Ribozymes: catalytic RNAs that cut things, make things, and do odd and useful jobs

Abstract

Catalytic RNAs, or ribozymes, are a fossil record of the ancient molecular evolution of life on earth and still provide the essential core of macromolecule synthesis in all life forms today. Are they also an avenue to the development of new catalysts to recreate evolution, or to use as therapeutics and molecule sensors.

Figure 1

The catalytic portfolio of ribozymes. (A) Hydrolysis (R’ = H) or transesterification (R’ = organic residue) of an RNA or DNA phosphoester linkage. R’ = H for RNase P, R’ = guanosine for group I introns, R’ = internal adenosine for group II introns. (B) RNA cleavage as catalysed by the small hammerhead, hairpin, and HDV ribozymes (B=base). (C) RNA chain elongation. (D) Peptidyl transfer (Nu = NH2 group of another amino acid), amide bond formation (Nu = 5’-NH2 of a modified RNA), or ester hydrolysis (Nu = water). (E) Isomerisation. (F) Diels-Alder cycloaddition.

Figure 2

What they look like: Schematic representations of the three-dimensional structures of three small ribozymes, engineered to act in trans on external substrates of choice. Long dashed lines, sequences removed to generate the trans-acting ribozymes; gold, substrates; arrows, cut sites. Additional colours used in the hairpin and HDV ribozymes correlate with those used in Figure 3.

Figure 3

Caught in the act: Details of the catalytic core of the hairpin and HDV ribozymes. The colour scheme is the same as in Figure 2. The red nucleotides are poised to act on the substrate by abstracting or donating a proton. Dashed purple tubes, hydrogen bonds to fix the substrate in place.

Figure 4

A ribosome’s true colours. (Top) The large subunit of the ribosome, with proteins in blue and RNA components in orange, grey, and burgundy. Green and red ribbons, tRNAs. (Bottom) The peptidyl transfer mechanism catalysed by the RNA components of the ribosome. A particular adenosine (A2451 in Escherichia coli) is rendered unusually basic by its environment within the folded structure; it is presumed to act as a base and abstract a proton as shown. Reprinted with permission from T R Cech (2000). Copyright 2000, American Association for the Advancement of Science.

Figure 5

Teaching an ancient dog new tricks by harnessing nature’s techniques: In vitro evolution of RNA. Starting from a library of many diverse molecules, the fittest ones for a certain function are selected, amplified, mutagenised, and re-selected until the winners fulfil a given task to perfection.