Scientists at the University of Wisconsin-Madison have begun a major effort to comprehend a poorly understood mechanism that keeps cells working smoothly. They are studying the main pathway that cells use to remove proteins they no longer need or want.
“There is nothing that goes on in a plant or animal that is not touched by this pathway,” says Richard Vierstra, a UW-Madison molecular biologist who is leading the research. “When it isn”t running correctly it can lead to diseases such as Parkinson”s, Alzheimer”s and numerous cancers. What”s even more surprising is that we didn”t know that this mechanism existed until recently.”
Discoveries about the pathway could lead to new approaches for preventing diseases in everything from crops to people, according to Vierstra, who is with the Department of Horticulture. Although he will be studying the pathway in plants, it is virtually identical to the one in animal cells. The National Science Foundation recently awarded Vierstra and colleagues at four other institutions a 4-year, $3.3 million grant to conduct the research.
The ultimate goal of researchers is to modify the pathway to benefit agriculture and medicine. For example, it may be possible to develop plants that resist viral diseases, according to Vierstra. Or, he says, scientists might be able to block the inflammation associated with arthritis, or the muscle wasting that occurs when people are bedridden.
The big question for Vierstra and his colleagues is how the pathway chooses which proteins to degrade. Each living cell is a complex factory that produces thousands of proteins to make its physical structure and its basic cellular machinery. It also produces a second group of 1,000 to 2,000 short-lived proteins that activate various parts of this machinery at the right time and place.
A cell isn”t just awash in the same proteins hour after hour. Cells tightly control the mix of proteins to regulate their activities as they change over time. Scientists once thought that cells regulated their activities just by selectively producing these proteins. But it now looks like the metabolic pathways that selectively break down proteins are also critical players – more critical then anyone first thought, Vierstra says.
Protein-breakdown pathways target two groups of proteins. First they screen all the proteins a cell produces to identify the ones that weren”t formed properly. Secondly they identify those short-lived proteins that must be cleared so a cell can change what it”s doing.
“The main pathway must identify which of these 1,000-plus, short-lived proteins to remove, and that”s an immense recognition problem,” Vierstra says. “We are just beginning to learn about these enzymes in plants, and how and why they target specific proteins.”
The main protein breakdown pathway involves hundreds of different enzymes, each of which recognizes a different protein or group of closely related proteins. When an enzyme identifies a protein that should be destroyed, the enzyme attaches a short protein called ubiquitin to it. The attached ubiquitin then serves as a tag, telling the cell to send that protein to a structure that acts as the cell”s garbage disposal. Like a garbage disposal, it has blades that chop proteins into their component amino acids, which can be reused to make new proteins.
Vierstra became interested in how cells destroy proteins in the late 1980s. He was studying phytochrome, a protein that plants make in order to sense light. As night turns to day, plants shift many of their activities.
“We were impressed by how quickly phytochrome disappeared from plant cells after they were exposed to light,” he says. “Scientists were just beginning to work on the ubiquitin protein-breakdown pathway and we were the first to show in nature that ubiquitin became attached to a protein – in this case phytochrome – before it disappeared.”
During the 1990s, Vierstra and those in his laboratory at the College of Agricultural and Life Sciences accelerated their research on the pathway. Now they are trying to identify all the genes and enzymes involved. They are also trying to determine which proteins are the targets for the ubiquitin tag and where that happens inside cells.
The grant is part of a National Science Foundation initiative to discover the functions of all the proteins of Arabidopsis thaliana, a small plant in the mustard family. Researchers use Arabidopsis to study biological processes common to all plants.
Vierstra will use the grant to study the enzymes that allow the pathway to be highly selective. He says that nearly five percent of the genes in Arabidopsis – approximately 1,250 genes – are involved in this mechanism for protein removal.
“That”s an amazing percentage of the genome to devote to one function,” he says. “Given this size there has to be lots of opportunities to change the pathway in ways that benefit agriculture and medicine.”