dictyNews Electronic Edition Volume 42, number 2 January 15, 2016 Please submit abstracts of your papers as soon as they have been accepted for publication by sending them to dicty@northwestern.edu or by using the form at http://dictybase.org/db/cgi-bin/dictyBase/abstract_submit. Back issues of dictyNews, the Dicty Reference database and other useful information is available at dictyBase - http://dictybase.org. Follow dictyBase on twitter: http://twitter.com/dictybase ========= Abstracts ========= The Physarum polycephalum Genome Reveals Extensive Use of Prokaryotic Two-Component andMetazoan-Type Tyrosine Kinase Signaling Pauline Schaap, Israel Barrantes, Pat Minx, Narie Sasaki, Roger W. Anderson, Marianne Benard, Kyle K. Biggar, Nicolas E. Buchler, Ralf Bundschuh, Xiao Chen, Catrina Fronick, Lucinda Fulton, Georg Golderer, Niels Jahn, Volker Knoop, Laura F. Landweber, Chrystelle Maric, Dennis Miller, Angelika A. Noegel, Rob Peace, Gerard Pierron, Taeko Sasaki, Mareike Schallenberg-Rüdinger, Michael Schleicher, Reema Singh, Thomas Spaller, Kenneth B. Storey, Takamasa Suzuki, Chad Tomlinson, John J. Tyson, Wesley C. Warren, Ernst R. Werner, Gabriele Werner-Felmayer, Richard K. Wilson,3 Thomas Winckler, Jonatha M. Gott, Gernot Glöckner , and Wolfgang Marwan Genome Biol. Evol. in press Physarum polycephalum is a well-studied microbial eukaryote with unique experimental attributes relative to other experimental 50 model organisms. It has a sophisticated life cycle with several distinct stages including amoebal, flagellated, and plasmodial cells. It is unusual in switching between open and closed mitosis according to specific life-cycle stages. Here we present the analysis of the genome of this enigmatic and important model organism and compare it with closely related species. The genome is littered with simple and complex repeats and the coding regions are frequently interrupted by introns with a mean size of 100 bases. Complemented with extensive transcriptome data, we define approximately 31,000 gene loci, providing unexpected insights into 55 early eukaryote evolution. We describe extensiveuse of histidine kinase-based two-component systems andtyrosine kinase signaling, the presence of bacterial and plant type photoreceptors (phytochromes, cryptochrome, and phototropin) and of plant-type pentatricopeptide repeat proteins, aswell asmetabolic pathways, and a cell cycle control system typically found in more complex eukaryotes. Our analysis characterizes P. polycephalumas a prototypical eukaryote with features attributed to the last common ancestor of Amorphea, that is, theAmoebozoa andOpisthokonts. Specifically, the presence of tyrosine kinases in Acanthamoeba and Physarum 60 as representatives of twodistantly related subdivisions of Amoebozoa argues against the lateremergence of tyrosine kinase signaling in the opisthokont lineage and also against the acquisition by horizontal gene transfer. submitted by: Gernot Glöckner [gernot.gloeckner@uni-koeln.de] ——————————————————————————————————————— Systematic evaluation of buffer influences on the development of Dictyostelium discoideum. Johanna Márquez López, Anja Sulzmann, Sascha Thewes. Institute for Biology – Microbiology; Department of Biology, Chemistry, Pharmacy; Freie Universität Berlin; Germany Development Genes and Evolution, in press Development and cell differentiation are key features of the social amoeba Dictyostelium discoideum. Already at early developmental stages the gene expression profile changes in the amoebae to make the cells aggregation-competent. In the laboratory development starts when the cells are washed free of nutrients. For this purpose various non-nutrient buffers are used in different laboratories. However, to date it is not clear if different buffers have different influences on the development of D. discoideum. Therefore we investigated systematically the influence of six widely used buffers on the development of D. discoideum. Investigation was done at the phenotypical, biochemical and molecular level. The results show that some of the investigated buffers show clear differences in the phenotypical outcome of the developmental cycle, at a biochemical level as measured in the response to cAMP, and/or at a molecular level as measured in the expression of early developmental marker genes. According to our results buffer compositions should be considered carefully for all developmental experiments with D. discoideum, especially when gene expression will be investigated. submitted by: Sascha Thewes [sascha.thewes@fu-berlin.de] ——————————————————————————————————————— Developmental accumulation of inorganic polyphosphate affects germination and energetic metabolism in Dictyostelium discoideum Thomas M. Livermore, Jonathan R. Chubb and Adolfo Saiardi Medical Research Council Laboratory for Molecular Cell Biology and Department of Cell and Developmental Biology, University College London, London WC1E 6BT, United Kingdom PNAS, in press Inorganic polyphosphate (polyP) is composed of linear chains of phosphate groups linked by high-energy phosphoanhydride bonds. However, this simple, ubiquitous molecule remains poorly understood. The use of nonstandardized analytical methods has contributed to this lack of clarity. By using improved polyacrylamide gel electrophoresis we were able to visualize polyP extracted from Dictyostelium discoideum. We established that polyP is undetectable in cells lacking the polyphosphate kinase (DdPpk1). Generation of this ppk1 null strain revealed that polyP is important for the general fitness of the amoebae with the mutant strain displaying a substantial growth defect. We discovered an unprecedented accumulation of polyP during the developmental program, with polyP increasing more than 100-fold. The failure of ppk1 spores to accumulate polyP results in a germination defect. These phenotypes are underpinned by the ability of polyP to regulate basic energetic metabolism, demonstrated by a 2.5-fold decrease in the level of ATP in vegetative ppk1. Finally, the lack of polyP during the development of ppk1 mutant cells is partially offset by an increase of both ATP and inositol pyrophosphates, evidence for a model in which there is a functional interplay between inositol pyrophosphates, ATP, and polyP. submitted by: Jonathan Chubb [j.chubb@ucl.ac.uk] ============================================================== [End dictyNews, volume 42, number 2]