Key cellular enzyme plays key role in gene regulation, CU team finds

By Ernie Mundell, Weill Cornell Medical College

A cellular enzyme known to biologists for years just got a startling makeover.

The discovery by a researcher with dual appointments at Cornell and Weill Cornell Medical College in New York City that poly (ADP-ribose) polymerase-1 (PARP-1) plays a pivotal role in gene transcription could open doors to new therapies for cancer and neurological disease. There are even hints at connections between the foods we eat and gene expression within our cells.

Kraus

"What's catching people's attention is that we have actually characterized a whole new activity for this long-studied protein," said W. Lee Kraus, associate professor of molecular biology and genetics at Cornell and adjunct associate professor of pharmacology at Weill Cornell.

"It's a very, very exciting story," added Anthony Sauve, an assistant professor of pharmacology at Weill Cornell, who is developing drugs that either activate or inhibit PARP-1.

"Dr. Kraus's work is really important," he said, "because he found that PARP-1 is regulating gene transcription -- converting DNA from an active to a silent state. So the real question is, what genes are affected? And for those genes that are either up-regulated in disease or down-regulated, is there a way we can target PARP-1 to turn the genes on or off?"

The findings were published in the Dec. 17, 2004, issue of Cell.

Atomic force microscopy (AFM) images of PARP-1-induced chromatin compaction. The image on the left shows a single molecule of chromatin in the absence of PARP-1. Individual nucleosomes (small white spheres) are clearly visible. The image on the right shows a single molecule of chromatin after the addition of PARP-1. The compact structure of the chromatin is evident. These images were produced by David Wacker, a biophysics graduate student in the Kraus lab, using an AFM instrument at the Cornell Nanobiotechnology Center in Duffield Hall. Photography by David Wacker

PARP-1 is the most abundantly expressed member of a family of proteins long known to be involved in the metabolism of nicotinamide adenine dinucleotide (NAD+), a cellular co-factor involved in both energy use and signaling within cells. According to Kraus, the enzyme also has been implicated in processes surrounding cellular stress and DNA damage.

In their experiments in both human and fly cells, Kraus and his colleagues discovered that PARP-1 also influences gene transcription within the cell nucleus. "We found that, on its own, PARP-1 binds very specifically to the chromatin structures that surround genes, called nucleosomes. When PARP-1 binds to chromatin, it actually tightens those structures -- closing up that architecture and making it much more difficult for genes to become expressed," he said.

But another natural mechanism also can release genes from PARP-1's repressive grip, the Cornell team found. When the enzyme binds with NAD+, this chemical partnership causes PARP-1 to convert the NAD+ into long chain polymers on its surface. Those polymers cause it to lose its connection to a gene's chromatin shell.

"PARP-1 then dissociates from chromatin, the structure opens up -- and genes are free to be expressed again," Kraus explained.

The implications of these discoveries could be profound, he said. By manipulating the NAD+/PARP-1 mechanism, scientists might find new pharmacological ways of switching genes on and off at will.

"Right now, no one is certain exactly which genes are going to be regulated by this system," Sauve said. "That's where the pharmacological approaches are going to be useful." His lab at Weill Cornell is attempting to identify candidate genes, as well as drugs that might intervene in the PARP-1 system.

It could take years before this type of gene therapy reaches patients. But studies are suggesting PARP-1 could play a role in a wide variety of conditions.

Because cancer is essentially driven by genetic abnormalities, it would seem to be an obvious research goal. But Sauve also pointed to recent animal studies that found inhibition of PARP-1 activity is associated with neurological and learning impairment. PARP-1 activity also has been implicated in immune responses, diabetes and aging.

There is the intriguing possibility that the NAD+/PARP-1 system might connect daily diet to genetic activity within cells. "For example, NAD+ is actually synthesized in a special biological pathway that uses niacin -- vitamin B3. It's not been proven yet, but it suggests that dietary effects could have a greater impact on gene expression than we even knew before," Kraus said. "That's another surprise PARP-1 may one day have in store."

Co-authors on the Cell study are all from Cornell, including John T. Lis, the McClintock Professor of Molecular Biology and Genetics, and postdoctoral researchers Mi Young Kim (lead author), Nicolas Gevry and Steven Mauro.

Kraus' work is funded by grants from both the National Institutes of Health and the American Cancer Society.