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dictyNews Volume 42 Number 02
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.
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Abstracts
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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]
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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]
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[End dictyNews, volume 42, number 2]
