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Physical Biology Oct 2018Understanding the relationship between the topology of a network and its function remains an important question in biological physics. However, this is not a one-to-one...
Understanding the relationship between the topology of a network and its function remains an important question in biological physics. However, this is not a one-to-one mapping. Often the behavior of a signaling system varies with the input signal it receives. For example, some biological systems show adaptation when they receive a low input signal while they show oscillation with a high input signal. We therefore set out to find all possible two-node and three-node networks that can perform both adaptation and oscillation with transcriptional regulation and enzymatic reactions. For two-node networks, we identified all bi-functional topologies by analyzing the Jacobean matrix. For three-node networks, they were identified by enumeration. We further investigated how the system can be transformed between these two functions. We found that the switching of functions can be achieved through changing anyone of the several key parameters, including the input signal level.
Topics: Adaptation, Physiological; Algorithms; Animals; Biocatalysis; Computer Simulation; Dictyostelium; Gene Regulatory Networks; Humans; Models, Biological; Protein Interaction Maps; Saccharomyces cerevisiae; Signal Transduction; Transcriptional Activation
PubMed: 30375366
DOI: 10.1088/1478-3975/aae74c -
PLoS Biology Mar 2020Loners-individuals out of sync with a coordinated majority-occur frequently in nature. Are loners incidental byproducts of large-scale coordination attempts, or are they...
Loners-individuals out of sync with a coordinated majority-occur frequently in nature. Are loners incidental byproducts of large-scale coordination attempts, or are they part of a mosaic of life-history strategies? Here, we provide empirical evidence of naturally occurring heritable variation in loner behavior in the model social amoeba Dictyostelium discoideum. We propose that Dictyostelium loners-cells that do not join the multicellular life stage-arise from a dynamic population-partitioning process, the result of each cell making a stochastic, signal-based decision. We find evidence that this imperfectly synchronized multicellular development is affected by both abiotic (environmental porosity) and biotic (signaling) factors. Finally, we predict theoretically that when a pair of strains differing in their partitioning behavior coaggregate, cross-signaling impacts slime-mold diversity across spatiotemporal scales. Our findings suggest that loners could be critical to understanding collective and social behaviors, multicellular development, and ecological dynamics in D. discoideum. More broadly, across taxa, imperfect coordination of collective behaviors might be adaptive by enabling diversification of life-history strategies.
Topics: Biological Evolution; Dictyostelium; Models, Biological; Quorum Sensing; Spatio-Temporal Analysis; Stochastic Processes
PubMed: 32191693
DOI: 10.1371/journal.pbio.3000642 -
Developmental Biology Jul 2014Continuous communication between cells is necessary for development of any multicellular organism and depends on the recognition of secreted signals. A wide range of... (Review)
Review
Continuous communication between cells is necessary for development of any multicellular organism and depends on the recognition of secreted signals. A wide range of molecules including proteins, peptides, amino acids, nucleic acids, steroids and polylketides are used as intercellular signals in plants and animals. They are also used for communication in the social ameba Dictyostelium discoideum when the solitary cells aggregate to form multicellular structures. Many of the signals are recognized by surface receptors that are seven-transmembrane proteins coupled to trimeric G proteins, which pass the signal on to components within the cytoplasm. Dictyostelium cells have to judge when sufficient cell density has been reached to warrant transition from growth to differentiation. They have to recognize when exogenous nutrients become limiting, and then synchronously initiate development. A few hours later they signal each other with pulses of cAMP that regulate gene expression as well as direct chemotactic aggregation. They then have to recognize kinship and only continue developing when they are surrounded by close kin. Thereafter, the cells diverge into two specialized cell types, prespore and prestalk cells, that continue to signal each other in complex ways to form well proportioned fruiting bodies. In this way they can proceed through the stages of a dependent sequence in an orderly manner without cells being left out or directed down the wrong path.
Topics: Cell Communication; Chemotaxis; Culture Media, Conditioned; Cyclic AMP; Cytokinins; Dictyostelium; Morphogenesis; Nucleic Acids; Peptides; Polyketides; Quorum Sensing; Receptors, G-Protein-Coupled; Signal Transduction; Steroids
PubMed: 24726820
DOI: 10.1016/j.ydbio.2014.04.001 -
The International Journal of... 2019Dictyostelium is a microorganism found in soils that are known as the battle fields of chemical warfare. Genome analysis of Dictyostelium revealed that it has great... (Review)
Review
Dictyostelium is a microorganism found in soils that are known as the battle fields of chemical warfare. Genome analysis of Dictyostelium revealed that it has great potential for the production of small molecules, including secondary metabolites such as polyketides and terpenes.Polyketides are a large family of secondary metabolites which have a variety of structures. In accordance with their structural variety, polyketides have a plethora of biological activities, including antimicrobial, antifungal, and antitumor activities. Unsurprisingly, they have exceptional medical importance. Polyketides in nature work as protective compounds and /or function in pheromonal communication. Terpenes belong to another family of structurally diverse secondary metabolites which play roles in ecological interactions, including defence against predators and formation of mutually beneficial alliance with other organisms. Polyketides and terpenes work as intra- or inter-species signalling compounds, i.e. they play the role of a chemical language. However, in Dictyostelium, they work as paracrine signalling compounds which control the organism's multicellular morphogenesis. This review is primarily focused on the small molecules that regulate pattern formation in the slug stage of the organism and their biosynthetic pathways. Current in vivo understandings of polyketide DIF-1 induced cell differentiation and DIF-1-dependent/independent pathways are also discussed.
