A prickly subject: The sea urchin genome is sequencedNovember 10, 2006
James Coffman, Ph.D., of the Mount Desert Island Biological Laboratory in Bar Harbor was one of the scientists who helped decode the 814 million pairs of nucleotide bases in the sea urchin's chromosomes. The Human Genome Sequencing Center at Baylor College of Medicine in Texas led the project and announced the completion of the three-year project today. Having the complete genome, Coffman says, "makes doing research on urchins so much easier."
Why would anyone want to do biomedical research on sea urchins? According to Coffman, sea urchins are remarkably similar to humans in many ways, sharing most of the same gene families, and yet differ in a few critical areas besides the obvious physical ones. For one thing, sea urchins have a "extraordinarily complex innate immune system" which is not based on antibodies, like that of jawed vertebrates, but is effective enough to give sea urchins a surprisingly long life span of up to a hundred years or more.
Innate immunity refers to a set of proteins that are "hard wired" to detect unique aspects of bacteria and signal to an organism's cells that there is an intruder. The rich repertoire of such proteins in sea urchins could end up providing new tools for use against infectious diseases.
Sea urchins are also extremely good at dealing with potential chemical threats in their environment through a "defensome" - a group of genes which can sense and then transform and eliminate threats from potentially toxic chemicals. Without this sophisticated response, these chemicals, including heavy metals, can lead to aging, illness and death, so it would be valuable to learn how sea urchins defend themselves against them.
In terms of evolution, sea urchins are in an interesting position between vertebrates and invertebrates. "The sea urchin fills a large evolutionary gap in sequenced genomes," said George Weinstock, Ph.D., co-director of the sea urchin sequencing project. Being more closely related to humans than other invertebrates such as flies and worms, "it allows us to see what went on in evolution after the split between the ancestors that gave rise to humans and insects. The sea urchin genome provided plenty of unexpected rewards and was a great choice for sequencing."
In the 1990s, sea urchins became a valuable fishery in Maine, but their stocks were quickly depleted. Linda Mercer, Director of the Bureau of Resource Management at Maine's Department of Marine Research, welcomed the news of the project's completion: "We are certainly interested in reestablishing the sea urchin population along the Maine coast, and any research that can continue to improve our understanding of sea urchin biology would be helpful."
The DNA that was sequenced came from a male California purple sea urchin, not one of the green sea urchins that live in Maine waters. Purple urchins are found along the west coast from Baja to Alaska, whereas the green ones, close relatives of the purple, are found in cold Northern waters on both the east and west coasts.
All sea urchins, however, have round shells covered with spines. Like the other members of the phylum Echinodermata, which includes starfish and sea cucumbers, they have fivefold symmetry and move by means of hundreds of tiny, adhesive "tube feet." They eat algae with a mouth surrounded by five teeth on the bottom of their shell and excrete through a hole at the top.
The sea urchin has long had a strong fan base among scientists. One reason it was chosen for the genome-sequencing project is the size of the sea urchin research community. Over 140 laboratories are using sea urchins as a primary research organism. Annotation of the sequenced genome was conducted by 240 scientists in 11 countries.
In fact, it was research conducted on sea urchins over a hundred years ago that led to one of the breakthroughs of modern biology, when Theodor Boveri discovered in 1902 that normal development requires that every cell in an embryo have a full set of chromosomes carrying the genetic or inherited material for an organism.
One reason sea urchins have been so popular with scientists is that they are easy to work with. They can live in a laboratory comfortably, release their eggs readily, and have transparent embryos. That makes it easy to observe their fertilization and development, which is surprisingly similar to human embryonic development in some ways. As Dr. Coffman says, "Studying gene function and regulation in early sea urchin embryos is relatively easy compared with other model organisms such as mice, and much faster."
Sea urchins are also incredibly fecund. A single female discharges millions of eggs. In fact, most of an urchin's body mass consists of its reproductive organs, and that's what people are consuming when they eat the "roe" from a sea urchin.
At first glance, sea urchins seem to be inanimate, although people who have been around sea urchins know that the spines will move quickly in reaction to a light touch. The genome project, however, revealed that urchins have genes encoding some of the same sensory proteins involved in vision and hearing in humans. Yet the sea urchin has no eyes and ears, at least as we know them. Some of the visual sensory proteins are localized to an appendage known as the tube foot, and probably function in sensory processes there.
"The sea urchin reminds us of the underlying unity of all life on earth," notes Erica Sodergren, Ph.D., co-leader of the sequencing project. At MDIBL, Dr. Coffman is hoping to exploit that unity to ultimately find new treatments for human diseases and is studying a sea urchin member of one of those shared families of genes known as the "Runx" genes. In vertebrates this family of genes is known to be important for developmental processes such as bone and blood formation, and its mutations are associated with bone disorders and a common form of childhood leukemia.
Now that the sea urchin's genome has been sequenced, Dr. Coffman's work should progress more quickly. "It's incredible," he says. "It's hard for me to imagine not having a genome now."
Mount Desert Island Biological Laboratory
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