Clams are an excellent model system – Hebrew University Professor Yosef Gruenbaum.They may not be kosher, but clams are providing Israeli researchers vital information about genetic diseases in humans. For that reason, Professors Avram Hershko of Technion-Israel Institute of Technology and Yosef Gruenbaum of Hebrew University of Jerusalem, joined American colleagues Robert Palazzo of Rensselaer Polytechnic Institute, and Robert Goldman of Northwestern University at the Marine Biological Laboratory in Woods Hole Massachusetts this summer.
The international team convened to pry open part of the clam genome by sequencing the surf clam’s active genes. The effort, called the Clam Project, is the first step toward sequencing the entire clam genome, and its goal is to provide scientists with better knowledge of the clam’s active DNA. Such information is crucial to the study of the basic cellular processes involved in many diseases such as cancer, premature aging, and muscular dystrophy. The scientists plan to use the new genetic information to create molecular tools such as antibodies, and DNA and RNA probes. And they hope to begin experiments impossible without those antibodies as soon as the project is complete.
“Clams are an excellent model system – in fact a Nobel prize has evolved from work on the clam cell cycle, and Professor Hershko made important discoveries during previous work with clams which helped explain how a cell divides,” Gruenbaum told ISRAEL21c. “Clams produce many ocytes (female sex cells) – they’re all synchronized and their early development can be easily followed. What is learned there can be applied to bio chemistry in large material.”
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.
“Without knowing the clam genome, it has been like walking in the dark with a flashlight, just finding things here and there,” said Gruenbaum.
Hershko agreed with his colleague – “We are reaching a barrier in our work, unless we obtain this molecular knowledge,” he told the MBL publication Lab Notes.
By this time next year, the team hopes 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.
“For us sequencing is a major tool – without it, we’re inhibited in our studies. Once we know the complete sequence, we can deduce the complete protein sequence which leads the way for analyzing important cellular and developmental functions,” said Gruenbaum.
“Sequencing the clam genome will be a quantum leap for our research,” added Hershko.
The four Clam Mini-Genome researchers all focus on mechanisms that regulate cell division.
“Each of the groups in Woods Hole worked on different aspects of the clam genome,” explained Gruenbaum. “Professor Hershko’s group was mostly interested in finding checkpoints of mytosis and myosis, while my team was investigating different aspects of nuclear envelope breakdown – specifically the protein of the inner nuclear membrane.”
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 has implications for the scientific community as it will attract more scientists to use clams as a model system to study areas like cancer development,” said Gruenbaum.
Hershko plans to continue his study of a protein called ubiquitin, 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,” said 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,” said 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.”
The Marine Biological Laboratory, the oldest private marine laboratory in the western hemisphere, is an independent scientific institution, founded in 1888, dedicated to improving the human condition through basic research and education in biology, biomedicine, and environmental science. The research for the Clam Project is made possible through the support of the Manhattan-based Gruss Lipper Family Foundation.
“We have positive results from the summer, but there’s still more to do. Most of the work now is in the hands of a company doing the sequencing for us. The initial results look promising, but we’re aiming for more,” said Gruenbaum.