Protein Discovery Could Reverse Genetic Disorders

Two UCSD biologists announced the discovery of a human protein last week that rewinds single-stranded DNA into its normal double-stranded form, potentially preventing critical genes — such as those responsible for genetic disorders — from forming. Previously, only proteins that unwound DNA were known to exist.

DNA is a double helix with four bases in the middle — guanine, cytosine, adenosine and thymine — whose sequence determines an organism’s genes. The two strands are complementary to each other, meaning that their bases fit together like puzzle pieces.

During replication and gene expression, the two strands come apart. This process is often facilitated by a protein called DNA helicase, which uses energy stored in the form of ATP to pull the strands apart. The newly discovered protein, known as HepA-Related Protein, does just the opposite.

“It is the first time anyone has observed DNA actively being rewound,” UCSD professor of biology and project supervisor Jim Kadonaga said. “Often, it has been presumed that the strands always find themselves.”

This DNA zipper binds at the fork, where double-stranded DNA becomes two strands of single-stranded DNA. The protein is actually a motor protein, which means that it travels along the DNA and burns ATP as its fuel source.

Scientists working on the project stumbled across the new function while studying mutations in HARP that cause the rare genetic disorder Schimke immuno-osseous dysplasia. Symptoms of the disease include strokes, congestive heart failure, kidney failure and premature death among children.

“We assumed that [the new protein] had a more mundane function,” Kadonaga said. “It was actually the reverse of that. We found that it binds to the fork and burns up ATP. ATP is like gasoline for a motor protein. If something binds a fork and burns up ATP, you would assume it is a helicase. Timur, who was doing the experiment, had the brilliant idea that it might be the reverse of a helicase.”

To confirm the new suspected function, the group created a number of bubbles; within each, double-stranded DNA separated into two strands and later rejoined as a single section of double-stranded DNA. The scientists then added HARP, which erased those bubbles.

The team — which includes Timur Yusufzai, a postdoctoral fellow in the lab — plans to examine the general cell processes in which the newly discovered protein may be involved, including DNA repair and general maintenance of human genes. They also hope to discover more enzymes of this class.

“There are many helicases,” Kadonaga said. “There are likely to be other reverse helicases like HARP. The other thing is that helicases are involved in separating DNA strands, RNA strands and DNA-RNA hybrids. There are probably reverse helicases that do the same things. This could be the beginning of a whole field.”

Kadonaga’s lab is searching for similar proteins in other organisms. Another reverse helicase was found in fruit flies, easy organisms on which to perform genetic studies due to their rapid rate of reproduction, allowing researchers to track the progress of the gene and to better understand mutations like those that cause the human disease Schimke immuno-osseous dysplasia.

“These things don’t happen that often — to find something so fundamental,” Kadonaga said. “There aren’t that many enzymes that alter the structure of DNA, and to add an entire new protein to this category is exciting.”