Programmed to Repeat

A team of Penn State scientists has uncovered the mechanism by which RNA viruses—which include those that cause the common cold, SARS, influenza, and polio—copy themselves. According to David Boehr, assistant professor of chemistry and a co-leader of the team, the discovery sheds light on a poorly understood region of an enzyme associated with the process of replicating genetic material, and could be an important step toward improving vaccine design.

Motif D shown next to a nucleotide
Boehr Lab

All organisms use enzymes called polymerases to "read" and copy their genetic material. Many of these polymerases are known to have a "cupped right hand" structure—a configuration of atoms that can be described as resembling a palm, fingers and thumb. Within the polymerases of RNA viruses, as in the example shown here, the "cupped hand" holds a loop known as motif D, whose function, until now, was a mystery.

As Boehr explains, all organisms use enzymes called polymerases to “read” and copy their genetic material. While the genetic material of RNA viruses is composed of single-stranded RNA, the genetic material of many other viruses, such as those that cause herpes and conjunctivitis, is composed of double-stranded DNA.

Regardless of whether the genetic material is DNA or RNA, viruses hijack a host cell’s machinery, forcing it to replicate the virus’s own genetic material and, ultimately, to make copies of the virus that will spread to and infect other cells.

Many of these polymerases, Boehr adds, are known to have a “cupped right hand” structure—a configuration of atoms that can be described as resembling a palm, fingers and thumb.

“We’ve known for some time that, in organisms that use DNA as their genetic material, within the ‘palm’ of the hand is a specific helical structure where much of the enzyme action takes place,” he says. “This ‘fidelity’ helix is where nucleotides—molecules that join to form RNA and DNA—are recognized and copied.

“However, the polymerases of RNA viruses do not have this helix structure. Instead, the ‘cupped hand’ holds a different structure—a loop known as motif D. Until now, the function of motif D was a mystery.”

To unravel that mystery, Boehr and his colleagues studied a strain of the poliovirus—an RNA virus that is similar to many other RNA viruses that affect humans. Using a technique called nuclear magnetic resonance spectroscopy, which probes the physical and chemical properties of atoms to determine the structure of organic compounds, they found that motif D is the functional equivalent of the helix structure found in the polymerases of other viruses.

“Previously, it was assumed that motif D had no function at all, or that it provided some sort of scaffolding to support the cupped palm structure,” Boehr says. “But we have found that it is responsible for identifying nucleotides and making sure that a new strand of RNA is replicated faithfully, with as few mistakes as possible.”

What he and his team discovered about motif D’s function in the polio strain, Boehr says, is applicable to many other RNA viruses, including the common cold. In addition, motif D may function similarly in retroviruses, such as HIV, that are replicated using an enzyme called reverse transcriptase to produce DNA from RNA genomes. “Additional studies will be necessary to confirm that motif D’s role is of equal importance in retroviruses,” Boehr notes.

He and his collaborators hope that motif D might provide a new direction for vaccine research. “Now that motif D has been identified as part of the mechanism by which genetic material is replicated accurately, it might be possible to use that information to create safer and more-efficient vaccines,” Boehr says.

As he explains, a vaccine, which is a weakened or harmless version of a virus, works by giving the vaccinated person’s immune system a “picture” of the enemy. Once the immune system knows what the virus looks like, it can recognize and defend against the pathogen when it comes into contact with the wild, harmful version.

But one concern of this strategy is the possibility that a weakened, vaccine version of a virus might evolve once it has been introduced into a population, eventually reverting back to a wild type and becoming harmful again.

“Ideally, every copy a vaccine virus makes of itself inside human cells will be the original, lab-created, harmless version,” Boehr says. “So by fine-tuning motif D—that is, by making this fidelity mechanism even more faithful—it might be possible to reduce the chances that the vaccine version of the virus will mutate and evolve on its own.“

Boehr adds that the research might also provide a new strategy to design vaccines for some of the RNA viruses for which vaccines have not yet been developed.

David Boehr, Ph.D., is assistant professor of chemistry, and can be reached at ddb12@psu.edu. Other Penn State scientists who contributed to the research include Xiaorong Yang, David Lum, and Jesse L. Welch, all of the Department of Chemistry; and Eric D. Smidansky, Kenneth R. Maksimchuk, Jamie J. Arnold, and Craig E. Cameron, all of the Department of Biochemistry and Molecular Biology.

This work was published in the September 5, 2012, issue of the Cell Press journal Structure, and was supported, in part, by the National Institutes of Health.

Last Updated October 04, 2012