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dictyNews Volume 33 Number 05
dictyNews
Electronic Edition
Volume 33, number 5
August 21, 2009
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.
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Abstracts
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CP250, a novel acidic coiled coil protein of the Dictyostelium centrosome,
affects growth, chemotaxis and the nuclear envelope
Rosemarie Blau-Wasser,*† Ursula Euteneuer,‡ Huajiang Xiong,*
Berthold Gassen,*† Michael Schleicher,‡ Angelika A. Noegel*†
*Center for Biochemistry, Medical Faculty,
†Center for Molecular Medicine Cologne (CMMC) and Cologne Excellence
Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD),
University of Cologne, 50931 Köln, Germany,
‡Institute of Anatomy and Cell Biology and Center for Integrated Protein
Science (CIPSM), Ludwig-Maximilians-University, 80336 München, Germany
Mol. Biol. Cell, in press
The Dictyostelium centrosome is a nucleus associated body consisting of a
box-shaped core surrounded by the corona, an amorphous matrix functionally
equivalent to the pericentriolar material of animal centrosomes which is
responsible for the nucleation and anchoring of microtubules. Here we describe
CP250 a component of the corona, an acidic coiled coil protein which is
present at the centrosome throughout interphase while disappearing during
prophase and reappearing at the end of late telophase. Amino acids 756-1148
of the 2,110 amino acids are sufficient for centrosomal targeting and cell
cycle dependent centrosome association. Mutant cells lacking CP250 are
smaller in size, growth on bacteria is delayed, chemotaxis is altered and
development is affected which, in general, are defects observed in
cytoskeletal mutants. Furthermore, loss of CP250 affected the nuclear
envelope and led to reduced amounts and altered distribution of Sun-1, a
conserved nuclear envelope protein that connects the centrosome to
chromatin.
Submitted by Angelika Nögel [noegel@uni-koeln.de]
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Role of a Cytoplasmic Dual-Function Glycosyltransferase in O2-Regulation
of Development in Dictyostelium
Zhuo A. Wang(1), Hanke van der Wel(1), Yusof Vohra(2), Therese Buskas(2),
Geert-Jan Boons(2), and Christopher M. West(1)
1Dept. of Biochemistry & Molecular Biology and Oklahoma Center for
Medical Glycobiology, University of Oklahoma Health Sciences Center,
Oklahoma City, OK 73104 USA;
2Dept. of Chemistry and Complex Carbohydrate Research Center, 315
Riverbend Road, University of Georgia, Athens, GA 30602 USA.
J. Biol. Chem., in press
In the social amoeba Dictyostelium, a terminal step in development is
regulated by environmental O2. Prolyl 4-hydroxylase-1 (P4H1) was
previously implicated in mediating the O2 signal, and P4H1-null cells
require elevated O2 to culminate. The E3-ubiquitin ligase adaptor Skp1
is a P4H1 substrate, and here we investigate the function of PgtA, a
dual function beta3-galactosyltransferase/alpha2-fucosyltransferase
that contributes the 2nd and 3rd sugars of the pentasaccharide cap
formed on Skp1 hydroxyproline. Although pgtA-null cells, whose Skp1
contains only a single sugar (N-acetylglucosamine or GlcNAc), show
wild-type O2-dependence of culmination, cells lacking AgtA, an
alpha3-galactosyltransferase required to extend the trisaccharide,
require elevated O2 as for P4H1-null cells. Skp1 is the only detectable
protein modified by purified PgtA added to pgtA-null extracts. The
basis for specificity of PgtA was investigated using native Skp1
acceptor glycoforms and a novel synthetic peptide containing
GlcNAcalpha1,4-hydroxy(trans)proline. Cysteine-alkylation of Skp1
strongly inhibited modification by the PgtA galactosyltransferase but
not the fucosyltransferase. Furthermore, native and synthetic Skp1
glycopeptides were poorly galactosylated, not processively fucosylated,
and negligibly inhibitory, whereas the fucosyltransferase was active
toward small substrates. In addition, the galactosyltransferase exhibited
an atypical concentration dependence on UDP-galactose. The results
provide the first evidence that Skp1 is the functional target of P4H1
in O2-regulation, indicate a gatekeeper function for the
beta3-galactosyltransferase in the PgtA-dual reaction, and identify
an unexpected P4H1-dependent yet antagonistic function for PgtA
that is reversed by AgtA.
