Scientists have unravelled the genetic code of the sea urchin, an animal whose evolutionary lineage may be key to understanding the relationship of humans and other vertebrates to invertebrates.
Purple sea urchins grazing on kelp
Analysis of the genome of the male California purple sea urchin (Strongylocentrotus purpuratus) has revealed many genes previously thought unique to vertebrates, along with an innovative immune system and a surprising array of sensory proteins.
"This was a big payoff genome," said Eric Davidson from the California Institute of Technology (Caltech).
"It is the first time in a while that a genome has been sequenced that's not closely related to another genome that's already been sequenced," explained the molecular biologist who was closely involved with the sequencing project, along with researchers at the Human Genome Sequencing Center (HGSC) at Baylor College of Medicine in Houston.
The results, appearing this week in the journal Science, with more than 40 more papers to follow in the December issue of Developmental Biology, are the culmination of three years of work by an international team of 240 scientists.
The group estimates the sea urchin has 23,300 genes. For comparison, the fruit fly has about 13,600 and humans 20,000 to 25,000.
"Any snorkeler who has ever marvelled at the spherical, almost otherworldly, symmetry of the sea urchin will be amazed to learn that this organism, so different in habitat and body plan from ourselves, actually shares a substantial number of the same genes and pathways," said Francis Collins, director of the National Human Genome Research Institute (NHGRI) which helped fund the project.
"It turns out that the sea urchin is very much like us," said George Weinstock, the co- director of the HGSC. "You wouldn't think it to look at it. But it's closer to us than a fly," he said.
Specific to the job
Along with the nematode worm, the fly's DNA was decoded early on; but flies and worms sit on a distant branch of the evolutionary tree.
We are more kindred to the sea urchin, an echinoderm whose spiny brethren include starfish and sea cucumbers. And like humans and other vertebrates, it is a deuterostome, a group identified by its embryonic development.
The sea urchin's significance is that it represents a hitherto un-sequenced branch of deuterostomes that split from the animals with vertebrae.
THE SEA URCHIN
Generally about 10cm in size; most are purple or pink
In most marine environments, from poles to equator
Some 800 species; fossils go back more than 440 million years
Sit in phylum Echinodermata, and classed as echinoids
Invertebrates; soft body parts covered by plated shell, or test
Complex mouth mechanism known as Aristotle's lantern
Have tube-like feet; eat seaweed, algae, animal debris
Clear embryo makes for ideal model to study biology
Provided first understanding of fertilisation process
For this reason, the sea urchin genome fills an important gap in mapped genomes and is in a position to illuminate what genetic characteristics define deuterostomes, vertebrates and, hence, human beings.
Scientists found several surprises in the sea urchin genome that begin immediately to address these questions.
Among them, the discovery of a diverse innate immune system - one that does not change over the course of the animal's life, unlike our acquired immunity which is modified depending on the bugs we interact with.
"It's an incredibly elaborate immune system," said Jonathan Rast, an immunologist at the University of Toronto, and a lead author of one of the Science papers. "The complexity is unprecedented."
The big switch-on
His team found that S. purpuratus carries a collection of genes that code for proteins to detect the presence of harmful bacteria.
At least two types had analogues in humans, he said, and the sea urchin has 10 times as many of those as we do. Scientists can only speculate why a marine invertebrate would have evolved such a diverse immune system.
"The aquatic environment, especially the sea bottom, is just filled with bacteria," said Courtney Smith, a biologist at the George Washington University and co-author of the study, suggesting the need for an innate defence system to fight invisible predators along with the pointed spines to fend off large ones.
Another possibility, says Dr Rast, may be the digestive function of symbiotic bacteria in the sea urchin's gut. In humans, the failure of these proteins can lead to autoimmune disorders such as Crohn's disease.
"It might mean that the sea urchins have to keep control of a lot of bacteria to help them digest their food," said Dr Rast, "and they need to keep alive the bacteria that are helping them, and keep the ones that could harm them in check."
The discovery is fascinating for what it reveals about the urchin's evolutionary innovation, said Dr Smith, and may help explain why the creature enjoys a long lifespan. Sea urchins live 30 to 60 years; some species live up to a century.
But the finding might also point to the origins of the human immune system and to the proteins that lead to specific diseases, said Erica Sodergren, the sea urchin project leader at HGSC.
"The sea urchin is just a wonderful paradigm for doing research because it has analogous genes for all the genes that we have in humans," she said. "It's just that they may have different numbers of them, and they're expressed differently."
Sensing the world
For more than a century, the sea urchin has been a useful experimental model, particularly in the area of embryonic development; its eggs are easy to isolate and fertilise.
Now, with a genome map in hand, researchers will hope to further their work by determining how regulatory genes guide an animal's earliest stages.
In other words, what leads an egg to become a sea urchin or a human being?
"All this information is coded in one cell," said Manoj Samanta, a scientist at the Systemix Institute in Los Altos, California. "At some point the cell says, 'okay, it's time to form a mouth or a leg'."
Tube-like feet help them move, eat and sense their surroundings
Scientists design specific experiments to discover how this is done. For example, they can knock out a particular gene in the embryo to interfere with its expression. When they see what goes wrong, they can determine what the gene does.
"And that way, you'll separate function, which we call phenotype, from the DNA sequence, which we call genotype," said Dr Weinstock.
"We have to show the genetic connection to the animal's lifestyle," he said. "Otherwise, the DNA sequence is just something we analyse with computers."
The experimental techniques may help scientists solve another surprising find in the genome: the discovery of hundreds of sensory perception genes that are associated with vision and smell in humans, but that are not expressed in the usual places.
Sea urchins have nothing that resembles an eye. "You can look with a microscope all you want, you will see no eyes or nose or antenna," said Dr Davidson said.
But scientists have determined that the sensory proteins which we use to see and smell are activated, among other places, in the tube feet, the waving appendages that the sea urchin uses to move and eat.
"So what you have here is a function that we're familiar with, mounted on a morphological structure that we're unfamiliar with," said Dr Davidson.
However, this observation does not solve the mystery of how the sea urchin uses these proteins to sense the environment. The genes are turned on in the tube feet and the creature is sensing something, but they're not seeing or smelling as we do.
If we figure out how the sea urchin senses the environment with its tube feet, and whatever other organs it uses, we may discover a new model for perception, said Dr Davidson.