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dictyNews Volume 30 Number 19
dictyNews
Electronic Edition
Volume 30, number 19
June 20, 2008
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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The Actinome of Dictyostelium discoideum in Comparison to Actins and
Actin-related Proteins from Other Organisms
Jayabalan M. Joseph 1, Petra Fey 2, Nagendran Ramalingam 1, XI Liu 3,
Meino Rohlfs 1, Angelika A. Noegel 4, Annette Mueller-Taubenberger 1,
Gernot Gloeckner 5 and
Michael Schleicher 1
1 ABI/Cell Biology and Center for Integrated Protein Science (CIPSM), LMU,
Muenchen, Germany
2 dictyBase, Center f. Genetic Medicine, Northwestern Univ., Chicago, IL, USA
3 Dept. Biol. II, LMU, Muenchen, Germany
4 Inst. f. Biochemistry I, Center f. Molecular Medicine Cologne (CMMC) and
Cologne Excellence Cluster on Cellular Stress Responses in
Aging-Associated Diseases (CECAD), Univ. of Cologne, Koeln, Germany
5 Leibniz-Inst. for Age Research - Fritz Lipmann Inst., Jena, Germany
PLoS ONE, in press
Actin belongs to the most abundant proteins in eukaryotic cells which harbor
usually many conventional actin isoforms as well as actin-related proteins
(Arps). To get an overview over the sometimes confusing multitude of actins
and Arps, we analyzed the Dictyostelium discoideum actinome in detail and
compared it with the genomes from other model organisms. The D. discoideum
actinome comprises 41 actins and actin-related proteins. The genome
contains 17 actin genes which most likely arose from consecutive gene
duplications, are all active, in some cases develomentally regulated and
coding for identical proteins (Act8-group). According to published data, the
actin fraction in a D. discoideum cell consists of more than 95% of these
Act8-type proteins. The other 16 actin isoforms contain a conventional
actin motif profile as well but differ in their protein sequences. Seven
actin genes are potential pseudogenes. A homology search of the human
genome using the most typical D. discoideum actin (Act8) as query sequence
finds the major actin isoforms such as cytoplasmic beta-actin as best hit.
This suggests that the Act8-group represents a nearly perfect actin
throughout evolution. Interestingly, limited data from D. fasciculatum, a more
ancient member among the social amoebae, show different relationships
between conventional actins. The Act8-type isoform is most conserved
throughout evolution. Modeling of the putative structures suggests that
the majority of the actin-related proteins is functionally unrelated to
canonical actin. The data suggest that the other actin variants are not
necessary for the cytoskeleton itself but rather regulators of its dynamical
features or subunits in larger protein complexes.
Submitted by: Michael Schleicher [schleicher@lrz.uni-muenchen.de]
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Genome-wide transcriptional changes induced by phagocytosis or growth on
bacteria in Dictyostelium.
Alessio Sillo*1, Gareth Bloomfield#°1, Alessandra Balest*, Alessandra Balbo*,
Barbara Pergolizzi*, Barbara Peracino*, Jason Skelton#, Alasdair Ivens#,
and Salvatore Bozzaro*§
BMC GENOMICS, in press
Background
Phagocytosis plays a major role in the defense of higher organisms against
microbial infection and provides also the basis for antigen processing in the
immune response. Cells of the model organism Dictyostelium are professional
phagocytes that exploit phagocytosis of bacteria as the preferred way to
ingest food, besides killing pathogens. We have investigated Dictyostelium
differential gene expression during phagocytosis of non-pathogenic bacteria,
using DNA microarrays, in order to identify molecular functions and novel
genes involved in phagocytosis.
Results
The gene expression profiles of cells incubated for a brief time with bacteria
were compared with cells either incubated in axenic medium or growing on
bacteria. Transcriptional changes during exponential growth in axenic medium
or on bacteria were also compared. We recognized 443 and 59 genes that are
differentially regulated by phagocytosis or by the different growth conditions
(growth on bacteria vs. axenic medium), respectively, and 102 genes regulated
by both processes. Roughly one third of the genes are up-regulated compared
to macropinocytosis and axenic growth. Functional annotation of differentially
regulated genes with different tools revealed that phagocytosis induces profound
changes in carbohydrate, aminoacid and lipid metabolism, and in cytoskeletal
components. Genes regulating translation and mitochondrial biogenesis are mostly
up-regulated. Genes involved in sterol biosynthesis are selectively up-regulated,
suggesting a shift in membrane lipid composition linked to phagocytosis. Very
few changes were detected in genes required for vesicle fission/fusion,
indicating that the intracellular traffic machinery is mostly in common between
phagocytosis and macropinocytosis. A few putative receptors, including GPCR
family 3 proteins, scaffolding and adhesion proteins, components of signal
transduction and transcription factors have been identified, which could be
part of a signalling complex regulating phagocytosis and adaptational
downstream responses.