Topics: Cell Differentiation; Cyclic AMP; Dictyostelium; Gene Expression Profiling; Genome; Models, Biological; Polyketide Synthases; Polyketides; STAT Transcription Factors; Signal Transduction; Terpenes; Transcription Factors
PubMed: 31840781
DOI: 10.1387/ijdb.190192ts -
Advances in Experimental Medicine and... 2020Dictyostelium cells are professional phagocytes that are capable of handling particles of variable shapes and sizes. Here we offer long bacteria that challenge the...
Dictyostelium cells are professional phagocytes that are capable of handling particles of variable shapes and sizes. Here we offer long bacteria that challenge the uptake mechanism to its limits and report on the responses of the phagocytes if they are unable to engulf the particle by closing the phagocytic cup. Reasons for failure may be a length of the particle much larger than the phagocyte's diameter, or competition with another phagocyte. A cell may simultaneously release a particle and engulf another one. The final phase of release can be fast, causing the phagosome membrane to turn inside-out and to form a bleb. Myosin-II may be involved in the release by generating tension at the plasma membrane, it does however not accumulate on the phagosome to act there directly in expelling the particle. Labeling with GFP-2FYVE indicates that processing of the phagosome with phosphatidylinositol 3-phosphate begins at the base of a long phagosome already before closure of the cup. The decision of releasing the particle can be made even at the stage of the processed phagosome.
Topics: Bacteria; Dictyostelium; Phagocytes; Phagocytosis; Phagosomes
PubMed: 32399826
DOI: 10.1007/978-3-030-40406-2_5 -
Current Topics in Developmental Biology 2015Macroautophagy (hereafter referred to as autophagy) is a process used by the cell to deliver cytoplasmic components to the lysosome for degradation. Autophagy is most... (Review)
Review
Macroautophagy (hereafter referred to as autophagy) is a process used by the cell to deliver cytoplasmic components to the lysosome for degradation. Autophagy is most often associated with cell survival, as it provides cells with molecular building blocks during periods of nutrient deprivation and also aids in the elimination of damaged organelles and protein aggregates. However, autophagy has also been implicated in cell death. Here, we review what is known about autophagy, its regulation, its role both in cell life and cell death, and what is known about autophagic cell death in vivo.
Topics: Animals; Apoptosis; Autophagy; Caenorhabditis elegans; Cell Death; Cell Survival; Dictyostelium; Drosophila melanogaster; Starvation; Vertebrates
PubMed: 26431564
DOI: 10.1016/bs.ctdb.2015.07.012 -
Current Opinion in Cell Biology Oct 2015Model organisms have been key to understanding many core biological processes. Dictyostelium amoebae have the attributes required to perform this role for chemotaxis,... (Review)
Review
Model organisms have been key to understanding many core biological processes. Dictyostelium amoebae have the attributes required to perform this role for chemotaxis, and by providing an evolutionary distant reference point to mammalian cells, they allow the central features of chemotaxis to be discerned. Here we highlight progress with Dictyostelium in understanding: pseudopod and bleb driven movement; the role of the actin cytoskeleton; chemotactic signal processing, including how cells adapt to background stimulation, and the controversial role of PIP3. Macropinocytosis and the axenic mutations are raised as potential confounding factors, while the identification of new players through proteomics holds great promise.
