International Team Finds Structure of Protein Important for Bacterial Virulence

By Mika Ono

A team of scientists at The Scripps Research Institute, Stanford Synchrotron Radiation Lightsource, the University of Tokyo, and other institutions has solved the structure of a protein that helps bacteria cause disease. The research provides new clues for understanding the mechanisms behind bacterial infections and for working toward the development of novel treatments to combat conditions including pneumonia, sepsis, and meningitis.

The research was published in the April 14, 2010 issue of Structure, a Cell Press journal.

"The study illuminates a novel structural arrangement in a protein called CvfB, found in a variety of virulent bacteria," said Scripps Research Professor Ian Wilson, senior author of the study and principal investigator of the Joint Center for Structural Genomics, a multi-institutional consortium. "This structure provides insights into an important piece of the puzzle to better understand how bacteria cause infection."

In the research, the scientists examined CvfB from the organisms Staphylococcus aureus (a common cause of potentially life-threatening staph infections, especially in hospital settings) and Streptococcus pneumoniae (a frequent cause of pneumonia, ear infections, sinus infections, and meningitis).

The study's results provide new insight into the structure and function of a key bacterial protein, which consists of an unusual combination of nucleic acid binding modules.

Parallel Paths

The new paper is the result of the convergence of research from two groups, one in the United States and one in Japan, which had both independently identified CvfB as warranting further investigation. CvfB is found in more than 300 bacteria species and has been linked to a gene network that controls virulence (ability to cause disease). CvfB is highly "conserved," meaning that it has remained essentially unchanged throughout evolution, probably due to its importance for the bacteria's survival.

In the United States, researchers at Scripps Research, the Stanford Synchrotron Radiation Lightsource/SLAC National Accelerator Laboratory, and other institutions came together under the umbrella of the Joint Center for Structural Genomics to conduct structural studies on CvfB.

The group used a technique called x-ray crystallography, in which scientists produce quantities of a protein and try to crystallize it. This crystal is then placed in a beam of x-rays, which diffract when they strike the atoms in the crystal. Based on the pattern of diffraction, scientists can reconstruct the three-dimensional atomic arrangement of the protein molecule.

Working with CvfB from several different organisms to increase the chance of success, the team was able to solve the structure of the protein from Streptococcus pneumoniae.

Excited by the results, the U.S. researchers reached out to a group in Japan that had been systematically testing proteins to find which ones were important in bacterial virulence and had initially identified CvfB.

"When we contacted them about a possible collaboration, they already had a preliminary paper written," said Qingping Xu of the Stanford Synchrotron, who is the lead crystallographer on the paper. "We found that our results corroborated each other perfectly."

The Japanese researchers had been studying CvfB from Staphylococcus aureus using biochemical techniques. After comparing their biochemical data with the structural findings, the team—now made up of scientists on both sides of the ocean—conducted some additional experiments and a paper was born.

In the end, the study showed that CvfB is made up of a unique combination of four modules, arranged in an L-shaped chain. Three consecutive modules are S1 RNA binding domains (named in accordance with the subunit of the ribosome which they are similar to, specifically small (S1 to S31) and large (L1 to L44)). The fourth module represents a motif known as a winged-helix domain, common for binding DNA but unusual for RNA binding.

The team also described exactly where and how CvfB bound to RNA.

"Even though all four of these domains are capable of binding RNA, we found that in this case only the last of the S1 domains and the winged-helix domain are involved in RNA binding," said Xu. "We think the protein is using the other two domains to interact with other machinery in the cell. What kind of machinery is currently not clear."

The team, however, continues to investigate the topic.

Yasuhiko Matsumoto of the University of Tokyo is first author of the paper "Structure of a Virulence Regulatory Factor CvfB Reveals a Novel Winged-helix RNA Binding Module," with Xu. In addition to Wilson, Xu, and Matsumoto, other authors include Shinya Miyazaki, Chikara Kaito, and Kazuhisa Sekimizu of the University of Tokyo; Carol Farr and Marc-André Elsliger of the Joint Center for Structural Genomics (JCSG) and Scripps Research; Herbert Axelrod, Hsiu-Ju Chiu, Mitchell Miller, and Ashley M. Deacon of JCSG and Stanford Synchrotron Radiation Lightsource; Heath E. Klock and Mark W. Knuth of the JCSG and the Genomics Institute of the Novartis Research Foundation; Adam Godzik of the JCSG and Sanford-Burnham Institute for Medical Research and University of California, San Diego; and Scott Lesley of JCSG and the Genomics Institute of the Novartis Research Foundation and Scripps Research. See http://www.cell.com/structure/abstract/S0969-2126(10)00099-7

The research was sponsored by the U.S. National Institutes of Health's National Institute of General Medical Sciences Protein Structure Initiative, by a grant-in-aid for Scientific Research (Japan), and by the Program for Promotion of Fundamental Studies in Health Sciences of the National Institute of Biomedical Innovation (Japan) and Genome Pharmaceuticals Institute Co., Ltd. (Japan). Portions of the research were carried out at the Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, a national user facility operated by Stanford University on behalf of the U.S. Department of Energy.

Send comments to: mikaono[at]scripps.edu

"This structure provides insights into an important piece of the puzzle to better understand how bacteria cause infection," says Professor Ian Wilson.