A cell for all reasons

Simple to Complex: The Role of Actin and Microtubules in Mitochondrial Dynamics in Amoeba, Yeast, and Mammalian Cells

Mitochondria are complex organelles that provide energy for the cell in the form of adenosine triphosphate (ATP) and have very specific structures. For most organisms, this is a reticular or tubular mitochondrial network, while others have singular oval-shaped organelles. Nonetheless, maintenance of this structure is dependent on the mitochondrial dynamics, fission, fusion, and motility. Recently, studies have shown that the cytoskeleton has a significant role in the regulation of mitochondrial dynamics. In this review, we focus on microtubules and actin filaments and look at what is currently known about the cytoskeleton’s role in mitochondrial dynamics in complex models like mammals and yeast, as well as what is known in the simple model system, Dictyostelium discoideum. Understanding how the cytoskeleton is involved in mitochondrial dynamics increases our understanding of mitochondrial disease, especially neurodegenerative diseases. Increases in fission, loss of fusion, and fragmented mitochondria are seen in several neurodegenerative diseases such as Parkinson’s, Alzheimer’s, and Huntington’s disease. There is no known cure for these diseases, but new therapeutic strategies using drugs to alter mitochondrial fusion and fission activity are being considered. The future of these therapeutic studies is dependent on an in-depth understanding of the mechanisms of mitochondrial dynamics. Understanding the cytoskeleton’s role in dynamics in multiple model organisms will further our understanding of these mechanisms and could potentially uncover new therapeutic targets for these neurodegenerative diseases.

Pursuit of food versus pursuit of information in a Markovian perception-action loop model of foraging

Efficient coding, redundancy reduction, and other information theoretic optimization principles have successfully explained the organization of many biological phenomena, from the physiology of sensory receptive fields to the variability of certain DNA sequence ensembles. Here we examine the hypothesis that behavioral strategies that are optimal for survival must necessarily involve efficient information processing, and ask whether there can be circumstances in which deliberately sacrificing some information can lead to higher utility? To this end, we present an analytically tractable model for a particular instance of a perception-action loop: a creature searching for a randomly moving food source confined to a 1D ring world. The model incorporates the statistical structure of the creature's world, the effects of the creature's actions on that structure, and the creature's strategic decision process. The underlying model takes the form of a Markov process on an infinite dimensional state space. To analyze it we construct an exact coarse graining that reduces the model to a Markov process on a finite number of "information states". This mathematical technique allows us to make quantitative comparisons between the performance of an information-theoretically optimal strategy with other candidate search strategies on a food gathering task. We find that 1. Information optimal search does not necessarily optimize utility (expected food gain). 2. The rank ordering of search strategies by information performance does not predict their ordering by expected food obtained. 3. The relative advantage of different strategies depends on the statistical structure of the environment, in particular the variability of motion of the source. We conclude that there is no simple relationship between information and utility. Even in the absence of information processing costs or bandwidth constraints, behavioral optimality does not imply information efficiency, nor is there a simple tradeoff between the two objectives of gaining information about a food source versus obtaining the food itself. For a wide range of values of the food source's movement parameter, the strategy of collecting the most information possible about the unknown source location carries an ineliminable structural cost, leading to a situation in which a foraging creature could actually choose to be less well-informed while simultaneously being, on average, better fed.

GPCR-controlled chemotaxis in Dictyostelium discoideum

Dictyostelium discoideum has been chosen as the key model organism for the study of eukaryotic chemotaxis. Studies in this lower eukaryotic organism have allowed us to discover eukaryotic chemotaxis behavior and to gradually understand the mechanism of chemotaxis. Investigations in this simple organism often guide the direction of chemotaxis studies in areas such as forming concepts, discovering molecular components, revealing pathways and networks. The cooperation between experimental approaches and computational modeling has helped us to comprehend the signaling network as a system. To further reveal the relationships among the molecular mechanisms of individual signaling steps, a continuous interplay between model development and refinement and experimental testing and verification will be useful. This article focuses on a chemoattractant G-protein-coupled receptor (GPCR)/G-protein gradient sensing machinery, which is monitored by PIP(3) responses and investigated by the interplay between live cell imaging experiments and computational modeling. We believe that such an approach will lead to a much better understanding of GPCR-controlled chemotaxis of all eukaryotic cells.

On the problem of establishing the subcellular localization of Dictyostelium retrotransposon TRE5-A proteins by biochemical analysis of nuclear extracts

At first sight a protein that is enriched in extracts prepared from nuclei by means of biochemical methods can be considered to be a nuclear protein in vivo. Although this assumption will hold true for most of the analyzed proteins, it could also lead to false interpretations. We analyzed the subcellular distribution of endogenous and plasmid-borne proteins derived from the retrotransposon TRE5-A of Dictyostelium discoideum. In biochemical fractionation experiments the proteins encoded by TRE5-A open reading frame 1 (ORF1p) and the putative endonuclease encoded in ORF2 (ENp) were found in the detergent-insoluble material containing the nuclei. However, salt extraction of isolated nuclei did not considerably release the TRE5-A proteins. Instead, the TRE5-A proteins were strongly enriched in a fraction that contained the chromosomal DNA after removal of most cytoskeletal and histone proteins. These observations implied that ORF1p and ENp were both attached to chromatin in vivo, but this conclusion was disproved by the expression of genetic fusions of green fluorescent protein with either ORF1p or ENp. We show conclusive evidence that both fusion proteins were located as large aggregates of native protein in the cytoplasm of D. discoideum cells.

Inhibition of multicellular development switches cell death of Dictyostelium discoideum towards mammalian-like unicellular apoptosis

The multicellular development of the single celled eukaryote Dictyostelium discoideum is induced by starvation and consists of initial aggregation of the isolated amoebae, followed by their differentiation into viable spores and dead stalk cells. These stalk cells retain their structural integrity inside a stalk tube that support the spores in the fruiting body. Terminal differentiation into stalk cells has been shown to share several features with programmed cell death (Cornillon et al. (1994), J. Cell Sci. 107, 2691-2704). Here we report that, in the absence of aggregation and differentiation, D. discoideum can undergo another form of programmed cell death that closely resembles apoptosis of most mammalian cells, involves loss of mitochondrial transmembrane potential, phosphatidylserine surface exposure, and engulfment of dying cells by neighboring D. discoideum cells. This death has been studied by various techniques (light microscopy and scanning or transmission electron microscopy, flow cytometry, DNA electrophoresis), in two different conditions inhibiting D. discoideum multicellular development. The first one, corresponding to an induced unicellular cell death, was obtained by starving the cells in a "conditioned" cell-free buffer, prepared by previous starvation of another D. discoideum cell population in potassium phosphate buffer (pH 6.8). The second one, corresponding to death of D. discoideum after axenic growth in suspension, was obtained by keeping stationary cells in their culture medium. In both cases of these unicellular-specific cell deaths, microscopy revealed morphological features known as hallmarks of apoptosis for higher eukaryotic cells and apoptosis was further corroborated by flow cytometry. The occurrence in D. discoideum of programmed cell death with two different phenotypes, depending on its multicellular or unicellular status, is further discussed.