Topics: Actin Cytoskeleton; Adaptation, Physiological; Chemotaxis; Dictyostelium; Phosphatidylinositols; Signal Transduction
PubMed: 26183444
DOI: 10.1016/j.ceb.2015.06.005 -
Accounts of Chemical Research Dec 2018The ability to navigate in chemical gradients, called chemotaxis, is crucial for the survival of microorganisms. It allows them to find food and to escape from toxins.... (Review)
Review
The ability to navigate in chemical gradients, called chemotaxis, is crucial for the survival of microorganisms. It allows them to find food and to escape from toxins. Many microorganisms can produce the chemicals to which they respond themselves and use chemotaxis for signaling, which can be seen as a basic form of communication, allowing ensembles of microorganisms to coordinate their behavior, for example, during embryogenesis, biofilm formation, or cellular aggregation. For example, Dictyostelium cells use signaling as a survival strategy: when starving, they produce certain chemicals toward which other cells show taxis. This leads to aggregation of the cells resulting in a multicellular aggregate that can sustain long starvation periods. Remarkably, the past decade has led to the development of synthetic microswimmers, which can self-propel through a solvent, analogously to bacteria and other microorganisms. The mechanism underlying the self-propulsion of synthetic microswimmers like camphor boats, droplet swimmers, and in particular autophoretic Janus colloids involves the production of certain chemicals. As we will discuss in this Account, the same chemicals (phoretic fields) involved in the self-propulsion of a (Janus) microswimmer also act on other ones and bias their swimming direction toward (or away from) the producing microswimmer. Synthetic microswimmers therefore provide a synthetic analogue to motile microorganisms interacting by taxis toward (or away from) self-produced chemical fields. In this Account, we review recent progress in the theoretical description of synthetic chemotaxis mainly based on simulations and field theoretical descriptions. We will begin with single motile particles leaving chemical trails behind with which they interact themselves, leading to effects like self-trapping or self-avoidance. Besides these self-interactions, in ensembles of synthetic motile particles each particle also responds to the chemicals produced by other particles, inducing chemical (or phoretic) cross-interactions. When these interactions are attractive, they commonly lead to clusters, even at low particle density. These clusters may either proceed toward macrophase separation, resembling Dictyostelium aggregation, or, as shown very recently, lead to dynamic clusters of self-limited size (dynamic clustering) as seen in experiments in autophoretic Janus colloids. Besides the classical case where chemical interactions are attractive, this Account discusses, as its main focus, repulsive chemical interactions, which can create a new and less known avenue to pattern formation in active systems leading to a variety of pattern, including clusters which are surrounded by shells of chemicals, traveling waves and more complex continuously reshaping patterns. In all these cases "synthetic signalling" can crucially determine the collective behavior of synthetic microswimmer ensembles and can be used as a design principle to create patterns in motile active particles.
Topics: Chemotaxis; Colloids; Dictyostelium; Models, Theoretical
PubMed: 30375857
DOI: 10.1021/acs.accounts.8b00215 -
Trends in Microbiology May 2024Metals and metalloids are used as weapons for predatory feeding by unicellular eukaryotes on prokaryotes. This review emphasizes the role of metal(loid) bioavailability... (Review)
Review
Metals and metalloids are used as weapons for predatory feeding by unicellular eukaryotes on prokaryotes. This review emphasizes the role of metal(loid) bioavailability over the course of Earth's history, coupled with eukaryogenesis and the evolution of the mitochondrion to trace the emergence and use of the metal(loid) prey-killing phagosome as a feeding strategy. Members of the genera Acanthamoeba and Dictyostelium use metals such as zinc (Zn) and copper (Cu), and possibly metalloids, to kill their bacterial prey after phagocytosis. We provide a potential timeline on when these capacities first evolved and how they correlate with perceived changes in metal(loid) bioavailability through Earth's history. The origin of phagotrophic eukaryotes must have postdated the Great Oxidation Event (GOE) in agreement with redox-dependent modification of metal(loid) bioavailability for phagotrophic poisoning. However, this predatory mechanism is predicted to have evolved much later - closer to the origin of the multicellular metazoans and the evolutionary development of the immune systems.
Topics: Metals; Phagocytosis; Dictyostelium; Biological Evolution; Acanthamoeba; Animals; Phagosomes; Zinc; Metalloids; Copper; Biological Availability; Mitochondria
PubMed: 38103995
DOI: 10.1016/j.tim.2023.11.008 -
Journal of Cell Science Oct 2023Mitogen-activated protein kinases (MAPKs) have been the focus of many studies over the past several decades, but the understanding of one subgroup of MAPKs, orthologs of... (Review)
Review
Mitogen-activated protein kinases (MAPKs) have been the focus of many studies over the past several decades, but the understanding of one subgroup of MAPKs, orthologs of MAPK15, known as atypical MAPKs, has lagged behind others. In most organisms, specific activating signals or downstream responses of atypical MAPK signaling pathways have not yet been identified even though these MAPKs are associated with many eukaryotic processes, including cancer and embryonic development. In this Review, we discuss recent studies that are shedding new light on both the regulation and function of atypical MAPKs in different organisms. In particular, the analysis of the atypical MAPK in the amoeba Dictyostelium discoideum has revealed important roles in chemotactic responses and gene regulation. The rapid and transient phosphorylation of the atypical MAPK in these responses suggest a highly regulated activation mechanism in vivo despite the ability of atypical MAPKs to autophosphorylate in vitro. Atypical MAPK function can also impact the activation of other MAPKs in amoeba. These advances are providing new perspectives on possible MAPK roles in animals that have not been previously considered, and this might lead to the identification of potential targets for regulating cell movement in the treatment of diseases.
Topics: Animals; Amoeba; Dictyostelium; Phosphorylation; MAP Kinase Signaling System; Gene Expression Regulation; Mitogen-Activated Protein Kinase Kinases
PubMed: 37850857
DOI: 10.1242/jcs.261447