cAMP receptor affinity controls wave dynamics, geometry and morphogenesis inDictyostelium

Bistable spiral wave dynamics in electrically excitable media

We show that a positive feedback loop between sodium current inactivation and wave-front ramp-up speed causes a saddle-node bifurcation to result in bistable planar and spiral waves in electrically excitable media, in which both slow and fast waves are triggered by different stimulation protocols. Moreover, the two types of spiral wave conduction may interact to give rise to more complex spiral wave dynamics. The transitions between different spiral wave behaviors via saddle-node bifurcation can be a candidate mechanism for transitions widely seen in cardiac arrhythmias and neural diseases.

Microbial models of development: Inspiration for engineering self-assembled synthetic multicellularity

While the field of synthetic developmental biology has traditionally focused on the study of the rich developmental processes seen in metazoan systems, an attractive alternate source of inspiration comes from microbial developmental models. Microbes face unique lifestyle challenges when forming emergent multicellular collectives. As a result, the solutions they employ can inspire the design of novel multicellular systems. In this review, we dissect the strategies employed in multicellular development by two model microbial systems: the cellular slime mold Dictyostelium discoideum and the biofilm-forming bacterium Bacillus subtilis. Both microbes face similar challenges but often have different solutions, both from metazoan systems and from each other, to create emergent multicellularity. These challenges include assembling and sustaining a critical mass of participating individuals to support development, regulating entry into development, and assigning cell fates. The mechanisms these microbial systems exploit to robustly coordinate development under a wide range of conditions offer inspiration for a new toolbox of solutions to the synthetic development community. Additionally, recreating these phenomena synthetically offers a pathway to understanding the key principles underlying how these behaviors are coordinated naturally.

Homogenisation for the monodomain model in the presence of microscopic fibrotic structures

Computational models in cardiac electrophysiology are notorious for long runtimes, restricting the numbers of nodes and mesh elements in the numerical discretisations used for their solution. This makes it particularly challenging to incorporate structural heterogeneities on small spatial scales, preventing a full understanding of the critical arrhythmogenic effects of conditions such as cardiac fibrosis. In this work, we explore the technique of homogenisation by volume averaging for the inclusion of non-conductive micro-structures into larger-scale cardiac meshes with minor computational overhead. Importantly, our approach is not restricted to periodic patterns, enabling homogenised models to represent, for example, the intricate patterns of collagen deposition present in different types of fibrosis. We first highlight the importance of appropriate boundary condition choice for the closure problems that define the parameters of homogenised models. Then, we demonstrate the technique's ability to correctly upscale the effects of fibrotic patterns with a spatial resolution of 10 µm into much larger numerical mesh sizes of 100- 250 µm . The homogenised models using these coarser meshes correctly predict critical pro-arrhythmic effects of fibrosis, including slowed conduction, source/sink mismatch, and stabilisation of re-entrant activation patterns. As such, this approach to homogenisation represents a significant step towards whole organ simulations that unravel the effects of microscopic cardiac tissue heterogeneities.

Mitochondrial Processes during Early Development of Dictyostelium discoideum: From Bioenergetic to Proteomic Studies

The slime mold Dictyostelium discoideum’s life cycle includes different unicellular and multicellular stages that provide a convenient model for research concerning intracellular and intercellular mechanisms influencing mitochondria’s structure and function. We aim to determine the differences between the mitochondria isolated from the slime mold regarding its early developmental stages induced by starvation, namely the unicellular (U), aggregation (A) and streams (S) stages, at the bioenergetic and proteome levels. We measured the oxygen consumption of intact cells using the Clarke electrode and observed a distinct decrease in mitochondrial coupling capacity for stage S cells and a decrease in mitochondrial coupling efficiency for stage A and S cells. We also found changes in spare respiratory capacity. We performed a wide comparative proteomic study. During the transition from the unicellular stage to the multicellular stage, important proteomic differences occurred in stages A and S relating to the proteins of the main mitochondrial functional groups, showing characteristic tendencies that could be associated with their ongoing adaptation to starvation following cell reprogramming during the switch to gluconeogenesis. We suggest that the main mitochondrial processes are downregulated during the early developmental stages, although this needs to be verified by extending analogous studies to the next slime mold life cycle stages.

Wild Dictyostelium discoideum social amoebae show plastic responses to the presence of nonrelatives during multicellular development

When multiple strains of microbes form social groups, such as the multicellular fruiting bodies of Dictyostelium discoideum, conflict can arise regarding cell fate. Both fixed and plastic differences among strains can contribute to cell fate, and plastic responses may be particularly important if social environments frequently change. We used RNA-sequencing and photographic time series analysis to detect possible conflict-induced plastic differences between wild D. discoideum aggregates formed by single strains compared with mixed pairs of strains (chimeras). We found one hundred and two differentially expressed genes that were enriched for biological processes including cytoskeleton organization and cyclic AMP response (up-regulated in chimeras), and DNA replication and cell cycle (down-regulated in chimeras). In addition, our data indicate that in reference to a time series of multicellular development in the laboratory strain AX4, chimeras may be slightly behind clonal aggregates in their development. Finally, phenotypic analysis supported slower splitting of aggregates and a nonsignificant trend for larger group sizes in chimeras. The transcriptomic comparison and phenotypic analyses support discoordination among aggregate group members due to social conflict. These results are consistent with previously observed factors that affect cell fate decision in D. discoideum and provide evidence for plasticity in cAMP signaling and phenotypic coordination during development in response to social conflict in D. discoideum and similar microbial social groups.

