An unusual RNA structure in the SARS virus

The SARS virus is a type of RNA virus, meaning that its genetic material is RNA rather than the more familiar DNA found in the chromosomes of everything from bacteria to humans. All RNA viruses have relatively high mutation rates, making their genomes highly variable. In HIV, for example, this high rate of mutation contributes to the rapid appearance of drug-resistant strains of the virus. In SARS and related viruses, however, one segment of the RNA genome--known as the s2m RNA--remains virtually unchanged.

"Because viral evolution has not been able to tamper with this sequence, it is clear that it must be of vital importance to the viruses that have it, but no one knows exactly what its function is," said William Scott, an associate professor of chemistry and biochemistry at UC Santa Cruz.

Scott's lab used the technique of x-ray crystallography to solve the structure of this RNA element with nearly atomic resolution, revealing where every one of the many thousands of atoms that make up the structure is situated. The results showed several unique and interesting features of the s2m RNA, including a distinctive fold that appears to be capable of binding to certain proteins involved in regulating protein synthesis in cells.

"The structure gives us strong hints about the function, because it forms a fold that has been implicated in binding a certain class of proteins," Scott said. "The structure itself also provides a starting point for designing antiviral drugs that might bind to this RNA and prevent it from doing whatever it is that is vital to the life cycle of the virus."

The UCSC researchers are publishing their findings in the journal PLoS Biology (Volume 3, Issue 1). The first author of the paper is Michael Robertson, a postdoctoral researcher in Scott's lab. Robertson and Scott purified large amounts of s2m RNA, crystallized it, bombarded the crystals with x-rays, and determined the structure from the resulting pattern of x-ray scattering.

The other coauthors, in addition to Scott, are Manuel Ares, professor of molecular, cell, and developmental biology and a Howard Hughes Medical Institute (HHMI) professor; Haller Igel, a research associate in the Ares lab; David Haussler, professor of biomolecular engineering and a HHMI investigator; and Robert Baertsch, a graduate student working with Haussler.

All of the authors are affiliated with UCSC's Center for Molecular Biology of RNA. The strong interdisciplinary connections within the RNA center were a key to making the project possible, Scott said. The investigation brought together bioinformatics experts Baertsch and Haussler, who performed the computational sequence analysis of the genomes of SARS and related viruses; molecular biologists Igel and Ares, who cloned and chemically characterized the s2m RNA; and RNA crystallography experts Robertson and Scott.

"It's true that exciting discoveries are often made at the interfaces between disciplines, but it's rare that you see it happening in such a vivid way. This is a great example of interdisciplinary science at work," said Harry Noller, Sinsheimer Professor of Molecular Biology at UCSC and director of the RNA center.

Different types of RNA perform a variety of critical tasks in all living cells. Messenger RNA is the intermediary that carries genetic information from the DNA in the chromosomes to the cellular protein factories, called ribosomes, where the genetic information is translated into proteins. The ribosomes themselves are made primarily of ribosomal RNA.

The SARS s2m RNA is in an untranslated section at one end of each of the messenger RNAs that direct the production of viral proteins in infected cells.

"It hangs on the tail end of the messenger RNA like a little molecular knob," Noller said.

Noller, an expert on the ribosome, noticed that a sharp, 90-degree bend in the s2m RNA structure is similar to a part of the ribosome. "It may only be a superficial resemblance, but you don't often see this kind of right-angle bend in RNA," Noller said.

This part of the ribosome and the proteins that bind to it are involved in the regulation of protein synthesis, leading Scott and his coauthors to hypothesize that the s2m RNA, by mimicking the ribosomal binding site, may serve to hijack the host cell's protein-synthesis machinery for use by the virus. This hypothesis will have to be tested by further studies, which are already under way in Ares's lab.

"The precise function is something they're going to figure out, no doubt about it, and it's bound to be something of major importance," Noller said. "When you see a whole class of viruses that have this absolutely conserved structural element, it tells you there's something really interesting going on here."

Sequence analysis by Haussler and Baertsch found that viruses in two families--coronaviruses (which include the SARS virus) and astroviruses--share the s2m element. About 75 percent of this sequence is absolutely invariant between viral species. Furthermore, an analysis of 38 different SARS variants found absolutely no variation within the s2m sequence.

Other scientists had previously noticed this highly conserved element in astroviruses and a few other viruses, and had given it the s2m name. But no one had any idea what the s2m RNA does that would explain why it is so highly conserved, Haussler said.

According to Scott, the UCSC team's investigation represents a novel approach in the field known as structural genomics. A more common approach in structural genomics is to determine the three-dimensional shape of a novel protein and compare it to the shapes of proteins with known functions to find clues to the function of the unknown protein.

"We have taken the methodology of conventional structural genomics and extended it to investigate the structure of the RNA genome itself," Scott said.

Ultimately, this research could lead to the development of antiviral drugs that would bind to the s2m RNA and prevent it from carrying out its function. Such drugs might be effective against a range of coronaviruses and astroviruses. While the SARS virus is the most deadly of these, other coronaviruses are common causes of respiratory infections in humans and other animals. Although none of the other human coronaviruses have the s2m RNA, several important animal pathogens do and would be susceptible to a drug that targets s2m.

Astroviruses, meanwhile, are a leading cause of gastrointestinal infections, second only to rotaviruses as a cause of childhood diarrhea. In developing countries, diarrhea is a major cause of death in children. A drug that blocks s2m could help alleviate this suffering, as well as provide another tool in the fight against SARS.

Source: University of California - Santa Cruz