Submitted by Chris West [Cwest2@ouhsc.edu]
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dictyExpress: A Dictyostelium discoideum gene expression database with an
explorative data analysis web-based interface
Gregor Rot*, Anup Parikh*, Tomaz Curk, Adam Kuspa, Gad Shaulsky and Blaz Zupan
Faculty of Computer and Information Science, University of Ljubljana, SI-1000
Ljubljana, Slovenia
Baylor College of Medicine, Houston, TX 77030, USA
* equal contribution
BMC Bioinformatics, in press
Background
Bioinformatics often leverages on recent advancements in computer science to
support biologists in their scientific discovery process. Such efforts include
the development of easy-to-use web interfaces to biomedical databases. Recent
advancements in interactive web technologies require us to rethink the standard
submit-and-wait paradigm, and craft bioinformatics web applications that share
analytical and interactive power with their desktop relatives, while retaining
simplicity and availability.
Results
We have developed dictyExpress, a web application that features a graphical,
highly interactive explorative interface to our database that consists of
more than 1000 Dictyostelium discoideum gene expression experiments. In
dictyExpress, the user can select experiments and genes, perform gene
clustering, view gene expression profiles across time, view gene co-expression
networks, perform analyses of Gene Ontology term enrichment, and simultaneously
display expression profiles for a selected gene in various experiments. Most
importantly, these tasks are achieved through web applications whose components
are seamlessly interlinked and immediately respond to events triggered by the
user, thus providing a powerful explorative data analysis environment.
Conclusions
dictyExpress is a precursor for a new generation of web-based bioinformatics
applications with simple but powerful interactive interfaces that resemble that
of the modern desktop. While dictyExpress serves mainly the Dictyostelium
research community, it is relatively easy to adapt it to other datasets. We
propose that the design ideas behind dictyExpress will influence the
development of similar applications for other model organisms.
Submitted by Gad Shaulsky and Blaz Zupan [gadi@bcm.edu]
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Self-organizing Actin Waves as Planar Phagocytic Cup Structures
Günther Gerisch1, Mary Ecke1, Britta Schroth-Diez2, Silke Gerwig2,
Ulrike Engel3, Lucinda Maddera4, and Margaret Clarke4
1 Max-Planck-Institut für Biochemie, Am Klopferspitz 18, D-82152
Martinsried, Germany.
2 Max-Planck-Institut für molekulare Zellbiologie und Genetik,
Pfotenhauerstrasse 108, D-01307 Dresden, Germany.
3 Nikon Imaging Center der Universität Heidelberg, Bioquant BQ 0004,
Im Neuenheimer Feld 267, D-69120 Heidelberg, Germany.
4 Program in Genetic Models of Disease, Oklahoma Medical Research
Foundation, Oklahoma City, OK 73121, USA.
Cell Adhesion & Migration, in press
Actin waves that travel on the planar membrane of a substrate-attached cell
underscore the capability of the actin system to assemble into dynamic
structures by the recruitment of proteins from the cytoplasm. The waves
have no fixed shape, can reverse their direction of propagation, and can
fuse or divide. Actin waves separate two phases of the plasma membrane that
are distinguished by their lipid composition. The area circumscribed by a
wave resembles in its phosphoinositide content the interior of a phagocytic
cup, leading us to explore the possibility that actin waves are in-plane
phagocytic structures generated without the localized stimulus of an attached
particle. Consistent with this view, wave-forming cells were found to exhibit
a high propensity for taking up particles. Cells fed rod-shaped particles
produced elongated phagocytic cups that displayed a zonal pattern that
reflected in detail the actin and lipid pattern of free-running actin waves.
Neutrophils and macrophages are known to spread on surfaces decorated with
immune complexes, a process that has been interpreted as “frustrated”
phagocytosis. We suggest that actin waves enable a phagocyte to scan a
surface for particles that might be engulfed.
Submitted by Günther Gerisch [gerisch@biochem.mpg.de]
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Food searching strategy of amoeboid cells by starvation induced run length
extension.