Collective cell migration of Dictyostelium without cAMP oscillations at multicellular stages

In Dictyostelium discoideum, a model organism for the study of collective cell migration, extracellular cyclic adenosine 3',5'-monophosphate (cAMP) acts as a diffusible chemical guidance cue for cell aggregation, which has been thought to be important in multicellular morphogenesis. Here we revealed that the dynamics of cAMP-mediated signaling showed a transition from propagating waves to steady state during cell development. Live-cell imaging of cytosolic cAMP levels revealed that their oscillation and propagation in cell populations were obvious for cell aggregation and mound formation stages, but they gradually disappeared when multicellular slugs started to migrate. A similar transition of signaling dynamics occurred with phosphatidylinositol 3,4,5-trisphosphate signaling, which is upstream of the cAMP signal pathway. This transition was programmed with concomitant developmental progression. We propose a new model in which cAMP oscillation and propagation between cells, which are important at the unicellular stage, are unessential for collective cell migration at the multicellular stage.

Migration of Dictyostelium discoideum to the Chemoattractant Folic Acid

Dictyostelium discoideum can be grown axenically in a cultured media or in the presence of a natural food source, such as the bacterium Klebsiella aerogenes (KA). Here we describe the advantages and methods for growing D. discoideum on a bacterial lawn for several processes studied using this model system. When grown on a bacterial lawn, D. discoideum show positive chemotaxis towards folic acid (FA). While these vegetative cells are highly unpolarized, it has been shown that the signaling and cytoskeletal molecules regulating the directed migration of these cells are homologous to those seen in the motility of polarized cells in response to the chemoattractant cyclic adenosine monophosphate (cAMP). Growing D. discoideum on KA stimulates chemotactic responsiveness to FA. A major advantage of performing FA-mediated chemotaxis is that it does not require expression of the cAMP developmental program and therefore has the potential to identify mutants that are purely unresponsive to chemoattractant gradients. The cAMP-mediated chemotaxis can appear to fail when cells are developmentally delayed or do not up-regulate genes needed for cAMP-mediated migration. In addition to providing robust chemotaxis to FA, cells grown on bacterial lawns are highly resistant to light damage during fluorescence microscopy. This resistance to light damage could be exploited to better understand other biological processes such as phagocytosis or cytokinesis. The cell cycle is also shortened when cells are grown in the presence of KA, so the chances of seeing a mitotic event increases.

A new HECT ubiquitin ligase regulating chemotaxis and development in Dictyostelium discoideum

Cyclic AMP (cAMP) binding to G-protein-coupled receptors (GPCRs) orchestrates chemotaxis and development in Dictyostelium. By activating the RasC-TORC2-PKB (PKB is also known as AKT in mammals) module, cAMP regulates cell polarization during chemotaxis. TORC2 also mediates GPCR-dependent stimulation of adenylyl cyclase A (ACA), enhancing cAMP relay and developmental gene expression. Thus, mutants defective in the TORC2 Pia subunit (also known as Rictor in mammals) are impaired in chemotaxis and development. Near-saturation mutagenesis of a Pia mutant by random gene disruption led to selection of two suppressor mutants in which spontaneous chemotaxis and development were restored. PKB phosphorylation and chemotactic cell polarization were rescued, whereas Pia-dependent ACA stimulation was not restored but bypassed, leading to cAMP-dependent developmental gene expression. Knocking out the gene encoding the adenylylcyclase B (ACB) in the parental strain showed ACB to be essential for this process. The gene tagged in the suppressor mutants encodes a newly unidentified HECT ubiquitin ligase that is homologous to mammalian HERC1, but harbours a pleckstrin homology domain. Expression of the isolated wild-type HECT domain, but not a mutant HECT C5185S form, from this protein was sufficient to reconstitute the parental phenotype. The new ubiquitin ligase appears to regulate cell sensitivity to cAMP signalling and TORC2-dependent PKB phosphorylation.

Self-organization of chemoattractant waves in Dictyostelium depends on F-actin and cell-substrate adhesion

In the social amoeba Dictyostelium discoideum, travelling waves of extracellular cyclic adenosine monophosphate (cAMP) self-organize in cell populations and direct aggregation of individual cells to form multicellular fruiting bodies. In contrast to the large body of studies that addressed how movement of cells is determined by spatial and temporal cues encoded in the dynamic cAMP gradients, how cell mechanics affect the formation of a self-generated chemoattractant field has received less attention. Here, we show, by live cell imaging analysis, that the periodicity of the synchronized cAMP waves increases in cells treated with the actin inhibitor latrunculin. Detail analysis of the extracellular cAMP-induced transients of cytosolic cAMP (cAMP relay response) in well-isolated cells demonstrated that their amplitude and duration were markedly reduced in latrunculin-treated cells. Similarly, in cells strongly adhered to a poly-l-lysine-coated surface, the response was suppressed, and the periodicity of the population-level oscillations was markedly lengthened. Our results suggest that cortical F-actin is dispensable for the basic low amplitude relay response but essential for its full amplification and that this enhanced response is necessary to establish high-frequency signalling centres. The observed F-actin dependence may prevent aggregation centres from establishing in microenvironments that are incompatible with cell migration.

Regulation of Spatiotemporal Patterns by Biological Variability: General Principles and Applications to Dictyostelium discoideum

Spatiotemporal patterns often emerge from local interactions in a self-organizing fashion. In biology, the resulting patterns are also subject to the influence of the systematic differences between the system’s constituents (biological variability). This regulation of spatiotemporal patterns by biological variability is the topic of our review. We discuss several examples of correlations between cell properties and the self-organized spatiotemporal patterns, together with their relevance for biology. Our guiding, illustrative example will be spiral waves of cAMP in a colony of Dictyostelium discoideum cells. Analogous processes take place in diverse situations (such as cardiac tissue, where spiral waves occur in potentially fatal ventricular fibrillation) so a deeper understanding of this additional layer of self-organized pattern formation would be beneficial to a wide range of applications. One of the most striking differences between pattern-forming systems in physics or chemistry and those in biology is the potential importance of variability. In the former, system components are essentially identical with random fluctuations determining the details of the self-organization process and the resulting patterns. In biology, due to variability, the properties of potentially very few cells can have a driving influence on the resulting asymptotic collective state of the colony. Variability is one means of implementing a few-element control on the collective mode. Regulatory architectures, parameters of signaling cascades, and properties of structure formation processes can be "reverse-engineered" from observed spatiotemporal patterns, as different types of regulation and forms of interactions between the constituents can lead to markedly different correlations. The power of this biology-inspired view of pattern formation lies in building a bridge between two scales: the patterns as a collective state of a very large number of cells on the one hand, and the internal parameters of the single cells on the other.

