Dictionary: ribozyme   (rī'bə-zīm')

An RNA segment that has the ability to catalyze the cleavage and formation of covalent bonds in RNA strands at specific sites.

[RIBO(NUCLEIC ACID) + (EN)ZYME.]

A ribonucleic acid (RNA) molecule that, like a protein, can catalyze specific biochemical reactions. Examples include self-splicing rRNA and RNase P, both involved in catalyzing RNA processing reactions (that is, the biochemical reactions that convert a newly synthesized RNA molecule to its mature form). Different ribozyme structures catalyze quite distinct RNA processing reactions, just as protein enzyme families that are composed of different structures catalyze different types of biochemical reactions.

Ribozymes share many similarities with protein enzymes, as assessed by two parameters that are used to describe a biological catalyst. The Michaelis-Menten constant K_m relates to the affinity that the catalyst has for its substrate, and ribozymes possess K_m values which are comparable to K_m values of protein enzymes. The catalytic rate constant describes how efficiently a catalyst converts substrate into product. The values of this constant for ribozymes are markedly lower than those values observed for protein enzymes. Nevertheless, ribozymes accelerate the rate of chemical reaction with specific substrates by 10¹¹ compared with the rate observed for the corresponding uncatalyzed, spontaneous reaction. Therefore, ribozymes and protein enzymes are capable of lowering to similar extents the activation energy for chemical reaction. See also Enzyme; Protein; Ribonucleic acid (RNA).

Ribozymes are RNA molecules that catalyze chemical reactions. Most biological processes do not happen spontaneously. For example, the cleavage of a molecule into two parts or the linkage of two molecules into one larger molecule requires catalysts, that is, helper molecules that make a reaction go faster. The majority of biological catalysts are proteins called enzymes. For many years scientists assumed that proteins alone had the structural complexity needed to serve as specific catalysts in cells, but around 1980 the research groups of Tom Cech and Sidney Altman independently discovered that some biological catalysts are made of RNA. These two scientists were honored with the Nobel Prize in chemistry in 1989 for their discovery.

Structure and Function

The RNA catalysts called ribozymes are found in the nucleus, mitochondria, and chloroplasts of eukaryotic organisms. Some viruses, including several bacterial viruses, also have ribozymes. The ribozymes discovered to date can be grouped into different chemical types, but in all cases the RNA is associated with metal ions, such as magnesium (Mg2+) or potassium (K+), that play important roles during the catalysis. Almost all ribozymes are involved in processing RNA. They act either as molecular scissors to cleave precursor RNA chains (the chains that form the basis of a new RNA chain) or as "molecular staplers" that ligate two RNA molecules together. Although most ribozyme targets are RNA, there is now very strong evidence that the linkage of amino acids into proteins, which occurs at the ribosome during translation, is also catalyzed by RNA. Thus, the ribosomal RNA is itself also a ribozyme.

In some ribozyme-catalyzed reactions, the RNA cleavage and ligation processes are linked. In this case, an RNA chain is cleaved in two places and the middle piece (called the intron) is discarded, while the two flanking RNA pieces (called exons) are ligated together. This reaction is called splicing. Besides ribozyme-mediated splicing, which involves RNA alone, there are some splicing reactions that involve RNA-protein complexes. These complexes are called small nucleus ribonucleoprotein particles, abbreviated as snRNPs. This class of splicing is a very common feature of messenger RNA (mRNA) processing in "higher" eukaryotes such as humans. It is not yet known if snRNP-mediated splicing is catalyzed by the RNA components. Note also that some RNA splicing reactions are catalyzed by enzymes made of only protein.

Some precursor RNA molecules have a ribozyme built into their own intron, and this ribozyme is responsible for removal of the intron in which it is found. These are called self-splicing RNAs. After the splicing reaction is complete, the intron, including the ribozyme, is degraded. In these cases, each ribozyme works only once, unlike protein enzymes that catalyze a reaction repeatedly. Examples of self-spliced RNAs include the ribosomal RNAs of ciliated protozoa and certain mRNAs of yeast mitochondria.

