ribozyme
American Heritage Dictionary:
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ri·bo·zyme
(rī'bə-zīm') 
n.
An RNA segment that has the ability to catalyze the cleavage and formation of covalent bonds in RNA strands at specific sites.
n.
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.]
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ribozyme
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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 Km relates to the affinity that the catalyst has for its substrate, and ribozymes possess Km values which are comparable to Km 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).
Gale Genetics Encyclopedia:
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Ribozyme
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
Biology Q&A:
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What are ribozymes?
Ribozymes are often referred to as "molecular scissors" that cut
RNA. They were discovered in the early 1980s by Sidney Altman (1939-) and
Thomas Cech (1947-), who won the Nobel Prize in Chemistry for their work
in 1989. The ability of ribozymes to recognize and cut specific sequences of
RNA allows certain genes to be turned off. Ribozymes are now being used in
human genetic studies.
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Oxford Dictionary of Biochemistry:
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ribozyme
an RNA molecule with catalytic activity. Such activity was first demonstrated in 1981 by Canadian-born US biochemist Sidney Altman (1939 — ) for RNase P. In 1982 the US biochemist Thomas R. Cech (1947 — ) discovered the catalysis by RNA of the reactions involved in the splicing of ribosomal RNA from Tetrahymena. In this process a 414-nucleotide intron is removed from a 6.4 kb precursor to yield the mature 26S rRNA. A guanine nucleotide is essential in the reaction, binding to the RNA and then attacking the 5′ splice site to form a phosphodiester bond with the 5′ end of the intron. The 414-nucleotide intron is then released and undergoes further splicing reactions to produce a linear RNA of 395 nucleotides which has lost 19 nucleotides and is named L19. L19 is catalytically active and acts both as a nuclease and a polymerase. The rate of conversion of a pentacytidylate into longer and shorter oligomers is about 1010 times the uncatalysed rate. Mg2+ plays an essential role. Much smaller ribozymes have been demonstrated, e.g. the viroids which infect plants and undergo self-splicing after replication. Comparisons of nucleotide sequences in the vicinity of specific cleavage sites suggest that the active site has a hammerhead secondary structure consisting of three helical regions radiating from a central core of unpaired nucleotides. mRNA precursors in the mitochondria of yeast and fungi also undergo self-splicing as do some RNA precursors in chloroplasts. Such reactions can be classified according to the nature of the unit that attacks the upstream splice site. Group I are mediated by a guanosine cofactor. In group II the attacking moiety is the 2′-OH of a specific adenylate of the intron. Such reactions resemble those that occur in the spliceosomes. Ribozymes are especially interesting in respect of theories on the origin of life because of the popular idea that the first macromolecules were composed of RNA. See also ribonuclease.
| ribovirus, ribothymidylyl, ribothymidylic acid | |
| ribulose-bisphosphate carboxylase, ricin, rickets |
Saunders Veterinary Dictionary:
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ribozyme
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.
Wikipedia on Answers.com:
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Ribozyme
This article is about the chemical. For the rock band, see Ribozyme (band).
A ribozyme is an RNA molecule with a well defined tertiary structure that enables it to catalyze a chemical reaction. Ribozyme means ribonucleic acid enzyme. It may also be called an RNA enzyme or catalytic RNA. It contains an active site that consists entirely of RNA. Many natural ribozymes catalyze either the cleavage of one of their own phosphodiester bonds (self-cleaving ribozymes), or the cleavage of bonds in other RNAs. Some have been found to catalyze the aminotransferase activity of the ribosome. Examples of ribozymes include the hammerhead ribozyme, the VS ribozyme and the hairpin ribozyme.
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 decomposes by cleavage of its phosphodiester bonds.[2] The "tC19Z" ribozyme can add up to 95 nucleotides with a fidelity of 0.0083 mutations/nucleotide.[3]
Some ribozymes may play an important role as therapeutic agents, as enzymes which tailor defined RNA sequences, as biosensors, and for applications in functional genomics and gene discovery.[4]
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Contents
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Discovery
Before the discovery of ribozymes, enzymes, which are defined as catalytic proteins,[5] 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. This idea was based upon the discovery that RNA can form complex secondary structures.[6] 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. These ribozymes were found in the intron of an RNA transcript, which removed itself from the transcript, as well as 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."[7] The term ribozyme was first introduced by Kelly Kruger et al. in 1982 in a paper published in Cell.[8]
It had been a firmly established belief in biology that catalysis was reserved for proteins. In retrospect, catalytic RNA makes a lot of sense. This is based on the old question regarding the origin of life: Which comes first, enzymes that do the work of the cell or nucleic acids that carry the information required to produce the enzymes? Ribo-Nucleic acids as catalysts circumvents this problem. RNA, in essence can be both the chicken and the egg.[9]
In the 1970s Thomas Cech, at the University of Colorado at Boulder, was studying the excision of introns in a ribosomal RNA gene in Tetrahymena thermophila. While trying to purify the enzyme responsible for splicing reaction, he found that intron could be spliced out in the absence of any added cell extract. As much as they tried, Cech and his colleagues could not identify any protein associated with the splicing reaction. After much work, Cech proposed that the intron sequence portion of the RNA could break and reform phosphodiester bonds. At about the same time, Sidney Altman, a professor at Yale University, was studying the way tRNA molecules are processed in the cell when he and his colleagues isolated an enzyme called RNase-P, which is responsible for conversion of a precursor tRNA into the active tRNA. Much to their surprise, they found that RNase-P contained RNA in addition to protein and that RNA was an essential component of the active enzyme. This was such a foreign idea that they had difficulty publishing their findings. The following year, Altman demonstrated that RNA can act as a catalyst by showing that the RNase-P RNA subunit could catalyze the cleavage of precursor tRNA into active tRNA in the absence of any protein component.