Pattern formation is abundant in nature—from the rich ornaments of sea shells and the diversity of animal coat patterns to the myriad of fractal structures in biology and pattern-forming colonies of bacteria. Particularly fascinating are patterns changing with time, spatiotemporal patterns, like propagating waves and aggregation streams. Bacteria form large branched and nested aggregation-like patterns to immobilize themselves against water flow. The individual amoeba in Dictyostelium discoideum colonies initiates a transition to a collective multicellular state via a quorum-sensing form of communication—a cAMP signal propagating through the community in the form of spiral waves—and the subsequent chemotactic response of the cells leads to branch-like aggregation streams. The theoretical principle underlying most of these spatial and spatiotemporal patterns is self-organization, in which local interactions lead to patterns as large-scale collective”modes” of the system. Over more than half a century, these patterns have been classified and analyzed according to a”physics paradigm,” investigating such questions as how parameters regulate the transitions among patterns, which (types of) interactions lead to such large-scale patterns, and whether there are "critical parameter values" marking the sharp, spontaneous onset of patterns. A fundamental discovery has been that simple local interaction rules can lead to complex large-scale patterns. The specific pattern "layouts" (i.e., their spatial arrangement and their geometric constraints) have received less attention. However, there is a major difference between patterns in physics and chemistry on the one hand and patterns in biology on the other: in biology, patterns often have an important functional role for the biological system and can be considered to be under evolutionary selection. From this perspective, we can expect that individual biological elements exert some control on the emerging patterns. Here we explore spiral wave patterns as a prominent example to illustrate the regulation of spatiotemporal patterns by biological variability. We propose a new approach to studying spatiotemporal data in biology: analyzing the correlation between the spatial distribution of the constituents’ properties and the features of the spatiotemporal pattern. This general concept is illustrated by simulated patterns and experimental data of a model organism of biological pattern formation, the slime mold Dictyostelium discoideum. We introduce patterns starting from Turing (stripe and spot) patterns, together with target waves and spiral waves. The biological relevance of these patterns is illustrated by snapshots from real and theoretical biological systems. The principles of spiral wave formation are first explored in a stylized cellular automaton model and then reproduced in a model of Dictyostelium signaling. The shaping of spatiotemporal patterns by biological variability (i.e., by a spatial distribution of cell-to-cell differences) is demonstrated, focusing on two Dictyostelium models. Building up on this foundation, we then discuss in more detail how the nonlinearities in biological models translate the distribution of cell properties into pattern events, leaving characteristic geometric signatures.

Promoting convergence: the Phi spiral in abduction of mouse corneal behaviors

Why do mouse corneal epithelial cells display spiraling patterns? We want to provide an explanation for this phenomenon by applying an idealized problem solving process. Specifically, we applied complementary line-fitting methods to measure transgenic epithelial reporter expression arrangements displayed on three mature, live enucleated globes to clarify the problem. Two prominent logarithmic curves were discovered, one of which displayed the ϕ ratio, an indicator of the optimal configuration in phyllotactic systems. We then utilized two different computational approaches to expose our current understanding of the behavior. In one procedure, which involved an isotropic mechanics-based finite element method, we successfully produced logarithmic spiral curves of maximum shear strain based pathlines but computed dimensions displayed pitch angles of 35° (ϕ spiral is ~17°), which was altered when we fitted the model with published measurements of coarse collagen orientations. We then used model-based reasoning in context of Peircean abduction to select a working hypothesis. Our work serves as a concise example of applying a scientific habit of mind and illustrates nuances of executing a common method to doing integrative science.

Delineating the core regulatory elements crucial for directed cell migration by examining folic-acid-mediated responses

Dictyostelium discoideum shows chemotaxis towards folic acid (FA) throughout vegetative growth, and towards cAMP during development. We determined the spatiotemporal localization of cytoskeletal and signaling molecules and investigated the FA-mediated responses in a number of signaling mutants to further our understanding of the core regulatory elements that are crucial for cell migration. Proteins enriched in the pseudopods during chemotaxis also relocalize transiently to the plasma membrane during uniform FA stimulation. In contrast, proteins that are absent from the pseudopods during migration redistribute transiently from the PM to the cytosol when cells are globally stimulated with FA. These chemotactic responses to FA were also examined in cells lacking the GTPases Ras C and G. Although Ras and phosphoinositide 3-kinase activity were significantly decreased in Ras G and Ras C/G nulls, these mutants still migrated towards FA, indicating that other pathways must support FA-mediated chemotaxis. We also examined the spatial movements of PTEN in response to uniform FA and cAMP stimulation in phospholipase C (PLC) null cells. The lack of PLC strongly influences the localization of PTEN in response to FA, but not cAMP. In addition, we compared the gradient-sensing behavior of polarized cells migrating towards cAMP to that of unpolarized cells migrating towards FA. The majority of polarized cells make U-turns when the cAMP gradient is switched from the front of the cell to the rear. Conversely, unpolarized cells immediately extend pseudopods towards the new FA source. We also observed that plasma membrane phosphatidylinositol 3,4,5-trisphosphate [PtdIns(3,4,5)P3] levels oscillate in unpolarized cells treated with Latrunculin-A, whereas polarized cells had stable plasma membrane PtdIns(3,4,5)P3 responses toward the chemoattractant gradient source. Results were similar for cells that were starved for 4 hours, with a mixture of polarized and unpolarized cells responding to cAMP. Taken together, these findings suggest that similar components control gradient sensing during FA- and cAMP-mediated motility, but the response of polarized cells is more stable, which ultimately helps maintain their directionality.

