Biologists Determine Genetic Blueprint Of Social Amoeba
By Kim McDonald
team that includes biologists at UCSD has determined the complete
genetic blueprint of Dictyostelium discoideum, a simple
social amoeba long used by researchers as a model genetic system,
much like fruit flies and laboratory mice, to gain a better
understanding of human diseases.
Credit: Dirk Dormann, University of Dundee
The scientific details
of this seven-yearlong genetic sequencing effort, which involved
97 scientists from 22 institutions in five countries, are contained
in a paper featured on the cover of the May 5 issue of the journal
team’s achievement will have an immediate application
for biomedical researchers, who can now mine the Dictyostelium
genome for a host of genes that cause human disease, thus gaining
a new and efficient way to study those human diseases with a
simple organism in their laboratories.
For evolutionary biologists,
the genetic blueprint of Dictyostelium, the first amoeba
genome to be sequenced, has clarified the place that Dictyostelium
occupies in the hierarchy of life.
patterns and divergence of organisms from the common ancestor
of plants and animals. Credit: William Loomis, UCSD
“It is more closely
related to fungi and animals than we had previously thought,”
says Adam Kuspa, a professor of biochemistry and molecular biology
at Baylor College of Medicine in Houston and a senior author
of the Nature paper.
The discovery will
also improve geneticists’ understanding of how the genes
from Dictyostelium and other genetic model organisms
have been conserved or adapted through evolution in humans and
Credit: Dirk Dormann, University of Dundee
“The cells which
gave rise to plants and animals had more types of genes available
to them than are presently found in either plants or animals,”
explains William Loomis, a professor of biology at UCSD and
one of the key members of the international sequencing effort.
“Specialization appears to lead to loss of genes as well
as the modification of copies of old genes. As each new genome
is sequenced, we learn more about the history and physiology
of the progenitors and gain insight into the function of human
In 1989, Loomis and
Kuspa, then a postdoctoral fellow in Loomis’ laboratory,
initiated a critical portion of the effort when they began the
arduous task of constructing a physical map of the genes located
on the six chromosomes of Dictyostelium.
The scientists mapped
the location of several hundred genes on those chromosomes based
on landmarks that had been discovered over the years, then created
a set of 5,000 large DNA clones, each about 200,000 nucleotide
bases long, that proved useful for other researchers in assembling
the genetic sequences of Dictyostelium’s genome.
Another UCSD biologist involved in the genome effort, Christophe
Anjard, an assistant project scientist in Loomis’ laboratory,
analyzed families of Dictyostelium genes and uncovered
relationships with these genes in both animals and plants.
is used as a model organism for studying cell polarity, how
cells move and the differentiation of tissues. It also exhibits
many of the properties of white blood cells.
Three years ago, another
team of UCSD biologists discovered that two genes that are used
by Dictyostelium to guide the organism to food sources
are also used to guide human white blood cells to the sites
of infections and play a role in the spread of cancer. (see:
usually exists as a single cell organism that inhabits forest
soil, consuming bacteria and yeast. When starved, however, the
single cells come together, differentiate into tissues and become
a true multicellular organism with a fruiting body composed
of a stalk with spores poised on top. This increases its utility
in a variety of studies.
relationship to humans depends on how related the proteins are
that are found in the two cell types,” says Kuspa. “You
can make direct analogies, or you could learn general principles
about how cells regulate their behavior. Both things will apply
in the studies we do.”
He and the other members
of the international sequencing team found that there are more
protein coding genes in the organism than they had thought and
nearly twice as many as there are in fungi. Their unraveling
of the genome also allowed Rolf Olsen, a postdoctoral fellow
working in Loomis’ laboratory, to generate a tree of life
and show that amoebozoa, the group to which Dictyostelium
belongs, evolved from the common ancestor of eukaryotes (the
group of organisms that contain all animals, plants, algae,
protozoa, slime mold and fungi) before fungi. Dictyostelium
has about 12,000 genes that produce a greater variety of proteins
than the approximately 6,000 found in fungi. And its genes are
more closely related to human genes than are the genes from
speaks to how much we will relate the gene function information
we find to humans,” Kuspa says. "It makes Dictyostelium
a better model for looking for targets against which drugs can
in the project at Baylor included Richard Gibbs and George Weinstock,
co-directors of Baylor’s Human Genome Sequencing Center,
and Richard Sucgang, an assistant professor of biochemistry.
Baylor performed about one half of the sequencing work.
The project was funded
by grants from the National Institute for Child Health and Development,
Deutsche Forschungsgemeinschaft, the Medical Research Council
and the European Union.
Comment: William Loomis
Media Contact: Kim McDonald