At the University of Texas Medical Branch (UTMB) NIEHS Center in Galveston, scientists see environmental health from all angles. Outside laboratory windows, industrial ships and barges crawl along the Houston Ship Channel, passing refineries that spew chalky smoke skyward. Inside, at the lab bench, researchers view twisted strands of DNA fraught with mutations caused by microscopic pollutants. Varying perspectives on health make the center--one of the newest environmental health science centers funded by the NIEHS--a unique place to work.
The center began with a southerly migration; a decade ago, UTMB administrators launched new programs in molecular and structural biology by luring senior scientists to Texas to work on the effort. From schools such as Harvard, Vanderbilt, and MIT, a string of researchers moved their laboratories to this industrial city on the Gulf Coast. By 1995, about 20 top researchers--primarily focused on researching DNA mutagenesis and repair--had gathered in Galveston. It was, as center director R. Stephen Lloyd says, a critical mass--and the motivation to establish the NIEHS Center, which was formed that year. "We're hoping to become a [scientific] powerhouse of the South," says Lloyd. The center is off to a good start. Already, the researchers have reconstituted key DNA repair systems and revealed the workings of several essential proteins.
Environmental assaults on DNA occur everywhere. The sun, auto exhaust, cigarettes, refinery emissions, and even food can send harmful chemicals into cells, where they can jumble the normal nucleotide sequence of DNA. Fortunately, roving enzymes usually spot such instances of mutated DNA, snip them, and stitch healthy genes back together. But sometimes the damage proves too much for repair proteins. When that happens, the mutated DNA may spin off abnormal cells that lead to cancer. The opportunity for environmental assault is all too present in Galveston. Here, lung cancer rates hover near the national high, and petrochemical plants and Superfund sites containing environmental pollutants abound. By sharing environmental health information with the community, center researchers have improved lives and inspired young students in Galveston. Eventually, their work could help treat--or better yet, prevent--some types of cancer nationwide.
Test tube city. Galveston, Texas, provides researchers at the University of Texas Medical Branch NIEHS Center with an environmental microcosm in which to study the effects of pollution on health.
Source: UTMB
Lloyd describes the advantage of the center in one word: synergy. Unlike colleagues who may span the country, center collaborators share the same hallways. Every week, scientists from different labs meet to swap ideas and research results. These brainstorming sessions speed up projects and spur new ones, Lloyd says. "We learn from each other's experiences, whether it's characterizing a set of enzymes or pursuing cutting-edge research."
Center scientists devote their synergies to four research areas: structural biology and physical biochemistry, DNA repair enzymology, signal transduction and control of gene expression, and DNA mutagenesis and molecular epidemiology. Each group gets a technical boost from UTMB's service cores in molecular biology, signal transduction, synthetic organic chemistry, and protein chemistry and purification. In the collaborations, the scientists study specific DNA mutations, how repair proteins respond, and what happens when the system breaks down.
Structural Biology and Physical Biochemistry
It all begins with structure. As every chemist knows, a molecule's form dictates its function. Similarly, the shape of a lesion-DNA complex determines its interaction with repair enzymes, polymerases, and other proteins. In the structural biology of DNA damage and repair research core, biochemists, molecular biologists, and structural biologists team up to unravel the structure of chemicals. They lay bare a chemical's anatomy with X-ray crystallography, nuclear magnetic resonance spectroscopy, and computer models. In particular, the researchers study how environmental toxins damage DNA structure and how the arrangement of a protein or nucleic acid affects its ability to respond to stimuli.
Led by David Gorenstein, the structural biology core is pursuing several projects. In one, scientists study the thermodynamics and kinetics of DNA helicases, enzymes essential to DNA metabolism and repair. Other researchers explore the transcription factor cAMP receptor protein, which activates or represses more than 20 Escherichia coli genes affected by the environment.
Gorenstein's own lab spotlights polycyclic aromatic hydrocarbons (PAHs), which attach to DNA, causing harmful mutations. Some PAHs that rapidly bind to DNA are particularly carcinogenic, and Gorenstein wants to know why. In a study published in the 16 September 1997 issue of Biochemistry, he applied various isomers of the compound benzo[a]pyrene to a known stretch of DNA. He found one common characteristic among the most harmful chemicals: flexibility. Some DNA lesions subtly change shape, hiding from repair proteins. Gorenstein is now investigating in three-dimensional studies how benzo[a]pyrene DNA adducts twist into these elusive conformations.
DNA Repair Enzymology
In the center's DNA repair enzymology and processes research core, a host of molecules--DNA polymerases, DNA-binding proteins, alkyltransferases, nucleases, recombinant proteins, and helicases--are examined under a high-powered microscope as center scientists probe basic questions of DNA damage such as how repair enzymes recognize damaged DNA, how they fix it, and why they sometimes fail. The answers promise new insight into cancer, the immune system, and even aging.