Chemoattractant-mediated Rap1 activation requires GPCR/G proteins

Rap1 is rapidly activated upon chemoattractant stimulation and plays an important role in cell adhesion and cytoskeletal reorganization during chemotaxis. Here, we demonstrate that G-protein coupled receptors and G-proteins are essential for chemoattractant-mediated Rap1 activation in Dictyostelium. The rapid Rap1 activation upon cAMP chemoattractant stimulation was absent in cells lacking chemoattractant cAMP receptors cAR1/cAR3 or a subunit of the heterotrimeric G-protein complex Gα2. Loss of guanylyl cyclases GCA/SGC or a cGMP-binding protein GbpC exhibited no effect on Rap1 activation kinetics. These results suggest that Rap1, a key regulator for the regulation of cytoskeletal reorganization during cell movement, is activated through the G-protein coupled receptors cAR1/cAR3 and Gα2 proteins in a way independent of the cGMP signaling pathway.

Ca2+ chemotaxis in Dictyostelium discoideum

Using a newly developed microfluidic chamber, we have demonstrated in vitro that Ca(2+) functions as a chemoattractant of aggregation-competent Dictyostelium discoideum amoebae, that parallel spatial gradients of cAMP and Ca(2+) are more effective than either alone, and that cAMP functions as a stronger chemoattractant than Ca(2+). Effective Ca(2+) gradients are extremely steep compared with effective cAMP gradients. This presents a paradox because there is no indication to date that steep Ca(2+) gradients are generated in aggregation territories. However, given that Ca(2+) chemotaxis is co-acquired with cAMP chemotaxis during development, we speculate on the role that Ca(2+) chemotaxis might have and the possibility that steep, transient Ca(2+) gradients are generated during natural aggregation in the interstitial regions between cells.

Collective cell migration in development

Collective cell migration is a key process during the development of most organisms. It can involve either the migration of closely packed mesenchymal cells that make dynamic contacts with frequently changing neighbour cells, or the migration of epithelial sheets that typically display more stable cell-cell interactions and less frequent changes in neighbours. These collective movements can be controlled by short- or long-range dynamic gradients of extracellular signalling molecules, depending on the number of cells involved and their distance of migration. These gradients are sensed by some or all of the migrating cells and translated into directed migration, which in many settings is further modulated by cell-contact-mediated attractive or repulsive interactions that result in contact-following or contact-inhibition of locomotion, respectively. Studies of collective migration of groups of epithelial cells during development indicate that, in some cases, only leader cells sense and migrate up an external signal gradient, and that adjacent cells follow through strong cell-cell contacts. In this Commentary, I review studies of collective cell migration of differently sized cell populations during the development of several model organisms, and discuss our current understanding of the molecular mechanisms that coordinate this migration.

Predicting spiral wave patterns from cell properties in a model of biological self-organization

In many biological systems, biological variability (i.e., systematic differences between the system components) can be expected to outrank statistical fluctuations in the shaping of self-organized patterns. In principle, the distribution of single-element properties should thus allow predicting features of such patterns. For a mathematical model of a paradigmatic and well-studied pattern formation process, spiral waves of cAMP signaling in colonies of the slime mold Dictyostelium discoideum, we explore this possibility and observe a pronounced anticorrelation between spiral waves and cell properties (namely, the firing rate) and particularly a clustering of spiral wave tips in regions devoid of spontaneously firing (pacemaker) cells. Furthermore, we observe local inhomogeneities in the distribution of spiral chiralities, again induced by the pacemaker distribution. We show that these findings can be explained by a simple geometrical model of spiral wave generation.

Oscillatory signaling and network responses during the development of Dictyostelium discoideum

Periodic biological variations reflect interactions among molecules and cells, or even organisms. The Dictyostelium cAMP oscillatory circuit is a highly robust example. cAMP oscillations in Dictyostelium arise intracellularly by a complex interplay of activating and inhibiting pathways, are transmitted extracellularly, and synchronize an entire local population. Once established, cAMP signal-relay persists stably for hours. On a two-dimensional surface, >100,000 cells may form a single coordinated territory. In suspension culture, >10(10) cells can oscillate in harmony. This review focuses on molecular mechanisms that cyclically activate and attenuate signal propagation and on chemotactic responses to oscillatory wave progression.

Highlighting the role of Ras and Rap during Dictyostelium chemotaxis

Chemotaxis, the directional movement towards a chemical compound, is an essential property of many cells and has been linked to the development and progression of many diseases. Eukaryotic chemotaxis is a complex process involving gradient sensing, cell polarity, remodelling of the cytoskeleton and signal relay. Recent studies in the model organism Dictyostelium discoideum have shown that chemotaxis does not depend on a single molecular mechanism, but rather depends on several interconnecting pathways. Surprisingly, small G-proteins appear to play essential roles in all these pathways. This review will summarize the role of small G-proteins in Dictyostelium, particularly highlighting the function of the Ras subfamily in chemotaxis.

Streamless aggregation of Dictyostelium in the presence of isopropylidenadenosin

Starving cells of Dictyostelium discoideum undergo a developmental cycle where cAMP is autocatalytically produced and relayed from cell to cell, resulting in the propagation of excitation waves over a spatially extended population. Later on the homogeneous cell layer transforms into a pattern of cell streams directed perpendicular to the cAMP waves. Here we chemically influence aggregation competent cells by isopropylidenadenosin (IPA), an adenosine derivative. It can be assumed, that IPA acts via specific adenosine binding sites localized in the cellular membrane. We find, however, that pattern formation and cellular aggregation under the influence of IPA differ considerably compared to experiments with adenosine. In particular, our observations point towards an inhibitory effect on adenylate cyclase (ACA), the key enzyme in the autocatalytic production process of cAMP inside the cell. Our results suggest the existence of a direct coupling (via intracellular affection) or indirect coupling (via inhibition of cAMP binding) of the specific adenosine receptors to the regulatory circuit that controls cyclic intra- and extracellular cAMP concentration.

