Editor’s note: Michael J. Smerdon, professor of biochemistry and biophysics, delivered the Washington State University Distinguished Faculty Address on Feb. 17. He is the 66th faculty member selected for the honor since the address was instituted as the Invited Address Series in 1958. The address is sponsored by WSU to honor its outstanding scholars; to stimulate creative activity; and to provide an opportunity for students, staff and friends of the university to become acquainted with the broader aspects of our cultural heritage and scientific achievements. The address is designed for an all-university audience.

Smerdon’s Research Focuses on DNA Repair

PULLMAN, Wash. — Solutions to puzzles often come as surprises, yet once found, the solutions make perfect sense. Michael Smerdon, professor of biochemistry and biophysics at Washington State University, has been surprised many times during his career. Maybe the first time was when he discovered that someone with a master’s degree in physics could be happy in the world of biology. Physicists often work with minute particles like photons and quarks, while biologists work with much bigger molecules, like DNA and proteins.

“Things as big as proteins make a physicist shudder,” says Smerdon.

Smerdon’s doctoral project involved studying how the proteins called histones fold and interact with each other. Histones are involved in compacting a cell’s DNA so that it will fit into the minuscule space of the cell’s nucleus.

DNA exists as two complementary strands that form a double helix or twisted ladder structure. The helix makes complexes with the histones to form chromatin, which is composed of repeating units called “nucleosomes.” When viewed through an electron microscope, nucleosomes look like beads on a string. The beads are DNA tightly wound around the histones, and the string is pure DNA.

Smerdon’s postdoctoral project examined the relationship between DNA repair and the structure of chromatin. By this time, researchers had determined that Xeroderma pigmentosum, a disease Smerdon had read about in the late 1960s, was caused by a defect in DNA repair. People with Xeroderma pigmentosum are 2,000 times more likely to develop skin cancers than those who do not.

DNA repair remains the focus of Smerdon’s research. While his work examines basic questions in science, his goal is to have what he learns extended to the clinical level and the prevention and treatment of cancer.

DNA repair is necessary because our cells’ DNA constantly is assaulted and damaged by ultraviolet light, toxic chemicals and even the by products of the cells’ own daily activities.

The amount of damage is staggering. Using oxygen and living at 98.6 degrees F, cells experience about 20 different types of DNA lesions. In one day, each cell in the body collects 10,000 to 20,000 of these lesions. If they remain unrepaired, the amount of damage is incompatible with life, says Smerdon.

Smerdon has spent two years on sabbatical in Switzerland working on yeast chromatin with professor Fritz Thoma at the ETH Hönggerberg. He and Thoma looked at the repair of DNA in yeast chromatin damaged by ultraviolet light. They examined DNA repair in each of the strands in a segment of DNA containing an active gene. Active genes are those actually being used to make the proteins a cell needs to function.

Their results showed that DNA damage within an active gene was repaired more rapidly than DNA damage elsewhere. Even more interesting, they found that only the one strand of DNA that actually codes for the protein was repaired quickly. The other strand was repaired at the same rate as DNA not encoding active genes. A group working on DNA repair at Stanford reported the same results in mammalian cells while Smerdon and Thoma were obtaining their findings in yeast.

“The results were a surprise,” says Smerdon. But they make sense. If a cell doesn’t repair damage to the DNA it needs for daily life, the cell dies. Other DNA is less immediately important.

Two other surprises were the result of work done by Jim Gale, a graduate student in Smerdon’s lab. To understand that work, it might help to think of the nucleosome as a two-strand braided rope wrapped around a rock. At regular intervals along the rope, one strand is next to the rock and the other is away from it.

Gale developed a way to determine, at any given location along the DNA, which strand was next to the histones. By combining that information with the location of an ultraviolet lesion in the same DNA strand, he could determine whether the lesion faced the histones.

Gale found that the DNA facing histones is damaged less by ultraviolet light than the DNA facing away. Initially, this didn’t make sense to the physicist in Smerdon, for he knew that the amount of ultraviolet light absorbed by each DNA strand was equal. But it did make sense when he and Gale considered the fact that the DNA next to histones is physically constrained by them. Damage caused by ultraviolet light makes the DNA change shape slightly, and if it’s difficult for the DNA to change shape, it’s harder for the damage to occur.

Karen Jensen, a research associate in Smerdon’s lab, used Gale’s technique to examine DNA repair in each of the DNA strands in the nucleosomes of human cells. She compared the rate of repair in DNA facing histones and DNA facing away. Smerdon expected that the rates would be different because the damaged sites next to the histones might be hidden from the repair machinery. Jensen’s experiments, however, showed that the rates were the same.

The work of Gale and Jensen is the result of an early tangent in Smerdon’s research, a surprise result that’s led to a major thread in his 20 years of research. While trying to determine whether the DNA in nucleosomes was repaired at the same rate as the DNA outside of them, he discovered that the nucleosomes did not remain intact during repair. They appeared to unfold before repair, then refold at the end of the repair process.

“This suggested that the DNA in the nucleosome and the DNA outside the nucleosome looked just the same to the repair enzymes,” says Smerdon. And it raised a series of questions that he’s still working to answer, such as how the repair machinery finds damage in chromatin.

Of course there have been other surprises along the way, as Smerdon’s knowledge of DNA and its repair has expanded, but one underlies them all.

“The incredible malleability of the DNA molecule and chromatin are a constant source of surprise to me,” says Smerdon.