Scientists Determine Structure Of Novel Protein-RNA Complex

BUFFALO, N.Y. -- At first glance, it might look like an artist's elegant design for a Christmas wreath, but the illustration on the cover of this week's Nature is actually a computer graphic of a strand of RNA that has bound to an unusually symmetrical protein by wrapping itself around the protein's outer edge.

Determined using X-ray crystallography at high-resolution by a team of scientists from the University at Buffalo and the University of York, it is the first 11-subunit protein bound to RNA that has ever been determined. It is one of only a few protein-RNA complexes that have been characterized and one of barely a handful of those that involve messenger RNA (mRNA).

"There are very few known and elucidated examples of complexes between protein and mRNA and very, very few that have been characterized to this level of detail," said Paul Gollnick, Ph.D., UB associate professor of biological sciences and senior author on the paper.

Gollnick conducted the work with co-authors Alfred Antson, Ph.D., and Guy Dodson, Ph.D., while on sabbatical at the University of York.

While the lion's share of genetic research in the past 20 years has focused on interactions between proteins and DNA, it only has been relatively recently that people have begun to appreciate and study the elements that control interactions between proteins and RNA. Probably the most famous example of such an interaction and the one that sparked much of the current interest in RNA was the discovery around 1990 that two RNA-protein interactions are involved in regulating the HIV virus that causes AIDS.

"The protein we study has no relation to HIV," explained Gollnick, "but at the fundamental level, if we can understand how this one works, it may have some relation to the genetic processes by which other proteins bind to RNA."

He explained that in terms of regulating the flow of genetic information from RNA to protein, binding mRNA is crucial.

"So if you want to regulate expression of a particular gene in a protein-RNA interaction, you would want to do it at the mRNA level," he said.

The protein involved is TRAP (Tryptophan RNA-binding Attenuator Protein), which is found in a family of bacteria called Bacilli.

The mechanism by which TRAP functions is called attenuation and several eukaryotic genes (genes found in multicellular organisms like humans), including several cancer genes, appear to be regulated by a similar mechanism.

"By understanding the simpler TRAP system in bacteria, we are beginning to develop a model for understanding more complex systems in some of the eukaryotic genes regulated by attenuation," said Gollnick.

In Bacillus subtilis, TRAP regulates the expression of genes that encode enzymes for the synthesis of the amino acid tryptophan, which is essential for protein-building in humans and also is related to circadian rhythms.

Gollnick explained that these bacteria only will make enzymes to synthesize tryptophan as necessary; if TRAP senses that there is enough in the cell, it automatically turns off gene expression for these enzymes.

"The virtually unique feature of TRAP is that it only binds RNA when it has first bound tryptophan," said Gollnick.

TRAP also has 11 identical subunits, a completely unique structure for a protein, which has scientists in Gollnick's lab at UB working to solve the mystery.

"Most proteins have one or two," said Gollnick. "Even four is odd and there are very few with eight. Why did this thing evolve to have 11?"

Another puzzling feature about the TRAP-mRNA complex is the lack of a folded structure in the RNA. "The RNA to which TRAP binds is entirely single-stranded," said Gollnick. "There is only one other similar example of this known to date."

The research was funded by the National Science Foundation and by The Pew Charitable Trusts.