Conclusions
The results highlight differences between phagocytosis and macropinocytosis,
and provide the basis for targeted functional analysis of new candidate genes
and for comparison studies with transcriptomes during infection with pathogenic
bacteria.
Submitted by: Salvo Bozzaro [salvatore.bozzaro@unito.it]
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Anna Maria Rosaria Colucci, Barbara Peracino, Salvatore Bozzaro,
Pietro Alifano and Cecilia Bucci
Dictyostelium discoideum as a model host for meningococcal pathogenesis
Medical Science Monitor, in Press
Background:
The aim of the present study was to evaluate the possibility of studying
meningococcal virulence in a new model organism, Dictyostelium discoideum,
a haploid social soil amoeba that has been established as a host model for
several human pathogens leading to discovery of novel virulence mechanisms.
Material and Methods:
A number of virulent and hyper-virulent N. meningitidis strains including a
pair of isogenic encapsulated and un-encapsulated derivatives were used to
test the ability of D. discoideum to internalize and grow in the presence of
dead or living bacteria. The intracellular survival of internalized bacteria
was also monitored.
Results:
Dead meningococci supported Dictyostelium growth and development
although with some difference between strains, which was partially related
to internalization rates. As well as in human cells, the capsule positively
affected survival of internalized bacteria in Dictyostelium cells. Interestingly,
at variance with dead meningococci, living meningococci progressively
killed Dictyostelium cells.
Conclusions:
Our results suggest that several meningococcal virulence determinants
such as the capsular polysaccharide may be remarkably effective also in
Dictyostelium cells stimulating the use of this model host to search for
novel meningococcal virulence determinants.
Submitted by: Salvo Bozzaro [salvatore.bozzaro@unito.it]
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A novel bioassay for evaluating soil bio-hazards using Dictyostelium as biosensor:
Validation and application to the Bio-Bio Project
Alessandra Balbo and Salvatore Bozzaro
Fresenius Environ. Bull., in press
An easy and cheap biosensor has been developed for assessing soil biohazards.
The toxicity assay is based on inhibition of Dictyostelium development, a soil
amoeba undergoing multicellular development and cell differentiation under
starving conditions. The sensitivity of the assay was assessed in soil samples
with increasing concentrations of heavy metals and by comparison with
standard bio-assays on a battery of soils collected from contaminated
industrial sites. Dictyostelium appears to be highly sensitive to polycyclic
aromatic hydrocarbons, mineral oil and, to a lesser extent, to heavy metals.
The assay has been applied in a concerted action with other bioassays within
the frame of the BIO-BIO project.
Submitted by: Salvo Bozzaro [salvatore.bozzaro@unito.it]
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A new protein carrying an NmrA-like domain is required for cell differentiation
and development in Dictyostelium discoideum
Beatriz Núñez-Corcuera, Ioannis Serafimidis, Ernesto Arias-Palomo,
Angel Rivera-Calzada and Teresa Suarez
Dev. Biol., in press
We have isolated a Dictyostelium mutant unable to induce expression of the
prestalk-specific marker ecmB in monolayer assays. The disrupted gene, padA,
leads to a range of phenotypic defects in growth and development. We show
that padA is essential for growth, and we have generated a thermosensitive
mutant allele, padA-. At the permissive temperature, mutant cells grow poorly;
they remain longer at the slug stage during development and are defective in
terminal differentiation. At the restrictive temperature, growth is completely
blocked, while development is permanently arrested prior to culmination.
padA- slugs are deficient in prestalkA cell differentiation and present an
abnormal ecmB expression pattern. Sequence comparisons and predicted
three-dimensional structure analyses show that PadA carries an NmrA-like
domain. NmrA is a negative transcriptional regulator involved in nitrogen
metabolite repression in Aspergillus nidulans. PadA predicted structure
shows a NAD(P)+-binding domain, which we demonstrate that is essential for
function. We show that padA- development is more sensitive to ammonia than
wild-type cells and two ammonium transporters, amtA and amtC, appear
derepressed during padA- development. Our data suggest that PadA belongs
to a new family of NAD(P)+-binding proteins that link metabolic changes
to gene expression and is required for growth and normal development.
Submitted by: Teresa Suarez [teresa@cib.csic.es]
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[End dictyNews, volume 30, number 19]