Center scientists are picking apart a number of DNA repair pathways. Satya Prakash, director of this research core, is teasing apart the mechanisms of nucleotide excision repair (NER), the cell's primary method for mending DNA damaged by ultraviolet (UV) light. When bombarded with UV rays, the DNA in skin cells can be jumbled, for example, by joining two thymines. Working together, roughly 30 repair proteins bind the mismatched DNA sequence, unwind and cut the misshapen DNA, and patch the healthy DNA back together.
Prakash and colleagues have identified the key proteins driving NER in yeast. Several yeast proteins, including Rad7 and Rad16, act as damage sensors, spotting UV-damaged DNA. Fueled by adenosine triphosphate, the Rad7-Rad16 complex binds to the altered DNA, flagging the spot for other repair proteins. From that point, a cast of proteins, endonucleases, and transcription factors cleave the mutated strand and carry on. "It's a complex process with a gamut of proteins," says Prakash. "After we used yeast as a model system to understand this DNA repair, other researchers began unraveling the system in humans." Prakash plans to continue breaking down NER in ever greater detail to answer questions such as how repair proteins first recognize DNA damage, and in what order they arrive at the damage site.
Ben Van Houten's lab in this core studies how the functions of the mitochondria gradually decline with age as cells weaken under relentless attack by free radicals. Researchers are testing this hypothesis of how aging occurs.
Signal Transduction and Gene Expression
Like a light switch, molecular signals "turn on" DNA repair genes, sending proteins to fix DNA damage. Scientists in the center's signal transduction and gene expression research core study how these signals regulate DNA repair genes and how the genes, in turn, call chemicals to the rescue. Researchers settle on a DNA repair process to study, and then systematically isolate and sequence the genes involved. In the long run, the research could lead to strategies for countering the DNA-damaging effects of pollution or chemotherapy.
Sankar Mitra, director of the core, focuses on free radicals, also called reactive oxygen species. Released as a result of infection, aging, environmental insult, and simply through breathing, free radicals are derived from oxygen molecules that recklessly ricochet about cells, damaging proteins, fats, and DNA. Researchers blame free radicals for many cancers and extoll the benefits of antioxidants such as vitamins A, C, and E, which apparently neutralize excess radicals.
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Getting down to molecules. Scientists at the center are studying the X-ray structures and molecular models of DNA adducts to learn how DNA is damaged by the environment and repaired by the body.
UTMB
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Mitra studies how free radicals affect DNA repair genes. Last spring, his lab reported that even small amounts of free radicals activate a major DNA repair system involving the enzyme apurinic/apyrimidinic endonuclease (APE). A cell under free radical attack may adapt by churning out higher levels of APE than normal. "It's an extension of the cell homeostasis hypothesis," says Mitra. The cell matches its reaction to the size of the damage it encounters. If a cell can't produce enough APE, it may be unable to fight free radical damage. Now, Mitra is tracking other enzymes that are enabled following free radical exposure. Combined, these proteins build a feedback loop or chain of defense that helps the cell respond to ongoing environmental assault, he says.
DNA Mutagenesis and Molecular Epidemiology
DNA glycosylases are the "proofreaders" of the cell, scanning for DNA damage or errors in replication that must be erased before the genes can be correctly replicated and transcribed. In the DNA mutagenesis and molecular epidemiology research core, scientists study how these proteins navigate around mutated DNA. When these enzymes succeed, damaged DNA is excised. But if the proteins falter, cancer-causing mutations make a home in every dividing cell. By learning just how repair proteins bypass or excise altered DNA, center researchers hope to find ways to bolster the effort with drugs.
One protein important in this process is MutY, a mismatch repair glycosylase that initiates repair of mismatched bases at the site of free radical damage in E. coli. Lloyd, who also heads this research core, recently solved a MutY mystery. For five years, scientists had tried to uncover MutY's crystal structure, but the protein's unstable domains resisted X-ray crystallization. In collaboration with John Tainer at the Scripps Research Institute in La Jolla, California, Lloyd took a different tack than previous researchers. He applied protease enzymes to MutY, chopping the protein until he found two stable domains, one with catalytic activity. By crystallizing just those domains, the team revealed MutY's basic structure--and possibly its function. "MutY is an extraordinarily important enzyme in preventing mutations where the cell might replicate mismatched DNA pairs," says Lloyd. "Now we hope to see whether changes in the protein affect its activity, making some people more susceptible to certain DNA mutations."
Reaching Out
Although it could be decades before the center's work leads to new drug therapies, the researchers are already making lives healthier through a number of outreach programs that cut across clinical program lines. By working with high school students, teachers, and community residents, center scientists spread the word about environmental health. Through educational programs and proactive therapy, UTMB researchers helped cut kids' emergency room visits for asthma by some 90% over the last few years. At a day camp called Camp Rad, children learn what triggers asthma attacks and how to prevent them. High school students work on year-long research projects with graduate students at the UTMB center and present their findings at a research symposium. Scientists also teach health care providers about environmental science at designated area health education centers. "Our main goal is basic science, but we also want to do something positive for the community," Lloyd says. "In both areas, I think we've got a good shot at success."
Kathryn S. Brown
Last Updated: October 29, 1998