Since Cech's and Altman's discovery, other investigators have discovered other examples of self-cleaving RNA or catalytic RNA molecules. Many ribozymes have either a hairpin – or hammerhead – shaped active center and a unique secondary structure that allows them to cleave other RNA molecules at specific sequences. It is now possible to make ribozymes that will specifically cleave any RNA molecule. These RNA catalysts may have pharmaceutical applications. For example, a ribozyme has been designed to cleave the RNA of HIV. If such a ribozyme was made by a cell, all incoming virus particles would have their RNA genome cleaved by the ribozyme, which would prevent infection.
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, composed of RNA tertiary structural motifs that are often coordinated to metal ions such as Mg2+ as cofactors. There is no requirement for divalent cations in a five-nucleotide RNA that can catalyze trans-phenylalanation of a four-nucleotide substrate which has three base complementary sequence with the catalyst. The catalyst and substrate were devised by truncation of the C3 ribozyme.[10]
RNA can also act as a hereditary molecule, which encouraged Walter Gilbert to propose that in the distant 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.[11]
Ribozymes have been shown to be involved in the viral concatemer cleavage that precedes the packing of viral genetic material into virions.[12][13]
Known ribozymes
Naturally occurring ribozymes include:
- Peptidyl transferase 23S rRNA
- RNase P
- Group I and Group II introns
- GIR1 branching ribozyme[14]
- Leadzyme - Although initially created in vitro, natural examples have been found
- Hairpin ribozyme
- Hammerhead ribozyme
- HDV ribozyme
- Mammalian CPEB3 ribozyme
- VS ribozyme
- glmS ribozyme
- CoTC ribozyme
Artificial 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[15] 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 artificial 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 transcribing 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.
Lincoln and Joyce developed an RNA enzyme system capable of self replication in about an hour. By utilizing molecular competition (in vitro evolution) of a candidate enzyme mixture, a pair of RNA enzymes emerged, in which each synthesizes the other from synthetic oligonucleotides, with no protein present.[16]
Applications
A type of synthetic ribozyme directed against HIV RNA called gene shears has been developed and has entered clinical testing for HIV infection.[17][18]
See also
References
- ^ Johnston WK, Unrau PJ, Lawrence MS, Glasner ME, Bartel DP (May 2001). "RNA-catalyzed RNA polymerization: accurate and general RNA-templated primer extension". Science 292 (5520): 1319–1325. doi:10.1126/science.1060786. PMID 11358999.
- ^ Zaher HS, Unrau PJ (July 2007). "Selection of an improved RNA polymerase ribozyme with superior extension and fidelity". RNA 13 (7): 1017–1026. doi:10.1261/rna.548807. PMC 1894930. PMID 17586759. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1894930.
- ^ Wochner A, Attwater J, Coulson A, Holliger P (April 2011). "Ribozyme-catalyzed transcription of an active ribozyme". Science 332 (6026): 209–212. doi:10.1126/science.1200752. PMID 21474753.
- ^ Hean J, Weinberg MS (2008). "The Hammerhead Ribozyme Revisited: New Biological Insights for the Development of Therapeutic Agents and for Reverse Genomics Applications". In Morris KL. RNA and the Regulation of Gene Expression: A Hidden Layer of Complexity. Norfolk, England: Caister Academic Press. ISBN 1-904455-25-5. http://www.horizonpress.com/rnareg.
- ^ Enzyme definition Dictionary.com Accessed 6 April 2007
- ^ Carl Woese, The Genetic Code (New York: Harper and Row, 1967).
- ^ The Nobel Prize in Chemistry 1989 was awarded to Thomas R. Cech and Sidney Altman "for their discovery of catalytic properties of RNA".
