University of Vermont

University Communications

Biologist Reports in Science on DNA Damage

Release Date: 05-25-2007

Author: Joshua E. Brown
Phone: 802-656-3039 Fax: (802) 656-3203

Whether a simple yeast or a breathtakingly complex mammal, like a human being, all of life requires a reliable source of genetic material to pass on to the next generation. And that means cells need a clean, accurate copy of their DNA before they replicate and divide. Problem is, DNA faces an array of enemies—like radiation and toxins—that threaten to corrupt the information coded within their elegant double helices.

In response to these threats, organisms have developed several clever mechanisms for repairing damaged DNA—all of which, in turn, rely on a clever system of proteins to sense various types of damage to DNA and coordinate a response. This signaling network (the “DNA damage response” or DDR) within a cell is only partially understood, but was known to involve some 30 proteins of the more than 10,000 types that any one cell might produce.

In a research article released today (5/25/07) in the journal Science, Bryan Ballif, assistant professor of biology at the University of Vermont, and a team of colleagues, show that this signaling network is much bigger than was previously understood; it likely involves at least 700 proteins. This discovery “paints a much broader landscape for the DDR than was previously appreciated and opens new avenues of investigation into the responses to DNA damage in mammals,” they write.

“The basic idea behind our study is that it’s very problematic when a cell has its DNA damaged because it can pass on mutations,” Ballif said, “and those mutations could lead to cancer or to a number of other diseases. Part of the reason we put sunblock on is to prevent damage from the sun to our DNA.”

“Once a cell senses the damaged DNA, it prevents itself from going on and replicating. It’s as if the cell is saying, “No, we cannot replicate this DNA, we’ve got to repair it first,’” he explains, “but first it’s got to sense it.”

In order to better understand this sensing system, the first author of the article, Shuhei Matsuoka, at Harvard Medical School, prepared protein extracts of human kidney cells, some of which were treated with radiation that damaged their DNA. Next, UVM’s Bryan Ballif, working in the laboratory of Steven Gygi, also at Harvard, went to work measuring the weights of these proteins in a machine called a mass spectrometer.

“One of the ways in which we determine which proteins are responding to this damage is that one of the master regulators of the DDR—a kinase—right after the DNA gets damaged, starts adding phosphate to other proteins,” Ballif said. “Phosphate has mass—when you add phosphate to something you’re adding atoms to it and you’re changing the mass of that protein.”

“One of the tools we used to detect the increase in mass of the added phosphate is a mass spectrometer—it basically weighs the protein,” he said.

“Our goal was to try to identify as many proteins as we could that might be getting this extra phosphate. We used some innovative technology to sort through all the proteins in the cell and fish out the ones that were specifically modified by this kinase—the results were surprising: we went from knowing 30 proteins that were involved to now as many as 700,” Ballif said.

“We show that perhaps 5-10% of the total protein types in the cell are being mobilized by DNA damage,” he said.

One pair of these proteins is the subject of another report in Science, also published today; Ballif is a co-author on this report as well.

Ballif’s work on the molecular mechanisms of cell signaling—like the DNA damage detection networks reported on today—continues on a mass spectrometer at UVM, provided by the Vermont Genetics Network, funded by the National Institutes of Health. Prior to his recent appointment at UVM, Ballif trained for three years at Harvard Medical School in the study of proteins through mass spectrometry.

For additional information, contact Bryan Ballif, assistant professor of biology, University of Vermont, (802) 656-1389,