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Clam Mini-Genome Project
International team of MBL scientists sequencing active
genes of the surf clam

Biomedical researchers the world over credit the study of marine organisms with major breakthroughs in topics as varied as vision, the functioning of nerves, and the cycle of cell division. Yet a lack of genetic information for some of the marine organisms most commonly used in biomedical research, such as the surf clam (Spisula solidissima), have all but halted efforts to explore some basic cellular mechanisms.

“We said that we would give it one more summer,” said Yosef Gruenbaum of Hebrew University of Jerusalem, whose research focuses on studying the structure and function of the nuclear envelope. “Without knowing the clam genome, it has been like walking in the dark with a flashlight, just finding things here and there.” Avram Hershko of Technion Israel Institute of Technology, who studies the regulation of cell division, shares Gruenbaum’s concerns. “We are reaching a barrier in our work, unless we obtain this molecular knowledge,” he said.

So Hershko and Gruenbaum, and collaborators Robert Palazzo of the Rensselaer Polytechnic Institute and Robert Goldman of Northwestern University, all summer researchers at the Marine Biological Laboratory, are teaming up to sequence all of the clam’s active genes, in an effort dubbed the Clam Mini-Genome Project. By this time next year, they plan to know the clam’s active DNA inside out, to have created antibodies from that information, and to have begun experiments impossible without those antibodies. “Sequencing the clam genome will be a quantum leap for our research,” said Hershko.

The four Clam Mini-Genome researchers all focus on mechanisms that regulate cell division. When this carefully scripted process goes awry, human diseases often result. In one such disease, progeria, children age unusually quickly. Goldman says that as rare as that disease is, the NIH has become interested because children with the disease display nearly all the symptoms of aging that the non-diseased elderly do. Understanding the aging process is becoming more and more critical as the elderly become an increasing portion of the American population.

Another group of diseases related to imperfect cell division includes muscular dystrophy, lipodystrophy, cardiomyopathy, neuropathology and mandibuloacral dysplasia. Then, of course, there is cancer, which results from uncontrolleed cell division. “I am sure we are just now hitting the tip of the iceberg with the number of diseases our research will inform,” said Goldman.

Because the goal of the Clam Mini-Genome Project is to sequence all RNA produced at any time in the clam’s life, Hershko’s team will sample RNA from fertilized clam eggs at different stages of development. This winter, the group plans to have matched all that RNA to the DNA that codes for it. Hershko expects the total number of active clam genes to come in at between 12,000 to 20,000 genes, though he said the actual number is impossible to predict. Researchers do not yet know the total number of genes in the clam genome.

The sequencing of the active clam genome will represent the creation of a powerful tool for yet further research. After posting the sequence to a public website, each of the four collaborators plans to use the new tool to inform their own experiments. Because so many basic cellular mechanisms have been conserved by evolutionary processes, Hershko and his team expect that their work will improve understanding of processes in other species whose genes have already been sequenced, including humans. “This is going to help us tremendously to make the clam more important as a cell biological, developmental, biochemical, and even molecular research tool,” says Goldman.

Research to be aided by the Mini-Genome Project

Hershko plans to continue his study of a protein called ubiquitin, which he discovered during previous work with clams, in the intricate ballet of molecular movement that makes up mitosis, one form of cell division. When cells divide correctly, they make perfect copies of their DNA. Usually, those DNA copies only split apart after each copy has been attached to a ‘thread’ within the cell. The threads pull the DNA copies into the nuclei of the newly forming cells. By duplicating and then evenly dividing DNA while cells reproduce, cells conserve genetic information critical to cell life and further division. Hershko hopes that the RNA sequencing will reveal new molecules in the biochemical pathways that usually allow the DNA copies to separate only after the threads are in place. Only a biochemical model constructed outside the cell, Hershko said, will allow him to determine the sequence of events in which different molecules regulate this process, and to learn why it sometimes goes wrong. As some experts believe that this incorrect division is important in the progression of cancer, Hershko’s work may move the world a step closer to understanding one fundamental part of the origin of cancer.

Gruenbaum’s research focuses on nuclear membranes and their role in nuclear envelope breakdown (NEBD) during meiosis, the form of cell division particular to the production of eggs and sperm. “It’s not clear what is going on. There are different models for NEBD, and the models do not all agree with each other,” says Gruenbaum. The clam, because the development of its eggs naturally pauses just before NEBD, is a great model to study the process. Researchers can fertilize eggs or stimulate them with salts, triggering instant breakdown of the nuclei as it releases its contents to form the nuclei of new cells. The ability to synchronize this stage of development in many different clam eggs makes it relatively easy to gather enough raw material to study particular stages of cell division.

Goldman’s experiments focus on the nuclear lamina, made up of proteins known as lamins. The lamina lies just inside the nuclear envelope. Goldman values the clams for the ease of gathering enough nuclear lamins to use for biochemical studies. Although responsible for everything from DNA replication and transcription to determining the size and shape of the nucleus, the lamins represent a relatively small quantity of the molecules that make up the cell. The nuclei, however, are rich with lamins, which help to give nuclei shape. “If you take a batch of eggs, within minutes you can have a test tube full of isolated nuclei,” says Goldman, “and the nuclei retain their cellular architecture beautifully.” Goldman also values the clam nuclei for apparently containing only one kind of lamin, instead of the several in frog eggs or the few in human eggs. This means that it is easier to create antibodies that interact with molecules from tissues other than the eggs, and easier to determine
which proteins are involved in the breakdown of the lamina during cell division. Antibodies are critical to biochemical investigations.

Palazzo is trying to understand what goes wrong when cells create too many centrosomes, subcellular structures responsible for physically organizing the cell before and after cell division. When incorrect numbers of centrosomes are produced and get involved in managing cell division, chromosomes can end up where they are not supposed to be. Many tumor cells, for example, have an abnormal number of centrosomes. Palazzo’s work may lead to a way to correct errant centrosome function in tumors, denying cancers the ability to grow further.

All the researchers agree that the MBL’s proximity to the waters where the clams are collected, and the ability to interact in person with fellow researchers, are the keys to success for this Mini-Genome Project. “Every technique, every idea, you have people to consult with,” says Gruenbaum. “You can exchange ideas, even get new ideas about how to proceed while eating clam chowder.”