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dictyNews Volume 18 Number 06
Dicty News
Electronic Edition
Volume 18, number 6
May 4, 2002
Please submit abstracts of your papers as soon as they have been
accepted for publication by sending them to dicty@northwestern.edu.
Back issues of Dicty-News, the Dicty Reference database and other useful
information is available at DictyBase--http://dictybase.org.
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Abstracts
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Rapid patterning and zonal-differentiation in a two-dimensional
Dictyostelium cell mass: a role of pH and ammonia.
Satoshi Sawai, Takashi Hirano, Yasuo Maeda and Yasuji Sawada
Graduate School of Information Sciences, Biological Institute,
Graduate School of Science and Research Institute of Electrical
Communication, Tohoku University, 2-1-1 Katahira, Aoba-ku,
Sendai 980-8577, Japan
J. Exp. Biol., in press
SUMMARY
Recently it was demonstrated that a rapidly forming self-organizing
pattern which emerges within two-dimensional Dictyostelium discoideum
cell cultures could later give rise to stripes of distinct zones, each
comprised of different cell-types. Here we report physiological aspects
of the initial rapid patterning and its relation to cell differentiation.
We found that as temperature is lowered the characteristic length of the
pattern increases. From this the activation energy of the patterning
kinetics was estimated. Fluorescence of fluorescein conjugated dextran
revealed that the cytosolic pH of cells in the zone inside becomes lower
than that in the other zone facing the air. The patterning could be
inhibited by addition of the plasma-membrane proton pump inhibitors
diethystilbestrol (DES) or miconazole. Preincubation of cells with weak
acid delayed the timing of the patterning, whereas weak base hastened it.
A pH indicating dye revealed localized accmulation of ammonia in the
extracelluar space. These results suggest that gradients of secreted
metabolites may be directly responsible for the rapid patterning and its
consequence on cell differentiation in confined geometry. Possible
diffusible candidate molecules and a reaction scheme coupled to the imposed
oxygen gradient is discussed.
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Sequence and Analysis of Chromosome 2 of Dictyostelium discoideum
Gernot Glckner*, Ludwig Eichinger , Karol Szafranski*, Justin A. Pachebat! ,
Alan T. Bankier! , Paul H. Dear! , Rdiger Lehmann*, Cornelia Baumgart*, Gens
Parra, Josep F. Abril, Roderic Guig, Kai Kumpf*, Budi Tunggal ,
the Dictyostelium Genome Sequencing Consortium, Edward Cox, Michael A.
Quail, Matthias Platzer*, Andr Rosenthal*# and Angelika A. Noegel
*IMB Jena, Dept of Genome Analysis, Beutenbergstr. 11, 07745 Jena, Germany
Center for Biochemistry, Medical Faculty, University of Cologne,
Joseph-Stelzmann-Str. 52, 50931 Kln, Germany ! PNAC Biotech, Laboratory of
Molecular Biology, MRC Centre, Hills Road, Cambridge CB2 2QH, UK Grup de
Recerca en Informatica Biomedica, Institut Municipal d'Investigaci Mdica,
Universitat Pompeu Fabra, Centre de Regulaci Genmica, 08003 Barcelona,
Spain Princeton University, Princeton, NJ 08544, USA The Sanger Centre,
Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
#Friedrich Schiller Universitt Jena, 07743 Jena, Germany
Nature, accepted
Abstract
The genome of the lower eukaryote Dictyostelium discoideum comprises six
chromosomes. Here we report the sequence of the largest, chromosome 2, which
at 8Mb represents about 25% of the genome. Despite an A+T content of nearly
80% the chromosome encodes 2,799 predicted protein coding genes and 73 tRNA
genes (http://genome.imb-jena.de/dictyostelium/chr2/Chr2map.html
and http://www.uni-koeln.de/dictyostelium/chr2/index.shtml). This gene
density, about 1 gene per 2.6kb, is surpassed only by Saccharomyces
cerevisiae (one per 2kb) and is similar to that of Schizosaccharomyces
pombe (one per 2.5kb). If we assume that the other chromosomes have a similar
gene density, we expect around 11,000 genes in the D. discoideum genome.
