Biologists Get First Look At DNA-Protein Binding Structure In An Archaeon

"The DNA has to store the genomic information, so the shape of its surface is variable," said Howard H. Robinson, a cell and structural biologist at the University of Illinois. "We've discovered that protein and DNA bind together in a more interesting way than was ever imagined. This research gives scientists a new avenue for looking at DNA-protein interactions."

In this case, the chromosomal protein Sac7d -- which to the DNA of a hyperthermophile archaeon is as abundant as the binding protein histone is to human DNA -- sticks itself snugly into small grooves between the rungs of DNA and causes the DNA to bend at a 72-degree angle.

"By knowing how this protein binds to DNA, we now understand which amino acids on the surface of the protein interact with the DNA," said Andrew H.-J. Wang, a professor of cell and structural biology. "The DNA-protein binding structure has been elusive. The way this protein binds to DNA, and how it distorts the DNA, is a very new finding. The protein kinks the DNA so that the DNA is sharply bent and stabilized."

To get this new view, the researchers formed a single crystal of the protein with pieces of DNA from the archaeons Sulfolobus acidocaldarius and S. solfataricus. After freezing the crystal with liquid nitrogen at minus 150 degrees Celsius, they were able to determine the three-dimensional structure of the binding complex using X-ray diffraction. The result is a definitive, very-detailed picture of protein binding with DNA.

The binding complex is "a buried box-shaped cavity" between the protein and DNA surfaces, where there are four water molecules, the authors wrote. The ability of the protein to accommodate the variable DNA surface is accomplished by the waters in the cavity reorganizing. The discovery, Wang and Robinson said, will allow researchers to look at other how other proteins might bind to DNA. Robinson and Wang teamed with Yi-Gui Gao, a research specialist in the U. of I. department of cell and structural biology, and Bradford S. McCrary, Stephen P. Edmonson and John W. Shriver, all of the department of medical biochemistry at the Southern Illinois University School of Medicine in Carbondale.

The research -- funded by the National Institutes of Health -- is part of efforts to answer the fundamental question of how DNA is packaged. In humans and other eukaryotes, DNA bends and compacts itself with histone into nucleosomes within cells. In the two other two branches of life, the bacteria and the archaea, the packing of DNA is much less clear, Wang said, because there are no chromosomes. The archaea used for this study are hyperthermophiles -- organisms that live in extreme conditions (in this case near the boiling point of water) -- and very primitive. That combination allows researchers to search for basic hints of how DNA was organized in ancient times.

By learning the structure of DNA-protein binding, Wang said, scientists may be able to obtain clues to how the proteins function in chromosomal organization and gene regulation, and eventually to manipulate proteins in such a way that would forge DNA into specific shapes for specific purposes.