Which came first, the chicken or the egg? A possible solution to this ancient evolutionary riddle is found in a single class of molecules that appears to have functioned figuratively as both chicken and egg early in the evolution of life, perhaps even providing the first method for primitive cells to reproduce.
On the cover of the Sept. 20 issue of the journal Science, colorful "snapshots" reveal the three-dimensional structure of a large molecule in this chicken-and-egg category -- a specialized ribonucleic acid RNA molecule called a RNA enzyme, or ribozyme. The images show how the ribozyme folds itself into a complex molecule capable of triggering cell activity
The discovery, which was made by a team of scientists led by Yale biochemist Jennifer Doudna, could help scientists design new drugs to fight lethal viruses, including the AIDS virus, and repair genetic errors that cause diseases ranging from cystic fibrosis to muscular dystrophy and sickle cell anemia. Collaborating on the research was Nobel laureate Thomas Cech of the Howard Hughes Medical Institute-University of Colorado. Other members of the research team were graduate student Jamie H. Cate and research assistant Kaihong Zhou of Yale; and Anne R. Gooding, Elaine Podell, Barbara L. Golden and Craig E. Kundrot of the University of Colorado.
The discovery of ribozymes, which earned Professor Cech and Yale biochemist Sidney Altman the 1989 Nobel Prize in chemistry, is the basis for a whole new branch of genetic engineering. Ribozymes of the type depicted in this new research, for example, are being developed to function as precision scissors that snip out flawed genetic segments from other RNA molecules and splice in corrected versions. The RNA scissors also can cut a virus's genetic code to shreds so it can't replicate.
One compact genetic package
Scientists had puzzled over which came first -- DNA genetic code or proteins. Without DNA, there would be no way to create proteins, which regulate all biological activity, including the building of bones, blood and muscles. But without proteins, there would be no activity to enable the cell to reproduce. Ribozymes, however, supply both the genetic code and the necessary activity for reproduction in one compact package.
Previously, most RNA molecules were thought to be passive genetic messengers responsible only for transcribing genetic code from DNA molecules and carrying that code to other sites in the cell for the production of proteins. It has recently been learned, however, that ribozymes, a type of RNA, can fold themselves directly into biologically active molecules following a self-contained genetic blueprint.
That discovery, made by Professors Altman and Cech in separate experiments performed in the late 1970s and early 1980s, forced the rewrite of many textbooks to remove the dogma that only proteins can trigger cell activity.
"This capability to serve as a catalyst makes ribozymes a good candidate for being the first method of genetic reproduction and may provide the missing link in our understanding of how the earliest life forms could have evolved," says Ms. Doudna, assistant professor of molecular biophysics and biochemistry.
The new X-ray crystallography snapshots, which capture one- half of a self-splicing ribozyme molecule, reveal a compact, hairpin-shaped structure that is secured by two chemical clamps. The experiments were performed on ribozymes that cut and splice RNA in Tetrahymena, which are single-cell, pond-dwelling creatures that Professor Cech used in his prize-winning research.
Largest ribozyme ever analyzed
The self-splicing ribozyme is by far the largest RNA molecule to have part of its 3-D chemical structure solved by X-ray crystallography in atomic detail. The resulting images provide tantalizing insights into why a RNA molecule can arrange itself into a biologically active molecule while DNA apparently cannot.
The images also have enough detail to help guide genetic engineering, Professor Doudna says, and show the 3-D composition of a recurring motif in all ribozymes -- a chemical unit that makes up one blade of the scissors that snip genetic code. Resolution of the images is precise to 2.8 Angstroms, which is the width of one water molecule, or about three atoms.
"We found that this RNA molecule, which has about 9,500 atoms, contains two regions of contact that hold the two halves of the molecular structure together," Professor Doudna says. "We also found that numerous metal ions -- specifically magnesium ions -- provide a scaffolding that stabilizes the structure. RNA also has a functional chemical group called a two-prime hydroxyl that can make numerous contacts to provide stability. That is one of the keys to why RNA can fold while DNA cannot."
According to Francois Michel and Eric Westhof, French biochemists who reflect on the recent discovery in a "Perspectives" article published in the same issue of Science, the images are "teeming with exciting detail. ... Now that the structural database for RNA is rapidly expanding, the prospects look brighter for eventually predicting RNA three-dimensional structure from its sequence" of chemical building blocks, without requiring complicated imaging methods.
"It would be an important accomplishment to solve a RNA structure simply by knowing its genetically specified sequence of nucleotides," Professor Doudna says. "If we had that kind of understanding of how atoms arrange themselves in three dimensions, it would not only speed drug design but also give us insights into how to fix genetic defects."