Researchers Develop Rapid Technique for Finding Genes That Govern Biochemical Activities Within Cells
November 04, 1999
In yeast cells, the process of finding individual genes is shortened from years to days; new technique will be applicable to the study of human genes
Results reported in November 5 issue of Science
Even with the most sophisticated equipment available, years of painstaking effort are often required to find the genes that trigger various biochemical activities within our bodies - such as the binding of oxygen molecules to hemoglobin in the blood, or the assembly of amino acids into proteins.
Today, however, researchers at the University of Rochester announced that they have developed a new technique that reduces this task - one of the most arduous in biomedical research - to a set of simple experiments that can be accomplished in a matter of days. The new technique is being reported in tomorrow's issue of the journal Science.
The technique was developed using genes from yeast cells, but will be applicable to the study of human genes once the human genome has been sequenced.
The announcement has profound implications for the fields of genetics and medicine. In addition to being able to quickly determine the identity of genes involved in a variety of biological processes, the new technique will allow scientists to screen large numbers of chemicals - ranging from prescription drugs to chemical pollutants in the air - in order to understand their effects on cells.
"More important than the development of this technique are the implications that it has for medical science," said Eric M. Phizicky, Ph.D., one of the authors of the report. "For example, the ability to quickly identify the individual genes involved in any biochemical activity will enable pharmaceutical companies to understand in greater detail how drugs work, and how they cause unwanted side-effects." The new information will help pharmaceutical companies modify the molecular design of their drugs in ways that make them more effective and simultaneously prevent side-effects.
How the technique works
Since 1990, an international effort known as the Human Genome Project has been underway to decipher the entire sequence of human DNA, a strand of three billion chemicals that contains the genetic instructions for carrying out every biological process in the human body. Along the length of the DNA molecule are about 100,000 individual genes, each of which contains the instructions for making one protein molecule that has a specific function in the body. Next year, scientists expect to complete the daunting task of finding the chemical sequence for all of the body's genes, which is collectively called the human genome.
Three years ago, however, other scientists quietly accomplished a similar feat on a much smaller scale: They decoded the entire genome of a single-cell organism, a species of yeast called Saccharomyces cerevisiae. While the human genome contains about 100,000 genes, the yeast genome contains about 6,100 genes.
Researchers at the University of Rochester used the information about the yeast genome to develop 6,144 stains of yeast, which were identical except for one feature: In each strain, they had attached a chemical tag to a different gene.
As the yeast cells were grown in test tubes, each gene provided instructions to make its respective protein molecule - or, in the language of biologists, to "express" its protein. But the instructions from the tagged genes included something else. When a tagged gene sent the instructions to express its protein, it also provided instructions for making the chemical tag. When a tagged gene expressed its protein, its protein was tagged, too, allowing it to be easily separated from its neighboring proteins within the cells. Scientists refer to the process as protein purification.
The researchers distributed the purified, tagged proteins from the 6,144 strains of yeast among a set of test tubes, creating a pool of about 100 different tagged proteins in each test tube. A corresponding chart was created to show which pool contained the proteins that had been derived from which genes.
The researchers tested each pool to discover the identify of three genes - two that are involved in the production of RNA within cells, and one that alters the structure of a protein found in mitrochondria, the energy factory of the cell. The proteins responsible for these activities tested positive by performing their function when the appropriate chemical substrate was placed in its pool. When chemical activity was observed in one of the pools, that pool was then divided into sub-pools to identify the responsible protein and its gene.
The research team is currently developing a second-generation strategy which will enable them to link any detectable biochemical activity in cells with the gene that triggers it in a single day. They expect to have the new system ready in three to four months.
Word of the new technique has spread to universities around the world, even before publication of the report in this week's issue of Science. The research team has had requests from more than 20 universities for materials that will enable them to apply the new technique in their research.
The new technique was developed by Eric M. Phizicky and Elizabeth J. Grayhack of the University of Rochester and Stanley Fields of the Howard Hughes Medical Institute at the University of Washington. Other members of the team include Mark R. Martzen, who built the genome library, as well as Steven M. McCraith, Sherry L. Spinelli, and Francy M. Torres.
The research was funded by the Merck Genome Research Institute, the National Institutes of Health, and the American Cancer Society.