A fast Ca2+-induced Ca2+-release mechanism in Dictyostelium discoideum

In vertebrate cells calcium-induced calcium release (CICR) is thought to be responsible for rapid cytosolic Ca(2+) elevations despite the occurrence of strong Ca(2+) buffering within the cytosol. In Dictyostelium, a CICR mechanism has not been reported. While analyzing Ca(2+) regulation in a vesicular fraction of Dictyostelium rich in Ca(2+)-flux activity, containing contractile vacuoles (CV) as the main component of acidic Ca(2+) stores and ER, we detected a rapid Ca(2+) change upon addition of Ca(2+) (CIC). CIC was three times larger in active stores accumulating Ca(2+) than before Ca(2+) uptake and in inactivated stores. Ca(2+) release was demonstrated with the calmodulin antagonist W7 that inhibits the V-type H(+)ATPase activity and Ca(2+) uptake of acidic Ca(2+) stores. W7 caused a rapid and large increase of extravesicular Ca(2+) ([Ca(2+)](e)), much faster and larger than thapsigargin (Tg), a Ca(2+)-uptake inhibitor of the ER. W7 treatment blocked CIC indicating that a large part of CIC is due to Ca(2+) release. The height of CIC depended on the filling state of the Ca(2+) stores. CIC was virtually unchanged in the iplA(-) strain that lacks a putative IP(3) or ryanodine receptor thought to be located at the endoplasmic reticulum. By contrast, CIC was reduced in two mutants, HGR8 and lvsA(-), that are impaired in acidic Ca(2+)-store function. Purified Ca(2+) stores enriched in CV still displayed CIC, indicating that CV are a source of Ca(2+)-induced Ca(2+) release. CIC-defective mutants were altered in their oscillatory properties. The irregularity of the HGR8 oscillation suggests that the principal oscillator is affected in this mutant.

Reconstruction of cellular variability from spatiotemporal patterns of Dictyostelium discoideum

Variability in cell properties can be an important driving mechanism behind spatiotemporal patterns in biological systems, as the degree of cell-to-cell differences determines the capacity of cells to locally synchronize and, consequently, form patterns on a larger spatial scale. In principle, certain features of spatial patterns emerging with time may be regulated by variability or, more specifically, by certain constellations of cell-to-cell differences. Similarly, measuring variability in a system (i.e. the spatial distribution of cell-cell differences) may help predict properties of later-stage patterns.Here we apply and compare different statistical methods of extracting such systematic cell-to-cell differences in the case of patterns generated with a simple model system of an excitable medium and of experimental data by the slime mold Dictyostelium discoideum. We demonstrate with the help of a correlation analysis that these methods produce systematic (i.e. stationary) results for cell properties. Furthermore, we discuss possible applications of our method, in particular how these cell properties may serve as predictors of certain later-stage patterns.

Dictyostelium discoideum chemotaxis: threshold for directed motion

The chemotactic response of Dictyostelium discoideum cells to stationary, linear gradients of cyclic adenosine 3',5'-monophosphate (cAMP) was studied using microfluidic devices. In shallow gradients of less than 10(-3) nM/microm, the cells showed no directional response and exhibited a constant basal motility. In steeper gradients, cells moved up the gradient on average. The chemotactic speed and the motility increased with increasing steepness up to a plateau at around 10(-1) nM/microm. In very steep gradients, above 10 nM/microm, the cells lost directionality and the motility returned to the sub-threshold level. In the regime of optimal response the difference in receptor occupancy at the front and back of the cell is estimated to be only about 100 molecules.

Geometric diagnostics of complex patterns: spiral defect chaos

Motivated by the observation of spiral patterns in a wide range of physical, chemical, and biological systems, we present an automated approach that aims at characterizing quantitatively spiral-like elements in complex stripe-like patterns. The approach provides the location of the spiral tip and the size of the spiral arms in terms of their arc length and their winding number. In addition, it yields the number of pattern components (Betti number of order 1), as well as their size and certain aspects of their shape. We apply the method to spiral defect chaos in thermally driven Rayleigh-Benard convection and find that the arc length of spirals decreases monotonically with decreasing Prandtl number of the fluid and increasing heating. By contrast, the winding number of the spirals is nonmonotonic in the heating. The distribution function for the number of spirals is significantly narrower than a Poisson distribution. The distribution function for the winding number shows approximately an exponential decay. It depends only weakly on the heating, but strongly on the Prandtl number. Large spirals arise only for larger Prandtl numbers (Pr approximately > 1). In this regime the joint distribution for the spiral length and the winding number exhibits a three-peak structure, indicating the dominance of Archimedean spirals of opposite sign and relatively straight sections. For small Prandtl numbers the distribution function reveals a large number of small compact pattern components.

