UH Scientists Help Analyze Sea Urchin, Honeybee Genomes

At first glance, the honeybee and sea urchin have little in common: One, an insect that lives tightly packed within the complex social system of a hive, significantly contributes to our food supply through pollination. The other, a spiny marine grazer that moves with hundreds of tiny tube feet, provides a preferred meal for crabs and lobsters.

Yet, according to recent genome sequencing projects involving two University of Houston genome composition specialists,  the two species—particularly the sea urchin—share a number of genetic characteristics with humans,

Dan Graur, UH John and Rebecca Moores Professor of Biology and Biochemistry, along with UH graduate student Eran Elhaik, took part in the compositional analyses of the genomes—chemical instructions for life contained in every cell of an organism.

The two UH scientists joined a large international group of researchers looking for clues into human development, in the case of the purple sea urchin, and sociality, in the case of the honeybee.

Their findings, titled “Insights into social insects from the genome of the honeybee Apis mellifera” and “The genome of the sea urchin Strongylocentrotus purpuratus,”  were published separately in the October 26, 2006, issue of Nature magazine and the November 3, 2006, issue of Science magazine, respectively.

“In general, the first report of a genomic sequence is only an appetizer that provides raw data for many other scientists to work on that sequence,” Graur explained.  “We got involved in these studies because we are interested in the evolution of compositional features of genomes, which are used to identify genes, predict levels of gene expression and find areas of the genome that are prone to mutations or insertions of foreign material.”

In characterizing the compositional prosperities of the genomes, Graur and Elhaik found those of both species exhibit a “power-law” distribution, indicating that compositionally homogeneous regions with the genome do not exhibit characteristic lengths. “This property has so far been found in all multicellular organisms but not in unicellular organisms such as bacteria and yeast,” Graur said.

Scientists fully sequenced only two insect genomes prior to the honeybee: the fruit fly and the malaria mosquito. Comparing the genomes, the latest sequencing hints that bees developed more slowly than either fruit flies or mosquitoes. Interestingly, the study found, some honeybee genes are more akin to those of mammals than to those of dipterans, the order of insects that includes flies. These genes include those that control internal clocks and circadian rhythms.

“The honeybee study revealed some puzzling features,” Graur said.  “While there was no genomic smoking gun to explain the honeybee’s most remarkable behavior—eusociality—the study does provide some interesting insights into honeybee biology.”

Eusociality refers to bees’ reproductive differentiation into two castes: sterile workers who care for the offspring-producing queens.

The researchers were surprised to find that compared to other insects the honeybee possesses only one-third as many genes associated with identifying and destroying bacteria responsible for disease. That’s despite spending most of its life in a congested, damp and warm indoor habitat conducive to disease. Apparently a bee’s genome is more focused on protecting the colony than with protecting the individual from disease. Bees are very clean and take precautionary steps such as immediately removing dead larva from the hive. When nurse bees feed the larvae, they secrete into the food substances that inhibit or kill bacteria and other microbes. Their main winter food source, honey, also does not foster the growth of microbes because it is high in sugar and low in water.

Bees also have a highly developed sense of smell, which appears to play a significant role in locating flowers and communicating with each other through chemicals known as pheromones, according to the findings.  The honeybee genome contains 170 olfactory-receptor genes, 157 of which belong to a gene family found to date exclusively in honeybees.  In comparison, fruit flies and mosquitoes have 62 and 79 genes, respectively.

Researchers selected the sea urchin for sequencing because supposedly it is the closest invertebrate to the chordates and because scientists have used it in hundreds of studies dealing with developmental biology, Graur said. Living more than 540 million years ago, a common ancestor of sea urchins and humans was an antecedent of the Deuterostome superphylum. Phyla constituting this group include echinoderms and chordates, the phyla to which humans and other vertebrates belong. The superphylum’s animals—including the sea urchin and humans—are more closely related to other Deuterostomes than they are to other animals, such as fruit flies and worms, outside the superphylum. 

In fact, the project found, the sea urchin shares most of the same gene families with man, although the size of the human gene families frequently are bigger. This indicates that after the sea urchin and human evolutionary lines separated two whole genome replications occurred as vertebrates evolved.

The immune system, however, was one area where a sea urchin gene family was found to be larger than in humans. Humans and sea urchins both possess inborn and acquired immune systems. Yet, although the sea urchin has some of the acquired immunity genes, it has 10 to 20 times as many innate immunity genes as humans. This finding could prove beneficial in learning more about combating infectious disease in humans.

Despite its apparent lack of eyes and ears, the sea urchin remarkably owns sensory protein genes associated with human sight and hearing. The proteins for sight may be located in the sea urchin’s tube feet.

“The findings of the sea urchin homologs for sensory proteins related to vision and hearing in humans may lead to interesting new concepts of perception, and the extraordinary organization of the sea urchin immune system is different from any animal yet studied,” according to the Science article.

The Human Genome Sequencing Center at Baylor College of Medicine led both sequencing projects. Funding for the honeybee sequencing came primarily from the National Human Genome Research Institute (NHGRI) of the National Institutes of Health with additional funding from other U.S and international sources. NHGRI provided most of the funding for the sea urchin sequencing.