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Sea Urchin Genome Yields New Understanding of “Chemical Defensome”

November 13, 2006

The Sea Urchin Genome Sequencing Consortium, a group of 240 researchers
from more than 70 institutions in 11 countries, recently announced the
sequencing of the California purple sea urchin, Strongylocentrotus purpuratus. 
Three biologists from the Woods Hole Oceanographic Institution (WHOI)
were among those participating in describing the sea urchin
genes.  They helped to identify a large group of genes encoding
proteins involved in protecting the sea urchin from toxic chemicals.
Reporting in the November 10 issue of the journal Science,
the consortium researchers announced the high-quality “draft” sequence,
covering more than 90 percent of the sea-urchin genome, and provided
detailed descriptions of genes involved in a variety of biological
processes ranging from immune function to sensory biology.  Those
descriptions appear in 41 papers in the December 1 issue of the journal
Developmental Biology.
The sea urchin genome contains over 814 million letters, spelling out
23,300 genes.  The WHOI scientists, in collaboration with
researchers from Stanford University’s Hopkins Marine Station and
several other institutions, identified over 400 of these genes that are
part of the “chemical defensome,” an integrated network of genes and
pathways that allow animals to mount an orchestrated defense against
toxic chemicals.  
The defensome genes include those for enzymes involved in
biotransformation — the conversion of chemicals to less-toxic
derivatives — as well as those encoding proteins involved in the
expulsion of chemicals or their metabolites from cells.  Also
included in the defensome are genes for proteins called transcription
factors, which sense the presence of toxic chemicals and turn on the
genes for biotransformation enzymes and transporters.
The defensome characterization was led by Jed Goldstone, a postdoctoral
scholar in the WHOI Biology Department, and Amro Hamdoun of Stanford
University, and also included two WHOI senior scientists, biologists
Mark Hahn and John Stegeman.  For many years, the WHOI group has
studied defensome genes in a variety of animals.  The sea urchin
research provides the first comprehensive, genome-wide assessment of
the defensome in any animal. The sea urchin defensome is notable
because several of the gene families in it have undergone expansion in
the sea urchin lineage, suggesting an especially important role for
chemical defense in these animals.
The overall sequencing project was led by Drs. Erica Sodergren,
George Weinstock, and Richard Gibbs at the Human Genome Sequencing
Center at Baylor College of Medicine, and Drs. Eric Davidson and Andrew
Cameron of the California Institute of Technology.
Sea urchins are echinoderms (Greek for “spiny skin”), marine animals
that originated over 540 million years ago and include starfish,
brittle stars, sea lilies, and sea cucumbers.  There was great
interest in the sea urchin as a target for genome sequencing because
these animals share a common ancestor with humans. That ancestor lived
over 540 million years ago and gave rise to the Deuterostomes, the
superphylum of animals that includes phyla such as echinoderms and
chordates, the phylum to which humans and other vertebrates
belong.  All Deuterostomes are more closely related to each other
than they are to any other animals not included in the Deuterostome
superphylum. For example, among sequenced genomes, the sea urchin
genome is closer to the human genome than to genomes of flies and
“Each genome that we sequence brings new surprises. This analysis shows
that sea urchins share substantially more genes and biological pathways
with humans than previously suspected,” said Dr. Francis S. Collins,
director of the National Human Genome Research Institute at the
National Institutes of Health. “Comparing the genome of the sea urchin
with that of the human and other model organisms will provide
scientists with novel insights into the structure and function of our
own genome, deepening our understanding of the human body in health and
The comparison of the genes of the sea urchin to the human gene list
shows which human genes are likely to be recent innovations in human
evolution and which are more ancient. It also shows which human genes
have changed slowly in the lineage from the ancestral Deuterostome
animal and which genes are evolving rapidly in response to natural
Although, as invertebrates, sea urchins have a radically different
morphology from humans and other vertebrates, their embryonic
development displays basic similarities, an important shared property
of Deuterostome animals.  The evolutionary relationship to humans
makes the sea urchin, with its many useful properties such as ease of
isolation of eggs and sperm and transparent embryos, a valuable model
to study the process of development and help understand human
development. The development of the animal occurs through a complex
network of genes, and the sea urchin is one of the main models for
systems biology, the description of how the building blocks of an
animal interact in time and space.
The chemical defensome described by the WHOI team and their colleagues
may be especially important for protecting sea urchin embryos from
toxic chemicals during embryonic development.  Indeed, the team
found that many of the defensome genes are expressed, or “turned on,”
in embryos.  In addition, based on comparisons with the previously
sequenced genomes of other invertebrates and vertebrates, the
researchers suggested that some defensome genes may have originally
functioned as part of the complex network of developmental regulatory
genes, and then later evolved their defensive roles.
The WHOI researchers were funded by grants from the National Institute
of Environmental Health Sciences, at part of the National Institutes of