Paxillin is required for cell-substrate adhesion, cell sorting and slug migration during Dictyostelium development

Paxillin is a key regulatory component of focal adhesion sites, implicated in controlling cell-substrate interactions and cell movement. We analyse the function of a Dictyostelium discoideum paxillin homologue, PaxB, which contains four highly conserved LD and four LIM domains, but lacks two characteristic tyrosine residues, that form the core of vertebrate SH2-binding domains. PaxB is expressed during growth and all stages of development, but expression peaks during slug formation. Using a paxB-gfp knockin strain we show the existence of focal adhesions and characterise their dynamics. During multicellular development PaxB is not only found in focal adhesions at the cell-substrate interface, but also in the tips of filopodial structures predominantly located at the trailing ends of cells. paxB- strains are less adhesive to the substrate, they can aggregate but multicellular development from the mound stage onwards is severely impeded. paxB- strains are defective in proper cell type proportioning, cell sorting, slug migration and form-defective fruiting bodies. Mutation of a conserved JNK phosphorylation site, implicated in the control of cell migration, does not have any major effects on cell sorting, slug migration or morphogenesis in Dictyostelium. PaxB does not appear to function redundantly with its closest relative Lim2 (paxA), which when deleted also results in a mound arrest phenotype. However, analysis of paxA- and paxB- single and double null mutants suggest that PaxB may act upstream of Lim2.

Ammonium transporter C of Dictyostelium discoideum is required for correct prestalk gene expression and for regulating the choice between slug migration and culmination

Ammonium transporter C (AmtC) is one of three transporters in Dictyostelium that have been proposed to regulate entry and exit of ammonia in a cell type dependent manner and to mediate ammonia signaling. Previous work demonstrated that disruption of the amtC gene results in a slugger phenotype in which the cells remain as migrating slugs when they should form fruiting bodies. More detailed studies on the null strain revealed that differentiation of prestalk cell types was delayed and maintenance of prestalk cell gene expression was defective. There was little or no expression of ecmB, a marker for the initiation of culmination. Normal expression of CudA, a nuclear protein required for culmination, was absent in the anterior prestalk zone. The absence of CudA within the tip region was attributable to the lack of nuclear localization of the transcription factor STATa, despite expression of adenylyl cyclase A mRNA in the slug tips. Disruption of the histidine kinase gene dhkC in the amtC null strain restored STATa and CudA expression and the ability to culminate. The results suggest that the lack of nuclear translocation of STATa results from low cAMP due to a misregulated and overactive DhkC phosphorelay in the amtC null strain.

Receptor Occupancy on an Ellipsoidal Cell in the Presence of a Point Source of a Chemoattractant

Diffusion of a chemoattractant from a micropipet is routinely used to examine the different aspects of a cell's chemotactic response. To quantify the effect of cell elongation on chemotactic sensitivity in the micropipet assay, the chemoattractant concentration at the cell plasma membrane was determined by solving the equation for diffusion from a point source in the presence of a prolate ellipsoid of varying eccentricity. The results show that cell elongation can significantly increase the difference in receptor occupancy between near and far cell ends and thereby enhance the sensitivity of chemotactic cells to shallow chemoattractant gradients.

Signaling to cytoskeletal dynamics during chemotaxis

We review insights in signaling pathways controlling cell polarization and cytoskeletal organization during chemotactic movement in Dictyostelium amoebae and neutrophils. We compare and contrast these insights with our current understanding of pathways controlling chemotactic movements in more-complex multicellular developmental contexts.

cGMP-phosphodiesterase antagonists inhibit Ca2+-influx in Dictyostelium discoideum and bovine cyclic-nucleotide-gated-channel

We used antagonists of cGMP-phosphodiesterases to examine the role of cGMP for light-scattering oscillations and cAMP-induced Ca(2+)-influx in Dictyostelium discoideum, however, SCH 51866 (cis-5,6a,7,8,9,9a-hexahydro-2-[4-(trifluoromethyl)phenylmethyl]-5-methyl-cyclopent[4,5]imidazo[2,1-b]purin-4(3H)-one) and sildenafil citrate (1-[[3-(6,7-dihydro-1-methyl-7-oxo-3-propyl-1-H-pyrazolo[4,3-d]pyrimidin-5-yl)-4-ethoxyphenyl]sulfonyl]-4-methylpiperazine citrate) were poor inhibitors of cGMP-hydrolysis. Instead, SCH 51866 (IC(50) = 16 microM) and sildenafil, blocked chemoattractant (cAMP)-induced Ca(2+)-influx as determined with a Ca(2+)-specific electrode. SCH 51866 (150 microM) affected neither spontaneous cGMP transients during light-scattering-oscillations nor cAMP-mediated K(+)-efflux. SCH 51866 and sildenafil are competitive inhibitors of cGMP phosphodiesterases. However, the activity of cGMP-dependent protein kinase Ialpha (PKGIalpha) was not altered by SCH 51866 (150 microM). By contrast, patch-clamp measurements of bovine cone cGMP-gated-channels (cyclic-nucleotide-gated-channel, CNGA3), stably expressed in human embryonic kidney cells, HEK 293 cells, revealed reversible, competitive and dose-dependent inhibition of sodium currents by SCH 51866 (IC(50) = 25 microM) and sildenafil, but not by another inhibitor of cGMP-phosphodiesterases, UK 114,542. The possibility that D. discoideum cells also express a cGMP-regulated channel is supported by our finding that LY 83583 (6-(phenylamino)-5,8-quinolinedione) (35 microM), known to inhibit cyclic-nucleotide-gated-channels as well as guanylyl-cyclases, reduced cAMP-induced Ca(2+)-influx in D. discoideum, but did not affect cAMP-induced cGMP accumulation. Utilizing a PDED null strain that exhibits a prolonged and elevated cGMP transient following receptor activation, we found that the inhibition of Ca(2+)-influx by SCH 51866 in the wildtype was absent in the mutant. Our results show that SCH 51866 and sildenafil are antagonists of a Ca(2+)-permeable channel (CNGA3) and that both compete with cGMP for a regulatory site of Ca(2+)-influx in D. discoideum.

Chemoattractant signaling in dictyostelium discoideum

Dictyostelium is an accessible organism for studies of signaling via chemoattractant receptors. Chemoattractant-mediated signaling events and components are reviewed and presented as a series of connected modules, including excitation, inhibition, G protein-independent responses, early gene expression, inositol lipids, PH domain-containing proteins, cyclic AMP signaling, polarization acquisition, actin polymerization, and cortical myosin. The network incorporates information from biochemical, genetic, and cell biological experiments carried out on living cells. The modules and connections represent current understanding, and future information is expected to modify and build upon this structure.

