Proteins are the indispensable catalytic workhorses, carrying out the processes essential to life in today's sophisticated organisms, but long ago ribonucleic acid (RNA) reigned supreme.

Researchers have produced an atomic picture that shows how two of these very old molecules interact with each other and it provides a rare glimpse into the transition from an ancient, RNA-based world to our present, protein-catalyst dominated world. 

The scientists show the atomic details of how ribonuclease P (RNase P) recognizes, binds and cleaves transfer RNA (tRNA). They used the powerful X-rays produced by the Advanced Photon Source at Argonne National Laboratory to obtain images from crystals formed by these two RNA molecules. The result is a snapshot of one of the most complex models of a catalytic RNA and its target.

Crystal structure of the T. maritima RNase P holoenzyme in complex with tRNA
Crystal structure of the T. maritima RNase P holoenzyme in complex with tRNA.  Credit: Nature

For billions of years and still to this day, the function of RNase P -- found in nearly all organisms, from bacteria to humans -- has been to cleave transfer tRNA. If the tRNA is not cleaved, it is not useful to the cell.

RNase P is formed by a large RNA core plus a small protein, illustrating the evolutionary shift from an RNA world toward a protein-dominated world. The protein helps recognize the tRNA, but most of the recognition occurs through RNA-RNA interactions involving shape complementarity and also base pairing.

"RNA is an ancient molecule, but it is pretty sophisticated," said Alfonso Mondragón, professor of molecular biosciences in the Weinberg College of Arts and Sciences at
Northwestern.   "Our crystal structure shows that it has many of the properties we ascribe to modern molecules. RNA is a catalyst that has much of the versatility and complexity of modern-day proteins."
The structure shows that once RNase P recognizes tRNA, it docks and, assisted by metal ions, cuts one chemical bond. This matures the tRNA, producing a smaller RNA molecule that now can contribute to fundamental processes in the cell. The RNA-based enzyme does this over and over, cutting each tRNA in exactly the same place every time.

"The discovery nearly 30 years ago that RNA molecules can have a catalytic function raised the idea that maybe RNA was the first molecule," Mondragón said. "Our work reinforces this notion of the existence of an RNA world when life first began."

Nicholas J. Reiter, Amy Osterman, Alfredo Torres-Larios, Kerren K. Swinger, Tao Pan, Alfonso Mondragón, 'Structure of a bacterial ribonuclease P holoenzyme in complex with tRNA',  Nature (14 November 2010) doi:10.1038/nature09516