Some RNA viruses, such as the hepatitis delta virus, also include a ribozyme as part of their inherited RNA molecule. During replication of the viral RNA, long strands containing repeats of the RNA genome (viral genetic information) are synthesized. The ribozyme then cleaves the long multimeric molecules into pieces that contain one genome copy, and fits that RNA piece into a virus particle.

Other ribozymes work on other RNA molecules. One ribozyme of this type is RNase P, which consists of one RNA chain and one or more proteins (depending on the organism). The catalytic mechanism of RNase P has been especially well-studied in bacteria. This ribozyme processes precursor transfer RNA (tRNA) by removing an extension from the 5-prime end, to create the 5-prime end of the "mature" tRNA (the two ends of an RNA molecule are chemically distinct and are called the 5-prime and 3-prime ends, referring to specific carbons in the sugar moiety of the terminal nucleotides). When the RNA molecule from bacterial RNase P is purified away from its protein, it can still cleave its precursor tRNA target, albeit at a very slow rate, proving that the RNA is the catalyst. Nevertheless, the protein(s) in RNase P also has important functions, such as maintenance of the proper conformation of the RNase P RNA and interaction with the precursor tRNA.

Relics of an "Rna World"

Many biologists hypothesize that ribozymes are vestiges of an ancient, prebiotic world that predated the evolution of proteins. In this "RNA world," RNAs were the catalysts of such functions as replication, cleavage, and ligation of RNA molecules. Proteins are hypothesized to have evolved later, and as they evolved they took over functions previously performed by RNA molecules. This may have happened because proteins are more versatile and efficient in their catalytic functions.

In today's world, most processing of precursor tRNA is performed by the ribozyme RNase P, as described above, but in some chloroplasts, this function is performed by a protein that apparently contains no RNA. This may be an example of the evolution of protein enzymes that replace ribozymes.

Intensive studies of ribozymes have provided rules for how they recognize their targets. Based on these rules, it has been possible to alter ribozymes to recognize and cleave new targets in RNA molecules that are normally not subject to ribozyme cleavage. These results raise the exciting possibility of using ribozymes for human therapy. For example, the abundance of disease-causing RNA molecules such as HIV, the cause of AIDS, could be reduced with artificial ribozymes. Considerable success has been achieved in testing these ribozymes in model cells. However, the biggest question remaining to be solved is how these potential "disease-fighting" ribozymes can be introduced into a patient and taken up by the appropriate cells.

Bibliography

Cech, T. R. "RNA as an Enzyme." Scientific American 255 (1986): 64-75.

Karp, Gerald. Cell and Molecular Biology, 3rd ed. New York: John Wiley & Sons, 2002.

—Lasse Lindahl

Enzyme whose catalytic function is carried out by an RNA subunit; of the four known classes, three carry out self processing reactions while the fourth, ribonuclease P (RNase P), is a true catalyst; discovered in the context of RNA splicing.

This article is about the chemical. For the rock band, see Ribozyme (band).

Schematic showing ribozyme cleavage of RNA.

A ribozyme (from ribonucleic acid enzyme, also called RNA enzyme or catalytic RNA) is an RNA molecule that catalyzes a chemical reaction. Many natural ribozymes catalyze either their own cleavage or the cleavage of other RNAs, but they have also been found to catalyze the aminotransferase activity of the ribosome. Investigators studying the origin of life have produced ribozymes in the laboratory that are capable of catalyzing their own synthesis under very specific conditions, such as an RNA polymerase ribozyme.^[1] Mutagenesis and selection has been performed resulting in isolation of improved variants of the "Round-18" polymerase ribozyme from 2001. "B6.61" is able to add up to 20 nucleotides to a primer template in 24 hours until it is decomposed by hydrolysis of the phosphodiester bonds.^[2]

Discovery

Before the discovery of ribozymes, enzymes, which are defined as catalytic proteins,^[3] were the only known biological catalysts. In 1967, Carl Woese, Francis Crick, and Leslie Orgel were the first to suggest that RNA could act as a catalyst based upon findings that it can form complex secondary structures.^[4] The first ribozymes were discovered in the 1980s by Thomas R. Cech, who was studying RNA splicing in the ciliated protozoan Tetrahymena thermophila and Sidney Altman, who was working on the bacterial RNase P complex. The ribozymes were found in the intron of an RNA transcript, which removed itself from the transcript and in the RNA component of the RNase P complex, which is involved in the maturation of pre-tRNAs. In 1989, Thomas R. Cech and Sidney Altman won the Nobel Prize in chemistry for their "discovery of catalytic properties of RNA."^[5] The term ribozyme was first introduced by Kelly Kruger et al. in 1982 in a paper published in Cell.