A paracrine loop between tumor cells and macrophages is required for tumor cell migration in mammary tumors

Invasion of tumor cells into the surrounding connective tissue and blood vessels is a key step in the metastatic spread of breast tumors. Although the presence of macrophages in primary tumors is associated with increased metastatic potential, the mechanistic basis for this observation is unknown. Using a chemotaxis-based in vivo invasion assay and multiphoton-based intravital imaging, we show that the interaction between macrophages and tumor cells facilitates the migration of carcinoma cells in the primary tumor. Gradients of either epidermal growth factor (EGF) or colony-stimulating factor 1 (CSF-1) stimulate collection into microneedles of tumor cells and macrophages even though tumor cells express only EGF receptor and macrophages express only CSF-1 receptor. Intravital imaging shows that macrophages and tumor cells migrate toward microneedles containing either EGF or CSF-1. Inhibition of either CSF-1- or EGF-stimulated signaling reduces the migration of both cell types. This work provides the first direct evidence for a synergistic interaction between macrophages and tumor cells during cell migration in vivo and indicates a mechanism for how macrophages may contribute to metastasis.

Chemotaxis: signalling the way forward

During random locomotion, human neutrophils and Dictyostelium discoideum amoebae repeatedly extend and retract cytoplasmic processes. During directed cell migration--chemotaxis--these pseudopodia form predominantly at the leading edge in response to the local accumulation of certain signalling molecules. Concurrent changes in actin and myosin enable the cell to move towards the stimulus. Recent studies are beginning to identify an intricate network of signalling molecules that mediate these processes, and how these molecules become localized in the cell is now becoming clear.

A G alpha-dependent pathway that antagonizes multiple chemoattractant responses that regulate directional cell movement

Chemotactic cells, including neutrophils and Dictyostelium discoideum, orient and move directionally in very shallow chemical gradients. As cells polarize, distinct structural and signaling components become spatially constrained to the leading edge or rear of the cell. It has been suggested that complex feedback loops that function downstream of receptor signaling integrate activating and inhibiting pathways to establish cell polarity within such gradients. Much effort has focused on defining activating pathways, whereas inhibitory networks have remained largely unexplored. We have identified a novel signaling function in Dictyostelium involving a Galpha subunit (Galpha9) that antagonizes broad chemotactic response. Mechanistically, Galpha9 functions rapidly following receptor stimulation to negatively regulate PI3K/PTEN, adenylyl cyclase, and guanylyl cyclase pathways. The coordinated activation of these pathways is required to establish the asymmetric mobilization of actin and myosin that typifies polarity and ultimately directs chemotaxis. Most dramatically, cells lacking Galpha9 have extended PI(3,4,5)P(3), cAMP, and cGMP responses and are hyperpolarized. In contrast, cells expressing constitutively activated Galpha9 exhibit a reciprocal phenotype. Their second message pathways are attenuated, and they have lost the ability to suppress lateral pseudopod formation. Potentially, functionally similar Galpha-mediated inhibitory signaling may exist in other eukaryotic cells to regulate chemoattractant response.

A cAMP receptor-like G protein-coupled receptor with roles in growth regulation and development

Dictyostelium discoideum uses G protein-mediated signal transduction for many vegetative and developmental functions, suggesting the existence of G protein-coupled receptors (GPCRs) other than the four known cyclic adenosine monophosphate (cAMP) receptors (cAR1-4). Sequences of the cAMP receptors were used to identify Dictyostelium genes encoding cAMP receptor-like proteins, CrlA-C. Limited sequence identity between these putative GPCRs and the cAMP receptors suggests the Crl receptors are unlikely to be receptors for cAMP. The crl genes are expressed at various times during growth and the developmental life cycle. Disruption of individual crl genes did not impair chemotactic responses to folic acid or cAMP or alter cAMP-dependent aggregation. However, crlA(-) mutants grew to a higher cell density than did wild-type cells and high-copy-number crlA expression vectors were detrimental to cell viability, suggesting that CrlA is a negative regulator of cell growth. In addition, crlA(-) mutants produce large aggregates with delayed anterior tip formation indicating a role for the CrlA receptor in the development of the anterior prestalk cell region. The scarcity of GFP-expressing crlA(-) mutants in the anterior prestalk cell region of chimeric organisms supports a cell-autonomous role for the CrlA receptor in prestalk cell differentiation.

The cyclase-associated protein CAP as regulator of cell polarity and cAMP signaling in Dictyostelium

Cyclase-associated protein (CAP) is an evolutionarily conserved regulator of the G-actin/F-actin ratio and, in yeast, is involved in regulating the adenylyl cyclase activity. We show that cell polarization, F-actin organization, and phototaxis are altered in a Dictyostelium CAP knockout mutant. Furthermore, in complementation assays we determined the roles of the individual domains in signaling and regulation of the actin cytoskeleton. We studied in detail the adenylyl cyclase activity and found that the mutant cells have normal levels of the aggregation phase-specific adenylyl cyclase and that receptor-mediated activation is intact. However, cAMP relay that is responsible for the generation of propagating cAMP waves that control the chemotactic aggregation of starving Dictyostelium cells was altered, and the cAMP-induced cGMP production was significantly reduced. The data suggest an interaction of CAP with adenylyl cyclase in Dictyostelium and an influence on signaling pathways directly as well as through its function as a regulatory component of the cytoskeleton.

