Researchers at Oregon State University have discovered how plants defend themselves against viruses at the most basic genetic and molecular levels, opening the way for important new advances in crop breeding, protection of plants against viral disease, and new applications of plants.

The findings, published in the journal Science, provide scientists a more complete understanding of how plants and viruses interact in a “molecular arms race” that began hundreds of millions of years ago, and ultimately explains how plant life has been able to survive in the face of constant attack.

The research also reveals yet another role for “small interfering RNA” molecules, an exploding area of research that has been called one of the most important scientific discoveries in years, and in which OSU experts in the Center for Genome Research and Biocomputing are international leaders.

The study showed that plants have a sophisticated system of “RNA silencing” that basically functions as a primitive immune system, in which plants recognize the double-stranded RNA of invading viruses and activate mechanisms to destroy it. The research also outlines how viruses have developed mechanisms to counteract this response for their own survival.

“The origin of RNA silencing probably dates back hundreds of millions of years, to before plants and animals diverged on separate evolutionary paths,” said James Carrington, professor and director of the Center for Genome Research and Biocomputing. “Animals still have this capability too, but in many cases, such as in humans, this ancient protective mechanism has been largely displaced by other, much more complex immune responses.”

“But in plants, this is still the primary way they protect themselves against viral attack,” Carrington said. “And for millions of years viruses have been developing ways to offset it. It’s a competitive arms race that has allowed both plant life and their viral attackers or parasites to survive, and now we’re learning in much more detail how it works.”

The human immune response is based on the body recognizing foreign proteins, and unleashing a defense involving antibodies, lymphocytes or other cellular mechanisms. By contrast, plants confronted with a virus recognize foreign RNA molecules.

The new study outlined how plants use two “dicer-like” enzymes to cut the RNA into smaller pieces, called small interfering RNA, or siRNA. These siRNA, in turn, act as a guide or steering mechanism to help the plant’s defense mechanism recognize the foreign RNA and destroy it, while leaving other RNA alone. Researchers also explained a redundant aspect of this process, in which multiple dicer enzymes were able and available to coordinate the antiviral defense in case one failed. The overall process of antiviral immunity is called RNA silencing.

“Plants have a silencing system to attack and destroy viral RNA, but what the system needs is something like a bar code or address so it knows how to recognize the virus as distinct from the normal cellular components,” Carrington said. “That’s what the dicer enzymes and siRNA provide.”

In response, the viruses have invented tricks of their own. Some viruses have created systems to tightly bind the siRNA and sequester it, preventing the attack mechanism from proceeding. Some suppressors also bind to and inactivate the dicers, and prevent siRNA from being made altogether.

This research was done with the model plant Arabidopsis, a small leafy plant in the mustard family. The entire genome of Arabidopsis has been decoded, making it an excellent model to understand broader details about plant genetics and function. Other plants such as rice, the researchers said, may have even more dicer enzymes that are involved in antiviral defense.

By knowing in detail how RNA silencing works, how the apparatus has been diversified to allow multiple lines of defense, and how viruses respond to counteract it, researchers believe they should be able to make more rapid progress in combating plant viral disease, a multi-billion dollar problem in many branches of agriculture.

It is possible to design better virus silencing mechanisms in genetically modified plants, they say, more easily identify individual plants that could have strong viral resistance, and ultimately create plants that have immunity to attack from certain kinds of viruses.

“The papaya industry in Hawaii was recently saved by researchers who were able to introduce some viral resistance in that species,” Carrington said. “But that was fortunate, because they didn’t really have the kind of detailed understanding and maps we’ll now have to do this type of work. By really knowing how the process works, we should be able to be far more precise, effective and faster.”

Resistance to viral attack through conventional crop breeding has been one key to major gains in agricultural productivity in the past century. That process may now accelerate, experts say.

This research was done in collaboration with scientists, led by Olivier Voinnet, at the Institut de Biologie Moleculaire des Plantes in France. It was supported by grants from the National Science Foundation, National Institutes of Health, and U.S. Department of Agriculture.

The Center for Genome Research and Biocomputing at OSU is helping to lead a revolution in the biological science by combining collaboration and service in genome-enabled and computationally intensive science.