A significant number of the genes show higher similarities to genes of
vertebrates than to those of other fully sequenced eukaryotes. This analysis
strengthens the view that the evolutionary position of D. discoideum is
located prior to the branching of metazoa and fungi but after the divergence
of the plant kingdom, placing it close to the base of metazoan evolution.
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Establishing direction during chemotaxis in eukaryotic cells
Wouter -Jan Rappel, Peter Thomas, Herbert Levine, and William F. Loomis
Departments of Physics and Biology, UCSD, La Jolla, CA 92093 and Salk
Institute for Biological Studies, La Jolla, CA 92186
Biophys. J (in press).
ABSTRACT
Several recent studies have demonstrated that eukaryotic cells including
amoeboid cells of Dictyostelium discoideum and neutrophils, respond to
chemoattractants by translocation of PH-domain proteins to the cell membrane
where these proteins participate in the modulation of the cytoskeleton and
relay of the signal. When the chemoattractant is released from a pipette,
the localization is found predominantly on the proximal side of the cell.
The recruitment of PH-domain proteins, particularly for Dictyostelium cells,
occurs very rapidly (<2 seconds). Thus, the mechanism responsible for the
first step in the directional sensing process of a cell must be able to
establish an asymmetry on the same time scale. Here, we propose a simple
mechanism in which a second messenger, generated by local activation of the
membrane, diffuses through the interior of the cell, suppresses the
activation of the back of the cell and converts the temporal gradient into
an initial cellular asymmetry. Numerical simulations show that such a
mechanism is plausible. Available evidence suggests that the internal
inhibitor may be cGMP which accumulates within less than a second following
treatment of cells with external cAMP.
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mRNA processing in Dictyostelium: sequence requirements for termination and
splicing
Francisco Rivero
Institut fr Biochemie I, Medizinische Fakultt, University of Cologne.
Joseph-Stelzmann-Strasse 52, D-50931 Kln, Germany
Protist, in press
Criteria for the identification of termination regions in Dictyostelium
discoideum genes have been established and the sequence requirements for
termination in 33 genes have been analyzed. A canonical hexamer signal AATAAA
was present 15-30 nucleotides upstream of the cleavage site, usually a TA,
and was embedded in a particularly A-rich environment. T- or GT-rich
downstream elements characteristic of animal cells could not be identified.
In a sample of 102 introns we have established the consensus AG/GTAAGT and
ATAG/ for the 5' and 3' splice sites, respectively. Most introns are 75-150
nucleotides long and the A+T content is high (90%). A putative branch point
was identified in half of the introns 20-60 nucleotides upstream of the 3'
splice site and the consensus TACTAAY was derived. A polypyrimidine tract
required for branching in vertebrates was not identified, but weak preference
for pyrimidine was found 10-45 nucleotides upstream of the 3' splice site.
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Brabek, J., Mojzita, D., Puta, F.
Folia Biologica(Prague)vol.48 p.73-76 (2002).
Abstract.
We achieved the production of the v-Src of the low-oncogenic strains Prague
C (PRC) and H19 in Dictyostelium discoideum, an emerging host system suitable
for the synthesis of heterologous proteins. To accomplish the expression,
the first 6 codons of the N-terminus of v-src had to be changed according to
the D. discoideum codon preference. Alternatively, N-terminal fusions, of
6xHis-tag or GFP, were sufficient to overcome the incompatibility in codon
usage. D. discoideum expressed v-Src kinases of expected molecular weight
were recognized by Src-specific antibodies; GFP-PRC was distributed uniformly
in the cytosol. In contrast to other lower eukaryotes, where the accumulation
of v-Src leads to growth inhibition, D. discoideum cells silenced the kinase
activity of PRC derived v-Src and showed no developmental or growth defects.
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[End Dicty News, volume 18, number 6]