Activity

Although most ribozymes are quite rare in the cell, their roles are sometimes essential to life. For example, the functional part of the ribosome, the molecular machine that translates RNA into proteins, is fundamentally a ribozyme. Ribozymes often have divalent metal ions such as Mg²⁺ as cofactors.

RNA can also act as a hereditary molecule, which encouraged Walter Gilbert to propose that in the past, the cell used RNA as both the genetic material and the structural and catalytic molecule, rather than dividing these functions between DNA and protein as they are today. This hypothesis became known as the "RNA world hypothesis" of the origin of life.

If ribozymes were the first molecular machines used by early life, then today's remaining ribozymes -- such as the ribosome machinery -- could be considered living fossils of a life based primarily on nucleic acids.

A recent test-tube study of prion folding suggests that an RNA may catalyze the pathological protein conformation in the manner of a chaperone enzyme.^[6]

Known ribozymes

Naturally occurring ribozymes include:

• RNase P
• Group I and Group II introns
• Leadzyme - Although initially created in vitro, natural examples have been found
• Hairpin ribozyme
• Hammerhead ribozyme
• HDV ribozyme
• Mammalian CPEB3 ribozyme
• Tetrahymena ribozyme
• VS ribozyme
• glmS ribozyme
• CoTC ribozyme

Synthetic ribozymes

Since the discovery of ribozymes that exist in living organisms, there has been interest in the study of new synthetic ribozymes made in the laboratory. For example, artificially-produced self-cleaving RNAs that have good enzymatic activity have been produced. Tang and Breaker^[7] isolated self-cleaving RNAs by in vitro selection of RNAs originating from random-sequence RNAs. Some of the synthetic ribozymes that were produced had novel structures, while some were similar to the naturally occurring hammerhead ribozyme.

The techniques used to discover synthetic ribozymes involve Darwinian evolution. This approach takes advantage of RNA's dual nature as both a catalyst and an informational polymer, making it easy for an investigator to produce vast populations of RNA catalysts using polymerase enzymes. The ribozymes are mutated by reverse transcibing them with reverse transcriptase into various cDNA and amplified with mutagenic PCR. The selection parameters in these experiments often differ. One approach for selecting a ligase ribozyme involves using biotin tags, which are covalently linked to the substrate. If a molecule possesses the desired ligase activity, a streptavidin matrix can be used to recover the active molecules.

See also

• Deoxyribozyme
• Spiegelman Monster

References

1. ^ Johnston W, Unrau P, Lawrence M, Glasner M, Bartel D (2001). "RNA-catalyzed RNA polymerization: accurate and general RNA-templated primer extension". Science 292 (5520): 1319-25. PMID 11358999. 
2. ^ Zaher HS, Unrau P (2007). "Selection of an improved RNA polymerase ribozyme with superior extension and fidelity". RNA 13 (7): 1017-26. PMID 17586759. 
3. ^ Enzyme definition Dictionary.com Accessed 6 April 2007
4. ^ Carl Woese, The Genetic Code (New York: Harper and Row, 1967).
5. ^ The Nobel Prize in Chemistry 1989 was awarded to Thomas R. Cech and Sidney Altman "for their discovery of catalytic properties of RNA".
6. ^ "Prion protein conversion in vitro" by S. Supattapone (2004) in Journal of Molecular Medicine Volume 82, pages 348-356. Entrez PubMed 15014886
7. ^ Jin Tang and Ronald R. Breaker (1997). "Structural diversity of self-cleaving ribozymes". Proceedings of the National Academy of Sciences 97 (11): 5784-5789. PMID 10823936. 

External links

• Ribozyme structures and mechanisms
• De novo synthesis and development of an RNA enzyme
• Directed evolution of nucleic acid enzymes.

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