Peter J.M. Van Haastert and Leonard Bosgraaf
Department of Cell Biochemistry, University of Groningen, Kerklaan 30,
9751 NN Haren, The Netherlands
PLoS ONE, in press
Food searching strategies of animals are key to their success in heterogeneous
environments. The optimal search strategy may include specialized random walks
such as Levy walks with heavy power-law tail distributions, or persistent walks
with preferred movement in a similar direction. We have investigated the
movement of the soil amoebae Dictyostelium searching for food. Dictyostelium
cells move by extending pseudopodia, either in the direction of the previous
pseudopod (persistent step) or in a different direction (turn). The analysis
of ~4000 pseudopodia reveals that step and turn pseudopodia are drawn from a
probability distribution that is determined by cGMP/PLA2 signaling pathways.
Starvation activates these pathways thereby suppressing turns and inducing
steps. As a consequence, starved cells make very long nearly straight runs
and disperse over ~30-fold larger areas, without extending more or larger
pseudopodia than vegetative cells. This ‘win-stay/lose-shift’ strategy for
food searching is called Starvation Induced Run-length Extension. The SIRE
walk explains very well the observed differences in search behavior between
fed and starving organisms such as bumble-bees, flower bug, hoverfly and
zooplankton.
Submitted by Peter Van Haastert [p.j.m.van.haastert@rug.nl]
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Navigation of chemotactic cells by parallel signaling to pseudopod persistence
and orientation.
Leonard Bosgraaf and Peter J.M. Van Haastert
Department of Cell Biochemistry, University of Groningen, Kerklaan 30,
9751 NN Haren, The Netherlands
PLoS ONE, in press
The mechanism of chemotaxis is one of the most interesting issues in modern
cell biology. Recent work shows that shallow chemoattractant gradients do not
induce the generation of pseudopods, as has been predicted in many models.
This poses the question of how else cells can steer towards chemoattractants.
Here we use a new computational algorithm to analyze the extension of
pseudopods by Dictyostelium cells. We show that a shallow gradient of cAMP
induces a small bias in the direction of pseudopod extension, without
significantly affecting parameters such as pseudopod frequency or size.
Persistent movement, caused by alternating left/right splitting of existing
pseudopodia, amplifies the effects of this bias by up to 5-fold. Known
players in chemotactic pathways play contrasting parts in this mechanism;
PLA2 and cGMP signal to the cytoskeleton to regulate the splitting process,
while PI 3-kinase and soluble guanylyl cyclase mediate the directional bias.
The coordinated regulation of pseudopod generation, orientation and
persistence by multiple signaling pathways allows eukaryotic cells to
detect extremely shallow gradients.
Submitted by Peter Van Haastert [p.j.m.van.haastert@rug.nl]
--------------------------------------------------------------------------------
The local cell curvature guides pseudopodia towards chemoattractants.
Peter J.M. Van Haastert and Leonard Bosgraaf
Department of Cell Biochemistry, University of Groningen, Kerklaan 30,
9751 NN Haren, The Netherlands
HFSP Journal, in press
Many eukaryotic cells use pseudopodia for movement towards chemoattractants.
We developed a computer algorithm to identify pseudopodia, and analyzed how
pseudopodia of Dictyostelium cells are guided towards cAMP. Surprisingly,
the direction of a pseudopod is not actively oriented towards the gradient,
but is always perpendicular to the local cell curvature. The gradient induces
a bias in the position where the pseudopod emerges: pseudopodia more likely
emerge at the side of the cell closer to the gradient where perpendicular
pseudopodia are pointed automatically towards the chemoattractant. A mutant
lacking the formin dDia2 is not spherical but has many invaginations. Although
pseudopodia still emerge at the side closer to the gradient, the surface
curvature is so irregular that many pseudopodia are not extended towards
cAMP. The results imply that the direction of pseudopod extension, and
therefore also the direction of cell movement, is dominated by two aspects:
the position at the cell surface where a pseudopod emerges, and the local
curvature of the membrane at that position.
Submitted by Peter Van Haastert [p.j.m.van.haastert@rug.nl]
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[End dictyNews, volume 33, number 5]