- ^ Kruger K, Grabowski PJ, Zaug AJ, Sands J, Gottschling DE, Cech TR (November 1982). "Self-splicing RNA: autoexcision and autocyclization of the ribosomal RNA intervening sequence of Tetrahymena". Cell 31 (1): 147–57. doi:10.1016/0092-8674(82)90414-7. PMID 6297745.
- ^ Visser CM (1984). "Evolution of biocatalysis 1. Possible pre-genetic-code RNA catalysts which are their own replicase". Orig. Life 14 (1–4): 291–300. Bibcode 1984OrLi...14..291V. doi:10.1007/BF00933670. PMID 6205343.
- ^ Turk RM, Chumachenko NV, Yarus M (March 2010). "Multiple translational products from a five-nucleotide ribozyme". Proc. Natl. Acad. Sci. U.S.A. 107 (10): 4585–4589. doi:10.1073/pnas.0912895107. PMC 2826339. PMID 20176971. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2826339.
- ^ Supattapone S (June 2004). "Prion protein conversion in vitro". J. Mol. Med. 82 (6): 348–356. doi:10.1007/s00109-004-0534-3. PMID 15014886.
- ^ Herpesviruses and Chromosomal Integration.
- ^ Cloning human herpes virus 6A genome into bacterial artificial chromosomes and study of DNA replication intermediates.
- ^ Nielsen H, Westhof E, Johansen S (2005). "An mRNA is capped by a 2', 5' lariat catalyzed by a group I-like ribozyme". Science 309 (5740): 1584–1587. doi:10.1126/science.1113645. PMID 16141078.
- ^ Tang J, Breaker RR (May 2000). "Structural diversity of self-cleaving ribozymes". Proc. Natl. Acad. Sci. U.S.A. 97 (11): 5784–5789. Bibcode 2000PNAS...97.5784T. doi:10.1073/pnas.97.11.5784. PMC 18511. PMID 10823936. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=18511.
- ^ Lincoln TA, Joyce GF (February 2009). "Self-sustained replication of an RNA enzyme". Science 323 (5918): 1229–1232. doi:10.1126/science.1167856. PMC 2652413. PMID 19131595. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2652413.
- ^ de Feyter R, Li P (June 2000). "Technology evaluation: HIV ribozyme gene therapy, Gene Shears Pty Ltd". Curr. Opin. Mol. Ther. 2 (3): 332–5. PMID 11249628.
- ^ Khan AU (May 2006). "Ribozyme: a clinical tool". Clin. Chim. Acta 367 (1–2): 20–27. doi:10.1016/j.cca.2005.11.023. PMID 16426595.
Further reading
- Astrid Sigel, Helmut Sigel and Roland K. O. Sigel, ed. (2011). Structural and catalytic roles of metal ions in RNA. Metal Ion in Life Sciences. 9. Cambridge, U.K.: RSC Publishing. doi:10.1039/9781849732512. ISBN 978-1-84973-251-2.
- Johnson-Buck, Alexander E.; McDowell, Sarah E.; Walter, Nils. G.. "Chapter 6. Metal Ions: Supporting Actors in the Playbook of Small Ribozymes". pp. 175–196. doi:10.1039/9781849732512-00175.
- Donghi, Daniela; Schnabl, Joachim. "Chapter 7. Multiple roles of metal ions in large ribozymes". pp. 197–234. doi:10.1039/9781849732512-00197.
- Trappl, Krista; Polacek, Norbert. "Chapter 9. The Ribosome: A Molecular Machine Powered by RNA". pp. 253–275. doi:10.1039/9781849732512-00253.
- Suga, Hiroaki; Futai, Kazuki; Jin, Koichiro. "Chapter 10. Metal Ion Requirements in Artificial Ribozymes that Catalyze Aminoacylation". pp. 277–297. doi:10.1039/9781849732512-00277.
- Wedekind, Joseph E.. "Chapter 11. Metal Ion Binding and Function in Natural and Artificial Small RNA Enzymes". pp. 299–345. doi:10.1039/9781849732512-00299.
- Doherty EA, Doudna JA (2001). "Ribozyme structures and mechanisms". Annu Rev Biophys Biomol Struct 30: 457–475. doi:10.1146/annurev.biophys.30.1.457. PMID 11441810.
- Joyce GF (2004). "Directed evolution of nucleic acid enzymes". Annu. Rev. Biochem. 73: 791–836. doi:10.1146/annurev.biochem.73.011303.073717. PMID 15189159.
- Ikawa Y, Tsuda K, Matsumura S, Inoue T (September 2004). "De novo synthesis and development of an RNA enzyme". Proc. Natl. Acad. Sci. U.S.A. 101 (38): 13750–13755. doi:10.1073/pnas.0405886101. PMC 518828. PMID 15365187. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=518828.
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