Long-range signal transmission in autocrine relays

Intracellular signaling induced by peptide growth factors can stimulate secretion of these molecules into the extracellular medium. In autocrine and paracrine networks, this can establish a positive feedback loop between ligand binding and ligand release. When coupled to intercellular communication by autocrine ligands, this positive feedback can generate constant-speed traveling waves. To demonstrate that, we propose a mechanistic model of autocrine relay systems. The model is relevant to the physiology of epithelial layers and to a number of in vitro experimental formats. Using asymptotic and numerical tools, we find that traveling waves in autocrine relays exist and have a number of unusual properties, such as an optimal ligand binding strength necessary for the maximal speed of propagation. We compare our results to recent observations of autocrine and paracrine systems and discuss the steps toward experimental tests of our predictions.

Computational approaches to cellular rhythms

Oscillations arise in genetic and metabolic networks as a result of various modes of cellular regulation. In view of the large number of variables involved and of the complexity of feedback processes that generate oscillations, mathematical models and numerical simulations are needed to fully grasp the molecular mechanisms and functions of biological rhythms. Models are also necessary to comprehend the transition from simple to complex oscillatory behaviour and to delineate the conditions under which they arise. Examples ranging from calcium oscillations to pulsatile intercellular communication and circadian rhythms illustrate how computational biology contributes to clarify the molecular and dynamical bases of cellular rhythms.

Cell movement patterns during gastrulation in the chick are controlled by positive and negative chemotaxis mediated by FGF4 and FGF8

During gastrulation in amniotes, epiblast cells ingress through the primitive streak and migrate away to form endodermal, mesodermal, and extraembryonic structures. Here we analyze the detailed movement trajectories of cells emerging at different anterior-posterior positions from the primitive streak, using in vivo imaging of the movement of GFP-tagged streak cells. Cells emerging at different anterior-posterior positions from the streak show characteristic cell migration patterns, in response to guidance signals from neighboring tissues. Streak cells are attracted by sources of FGF4 and repelled by sources of FGF8. The observed movement patterns of anterior streak cells can be explained by an FGF8-mediated chemorepulsion of cells away from the streak followed by chemoattraction toward an FGF4 signal produced by the forming notochord.

CulB, a putative ubiquitin ligase subunit, regulates prestalk cell differentiation and morphogenesis in Dictyostelium spp

Dictyostelium amoebae accomplish a starvation-induced developmental process by aggregating into a mound and forming a single fruiting body with terminally differentiated spores and stalk cells. culB was identified as the gene disrupted in a developmental mutant with an aberrant prestalk cell differentiation phenotype. The culB gene product appears to be a homolog of the cullin family of proteins that are known to be involved in ubiquitin-mediated protein degradation. The culB mutants form supernumerary prestalk tips atop each developing mound that result in the formation of multiple small fruiting bodies. The prestalk-specific gene ecmA is expressed precociously in culB mutants, suggesting that prestalk cell differentiation occurs earlier than normal. In addition, when culB mutant cells are mixed with wild-type cells, they display a cell-autonomous propensity to form stalk cells. Thus, CulB appears to ensure that the proper number of prestalk cells differentiate at the appropriate time in development. Activation of cyclic AMP-dependent protein kinase (PKA) by disruption of the regulatory subunit gene (pkaR) or by overexpression of the catalytic subunit gene (pkaC) enhances the prestalk/stalk cell differentiation phenotype of the culB mutant. For example, culB- pkaR- cells form stalk cells without obvious multicellular morphogenesis and are more sensitive to the prestalk O (pstO) cell inducer DIF-1. The sensitized condition of PKA activation reveals that CulB may govern prestalk cell differentiation in Dictyostelium, in part by controlling the sensitivity of cells to DIF-1, possibly by regulating the levels of one or more proteins that are rate limiting for prestalk differentiation.

Cell-cell adhesion and signal transduction duringDictyosteliumdevelopment

The development of the non-metazoan eukaryote Dictyostelium discoideum displays many of the features of animal embryogenesis, including regulated cell-cell adhesion. During early development, two proteins, DdCAD-1 and csA, mediate cell-cell adhesion between amoebae as they form a loosely packed multicellular mass. The mechanism governing this process is similar to epithelial sheet sealing in animals. Although cell differentiation can occur in the absence of cell contact, regulated cell-cell adhesion is an important component of Dictyostelium morphogenesis, and a third adhesion molecule, gp150, is required for multicellular development past the aggregation stage.

Cell-cell junctions that appear to be adherens junctions form during the late stages of Dictyostelium development. Although they are not essential to establish the basic multicellular body plan, these junctions are required to maintain the structural integrity of the fruiting body. The Dictyostelium β-catenin homologue Aardvark (Aar) is present in adherens junctions, which are lost in its absence. As in the case of its metazoan counterparts, Aar also has a function in cell signalling and regulates expression of the pre-spore gene psA.

It is becoming clear that cell-cell adhesion is an integral part of Dictyostelium development. As in animals, cell adhesion molecules have a mechanical function and may also interact with the signal-transduction processes governing morphogenesis.

Propagating chemoattractant waves coordinate periodic cell movement inDictyosteliumslugs

Migration and behaviour of Dictyostelium slugs results from coordinated movement of its constituent cells. It has been proposed that cell movement is controlled by propagating waves of cAMP as during aggregation and in the mound. We report the existence of optical density waves in slugs; they are initiated in the tip and propagate backwards. The waves reflect periodic cell movement and are mediated by cAMP, as injection of cAMP or cAMP phosphodiesterase disrupts wave propagation and results in effects on cell movement and, therefore, slug migration. Inhibiting the function of the cAMP receptor cAR1 blocks wave propagation, showing that the signal is mediated by cAR1. Wave initiation is strictly dependent on the tip; in decapitated slugs no new waves are initiated and slug movement stops until a new tip regenerates. Isolated tips continue to migrate while producing waves. We conclude from these observations that the tip acts as a pacemaker for cAMP waves that coordinate cell movement in slugs.Movies available on-line