Ribozymes

As a student at Grinnell College, I wanted to be a physical chemist. By the time I entered graduate school at UC Berkeley, however, I was very uncertain. Research in gas-phase physical chemistry depended on complex, custom-built machines, and a long time elapsed between designing an experiment and seeing the results. These features didn't match my impatient temperament. Fortunately, I met Professor John Hearst, a physical chemist bursting with excitement about unraveling chromosome structure and function. His enthusiasm was infectious, and as I took up my graduate research, I found myself spending more and more time catching up on molecular biology.

Eight years later, I had my own research group in Boulder, Colorado. I was still studying chromosomes, now in Tetrahymena. This ciliated protozoan has 10,000 copies per cell of a minichromosome encoding the ribosomal RNA, making it advantageous for studies of gene expression. Although we started out exploring gene expression, my group and I soon became sidetracked by an intriguing RNA molecule, initially transcribed as part of the ribosomal RNA precursor and subsequently spliced out. This RNA had not read the biology textbooks, and did not know that biological catalysis was supposed to be the sole realm of protein enzymes; it contained a catalytic active site built of ribonucleotides.

Unknown to us at the time, this "ribozyme" was a molecule long awaited by those considering the origins of life. If a molecule could both carry information and function as a biocatalyst, it might have constituted the primordial self-replicating system. Later, the ability of ribozymes to recognize, cleave, and thereby inactivate disease-causing viral or cellular RNAs would spawn a subfield of biotechnology. These were grand possibilities. What really drove most of our day-to-day research, however, was another sort of question: how can RNA act as a catalyst?

Catalytic RNA molecules, like proteins, are intricate molecular machines. We want to know how these atomic-level machines are assembled, how they work, and how they interact with other cellular components. Our investigations of catalysis by RNA have revealed striking similarities with catalysis carried out by protein enzymes: the RNA provides specific binding sites to line up the reacting groups, and it positions metal ions to speed up the bond breakage and formation steps. This work gets very chemical. Sometimes it almost seems we are treating RNA like a sample of NaCl pulled off the reagent shelf. Yet, we remember that biochemistry is most powerful when it keeps one foot in biology, so we try to incorporate genetic approaches.

Where is this field going? On the biomedical front, the next decade will see critical tests of the utility of ribozymes as pharmaceuticals. This depends in part on advancements in gene therapy, whereby ribozyme-producing genes could be delivered to cells and confer protection against viruses or regulate cell proliferation. Advances in X-ray crystallography, which have provided so many breathtaking pictures of proteins, should allow large ribozymes to be visualized in atomic detail. Finally, there may be conclusive evidence as to whether the ribosome, responsible for protein synthesis in all earthly life, uses its RNA directly for catalysis. If so, the ribosome may be the most important ribozyme.