News Of The Week
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July 24, 2000 - Volume 78, Number 30
- CENEAR 78 30 pp. 11-12
- ISSN 0009-2347
Versatile RNA Folds Into Two Ribozymes
Rebecca Rawls
Courtesy of Erik A. Schultes |
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A single RNA sequence (at top) represented as beads on a string, is capableof folding into active ligase and HDV conformations. The beads (nucleotides) are color coded to reflect regions of hydrogen bonding in the ligase conformation, which do not carry over into HDV structure. |
For proteins, amino acid sequence determines structure, which in turn determines function. But catalytic RNAs don't necessarily play by the same rules, according to biology associate professor David P. Bartel and postdoctoral fellow Erik A. Schultes of Massachusetts Institute of Technology and the Whitehead Institute for Biomedical Research. To prove their point, the researchers have constructed an RNA sequence that can fold two different ways, and each configuration has its own quite different catalytic activity [Science, 289, 448 (2000)].
Compared with other ribozymes, the new sequence isn't a very good catalyst in either of its possible configurations. But the mere fact that it can take on two different shapes and functions at all upsets one of the canons of molecular biology. It means that, at least some of the time, ribozymes can evolve new capabilities without first acquiring mutations that change their RNA.
Bartel and Schultes study how, in the course of evolution, new RNA folds develop and thereby new functions develop. Both theoretical arguments and an examination of the sequences of naturally occurring ribozymes show that a wide variety of very different sequences can all produce the same basic fold. That means that RNA sequences can accumulate a lot of changes that do not affect their folding or catalytic function. "Sequences can drift very, very far," Bartel says, "so far that they approach the sequences of other ribozymes with other folds and other functions." The researchers wanted to test whether these regions of drift could actually overlap, so that the same sequence could fold in two different ways to become, in effect, two different ribozymes.
To test this possibility, they chose two ribozymes of the same size but with different structures and catalytic functions. One is the hepatitis delta virus (HDV) ribozyme, a naturally occurring ribozyme that catalyzes a reaction that cleaves RNA. The other is a class III ligase generated in the laboratory by "test-tube" evolution that catalyzes formation of a phosphodiester bond.
"When you know the sequence requirements for both ribozymes, you can write down sequences that you think might be able to fold into one or the other ribozyme and catalyze the two reactions," Bartel says. "We've done that, and in the couple that we have tested, they do have a little bit of the activity for both enzymes."
The resulting sequence is more likely to fold into the shape of the ligase ribozyme, where it produces a 460-fold improvement over the uncatalyzed rate of reaction. But sometimes it folds into the HDV ribozyme shape, where it improves RNA cleavage rates about 70-fold. By making one or two key changes to the RNA sequences, the researchers can greatly improve the ribozyme's catalytic ability for either reaction, but when they do so, they lose all crossover capability.
Although Bartel makes finding the right sequence seem a simple matter, it is "no mean feat," writes Gerald F. Joyce , professor of chemistry at Scripps Research Institute , La Jolla, Calif., in a commentary accompanying publication of the MIT work. "Imagine generating a string of text that, without changing the order of a single letter, could be grouped into different words so as to provide two paragraphs that have entirely different meanings," he writes. Such a task would be nearly impossible using the standard 26-letter alphabet or the 20-letter amino acid "alphabet" used to construct proteins. It can be done with RNA, however, because it is constructed from a four-letter alphabet of nucleic acids.
- Chemical & Engineering News
- ISSN 0009-2347
- Copyright © 2006 American Chemical Society
