Ribozymes are RNA molecules that are capable of catalyzing a chemical reaction. Ribozymes occur naturally inside cells where they play an essential role in the ribosome, joining amino acids together to form protein chains. Ribozymes also play a role in other vital reactions such as RNA splicing, transfer RNA biosynthesis and viral replication.
For many years, researchers thought that only proteins and their cofactors had the structural complexity required to catalyze specific reactions in cells. However, in around 1980, researchers led by Tom Cech’s and Sidney Altman discovered that some enzymes are made of RNA. The first breakthrough was that Cech’s team at the University of Colorado found that an RNA was present in a protozoa called Tetrahymena thermophila that was capable of splicing itself, independently of an outside protein or energy source.
Next, Altman’s team at Yale University discovered another independent RNA in an enzyme called ribonuclease P, which is found in Escherichia coli. The concept of enzymes made of RNA gained credence and overturned the notion that RNA was merely an intermediate in the process of protein synthesis from DNA. Instead, the intrinsic catalytic activity of RNA itself was revealed, a finding for which the two scientists were awarded the Nobel Prize in chemistry in 1989. These ribozymes exhibit all the same features as a protein enzyme including transition state stabilization, specificity and Michaelis Menten Kinetics.
Ribozymes are present in the nucleus, mitochondria and chloroplasts of eukaryotes, as well as in some viruses. These RNA catalysts are grouped by their chemical type, but regardless of the type, all RNA is associated with metal ions such as potassium (K+) or magnesium (Mg2+), which play essential roles in catalysing reactions.
Most ribozymes are involved in the processing of RNA. They either serve as “molecular scissors” and cleave chains of precursor RNA or they serve as “staplers” that ligate two molecules of RNA together. Although most targets of ribozymes are RNA, evidence suggests that the assembly of amino acids into a protein that occurs during translation is also catalyzed by RNA, meaning the ribosomal RNA itself is also a ribozyme.
As well as Cech’s work showing that enzymes made of RNA exist, it also demonstrated that introns, which had previously been considered as non-coding genetic sequences were not actually “junk” at all. The tetrahymena ribozyme Cech’s team discovered was an intron itself and evidence has since demonstrated that as well as having intrinsic catalytic activity, some introns code for proteins that are needed for DNA and RNA to be processed.
RNA was therefore found to have several functions, both as a genetic code repository and as a catalyst in protein synthesis. As the notion that RNA had properties essential to the creation of human life gained credence, the “RNA world” hypothesis was born, which stated that life based on DNA and protein was preceded by RNA, where RNA acted both as cellular enzymes and genetic material. In the process of cellular metabolism becoming more advanced, there was an increasing need to transit to enzymes based on protein and for genetic material to be more stable, in the form of DNA. Researchers excited by this hypothesis started to search many organisms in the hunt for more ribozyme “fossils”.
Researchers have developed synthetic ribozymes in the laboratory that are able to catalyze their own synthesis under specific conditions. One important example is the RNA polymerase ribozyme. Using mutagenesis and selection, scientists have managed to develop and improve variants of the Round-18 polymerase ribozyme from 2001. The most successful of these is called B6.61, which can add up to 20 nucleotides to a primer template over a period of 24 hours.
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