When Ray Deshaies went to Cornell University in 1979, he thought he might become a horticulturalist. But when he discovered that molecular mechanisms interested him more than growing plants, he decided to major in biochemistry. Moreover, a summer job just before his senior year uncovered his aptitude for research. His older brother, a former budget officer at the National Institutes of Health, counseled him to avoid academia, however, because funding was so scarce.
Deshaies decided he would take his brother's advice if he was unable to gain admission to a top-tier graduate school. Instead, he had the good fortune to choose among several, and ended up at the University of California, Berkeley. Now at Caltech, his lab is working hard to determine how cells destroy unwanted proteins. Deshaies has also cofounded a biotech company to develop cancer drugs that inhibit protein destruction.
Deshaies obtained his Ph.D. in 1988, and left Berkeley in 1990 to move across the bay to the University of California, San Francisco. As a postdoc there, he began to study cell division. The lab in which he performed this work had determined that a protein called ubiquitin plays an important role in the cell cycle (the series of events between one cell division and the next). In 1992, Deshaies made the chance observation that CLN2, one of the proteins involved in a different stage of the cell cycle, is modified by ubiquitin. "In a matter of days, I shifted my research program to study the mechanism of how CLN2 was being modified," Deshaies says.
A few years earlier, Israeli and American scientists who would win a Nobel Prize in 2004 had discovered that ubiquitin gives the kiss of death to unwanted proteins by tagging them for destruction. Over the years, it has become clear that ubiquitin plays roles in almost every important biological process. "What is particularly exciting," Deshaies says, "is that ubiquitin plays a direct role in controlling many of the things that happen in cells."
One of ubiquitin's important functions is to rid cells of old or damaged proteins. Deshaies likens unwanted proteins to milk and meat that are removed from a supermarket when they reach their expiration dates. Ubiquitin is like a brightly colored sticker placed on packages that need to be pulled from the shelves. If these products were not removed, the supermarket would fill up with spoiled food. Similarly, cells would become clogged with outdated proteins if they had no way to remove them. However, they need to differentiate unwanted proteins from those that are still needed. About a third of the proteins in human cells are in flux, so ubiquitin "stickers" are applied constantly.
Deshaies continued to study ubiquitin's involvement in the cell cycle when he joined the Caltech faculty in 1994. In 1997, his group reported in Cell that they had identified a counterpart of the supermarket worker who pastes stickers onto milk—the enzyme complex, known as a ubiquitin ligase, that attaches ubiquitin to CLN2 and another cell cycle regulator. Deshaies's group reconstituted this complex from four known cell cycle proteins. When part of the complex bound to a protein that prevents cells from duplicating their DNA, the protein became a target for ubiquitin and therefore was destroyed. Removal of this protein would permit the cell to progress to the next stage of its cycle.
Identification of this complex, called SCF, opened a new field of inquiry. Subsequent studies have uncovered a large family of SCF-like ubiquitin ligases that may have as many as 300 members. This family exists in all eukaryotic organisms, including humans and plants, and the various ligases target different types of proteins (as if some supermarket workers placed stickers on milk nearing its expiration date and other workers placed them on meat). "The discovery of SCF that established the paradigm of this superfamily was one of the most important things we've done," Deshaies says, noting that the Cell paper has been cited more than 400 times.
At the same time, Deshaies's group reported in Science that SCF attaches ubiquitin only to proteins that have been modified by phosphorylation (the addition of a phosphate group). For many proteins, the same phosphorylation that switches them on when certain signals are transmitted through the cell causes them to be modified with ubiquitin by SCF and then broken down. Thus, as soon as the signal disappears, so does the "switched on" form of the protein. "This is a nice way of making sure that whatever the signaling activates is only activated while the signal is present," Deshaies says.
As more investigators began to study ubiquitin, the system's size and complexity became apparent. "There were a huge number of parts," Deshaies says, "and most of them were poorly studied." In 1999, his lab and a couple of others identified the enzymatic core of SCF as a RING domain. These proteins were known previously, but their functions were unclear. It now appears that most RING-domain proteins (which may number as many as 300) are ubiquitin ligases. Two of these RING proteins are used to assemble the entire superfamily of up to 300 SCF-like ubiquitin ligases.
In 2001, the group determined the function of a protein complex that was known, through genetic studies, to help transmit light signals in plant cells. They determined that this complex, called the COP9 signalosome, is an enzyme that controls SCF activity by clipping a ubiquitin-like protein from one of the ligase's subunits. The next year, they found that the signalosome's enzymatic activity resides in a protein-cleaving subunit that requires zinc. A related complex known as the "lid" of the proteasome (the large enzyme complex that shreds ubiquitinated proteins) also uses a zinc-binding enzyme to cleave ubiquitin from proteins that are being shredded. "Finding that the signalosome and lid were using an enzymatic site that had not previously been discovered was one of the most surprising findings my group has made," Deshaies says.
Although Deshaies's major focus was ubiquitin by this time, some of his work still involved the cell cycle. In 1999, his group discovered that a protein called a phosphatase that is needed to propel cells out of mitosis (the cell cycle stage that duplicates chromosomes) is sequestered in a region of the nucleus called the nucleolus. At the end of mitosis, the phosphatase is released. "That established the paradigm that you can control protein activity by reversibly storing a protein in the nucleolus and releasing it when you want it to be active," Deshaies says. In 2004, his group demonstrated that the protein that tethers the phosphatase to the nucleolus loses its grip when it becomes phosphorylated at the end of mitosis. Other labs have since uncovered several important examples of protein regulation by nucleolar sequestration.
Although Deshaies has spent most of his career unraveling the mechanisms, functions, and regulation of ubiquitin ligases, he has been keenly aware of the connections between the ubiquitin system and human disease. For example, cancer cells depend heavily on this system to degrade abnormal proteins and might therefore be more sensitive than normal cells to inhibitors of protein breakdown. With this idea in mind, Deshaies cofounded the biotech company Proteolix in 2003. Proteolix has developed a drug that inhibits the proteasome in a completely different way than the proteasome inhibitor already on the market. The drug's efficacy is now being tested in small clinical trials. "We have seen some very positive responses in patients with multiple myeloma," Deshaies says.