Ribozyme
Encyclopedia
Molecule
A molecule is an electrically neutral group of at least two atoms held together by covalent chemical bonds. Molecules are distinguished from ions by their electrical charge...
with a well defined tertiary structure that enables it to catalyze
Catalysis
Catalysis is the change in rate of a chemical reaction due to the participation of a substance called a catalyst. Unlike other reagents that participate in the chemical reaction, a catalyst is not consumed by the reaction itself. A catalyst may participate in multiple chemical transformations....
a chemical reaction
Chemical reaction
A chemical reaction is a process that leads to the transformation of one set of chemical substances to another. Chemical reactions can be either spontaneous, requiring no input of energy, or non-spontaneous, typically following the input of some type of energy, such as heat, light or electricity...
. Ribozyme means ribonucleic acid enzyme. It may also be called an RNA
RNA
Ribonucleic acid , or RNA, is one of the three major macromolecules that are essential for all known forms of life....
enzyme
Enzyme
Enzymes are proteins that catalyze chemical reactions. In enzymatic reactions, the molecules at the beginning of the process, called substrates, are converted into different molecules, called products. Almost all chemical reactions in a biological cell need enzymes in order to occur at rates...
or catalytic RNA. Many natural ribozymes catalyze either the hydrolysis
Hydrolysis
Hydrolysis is a chemical reaction during which molecules of water are split into hydrogen cations and hydroxide anions in the process of a chemical mechanism. It is the type of reaction that is used to break down certain polymers, especially those made by condensation polymerization...
of one of their own phosphodiester bond
Phosphodiester bond
A phosphodiester bond is a group of strong covalent bonds between a phosphate group and two 5-carbon ring carbohydrates over two ester bonds. Phosphodiester bonds are central to all known life, as they make up the backbone of each helical strand of DNA...
s (self-cleaving
Bond cleavage
Bond cleavage, or scission, is the splitting of chemical bonds.If the two electrons in a cleaved covalent bond are divided between the products, the process is known as homolytic fission and free redicals are generated by homolytic cleavage the process is known as homolytic fission or homolysis...
ribozymes), or the hydrolysis of bonds in other RNAs. Some have been found to catalyze the aminotransferase activity of the ribosome
Ribosome
A ribosome is a component of cells that assembles the twenty specific amino acid molecules to form the particular protein molecule determined by the nucleotide sequence of an RNA molecule....
. Examples of ribozymes include the hammerhead ribozyme
Hammerhead ribozyme
Hammerhead RNAs are RNAs that self-cleave via a small conserved secondary structural motif termed a hammerhead because of its shape. Most hammerhead RNAs are subsets of two classes of plant pathogenic RNAs: the satellite RNAs of RNA viruses and the viroids. The self-cleavage reactions, first...
, the VS ribozyme
VS ribozyme
The Varkud satellite ribozyme is an RNA enzyme that carries out the cleavage of a phosphodiester bond.-Structure:The VS ribozyme is composed of 5 helices that form an H shape...
and the hairpin ribozyme
Hairpin ribozyme
The hairpin ribozyme is a small section of RNA that can act as an enzyme known as a ribozyme. Like the hammerhead ribozyme it is found in RNA satellites of plant viruses...
.
Investigators studying the origin of life have produced ribozymes in the laboratory that are capable of catalyzing their own synthesis
Autocatalysis
A single chemical reaction is said to have undergone autocatalysis, or be autocatalytic, if the reaction product itself is the catalyst for that reaction....
under very specific conditions, such as an RNA polymerase
RNA polymerase
RNA polymerase is an enzyme that produces RNA. In cells, RNAP is needed for constructing RNA chains from DNA genes as templates, a process called transcription. RNA polymerase enzymes are essential to life and are found in all organisms and many viruses...
ribozyme. 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 hydrolysis of its phosphodiester bonds. The "tC19Z" ribozyme can add up to 95 nucleotides with a fidelity of 0.0083 mutations/nucleotide.
Some ribozymes may play an important role as therapeutic agents, as enzymes which tailor defined RNA sequences, as biosensor
Biosensor
A biosensor is an analytical device for the detection of an analyte that combines a biological component with a physicochemical detector component.It consists of 3 parts:* the sensitive biological element A biosensor is an analytical device for the detection of an analyte that combines a biological...
s, and for applications in functional genomics
Functional genomics
Functional genomics is a field of molecular biology that attempts to make use of the vast wealth of data produced by genomic projects to describe gene functions and interactions...
and gene discovery.
Discovery
Enzyme
Enzymes are proteins that catalyze chemical reactions. In enzymatic reactions, the molecules at the beginning of the process, called substrates, are converted into different molecules, called products. Almost all chemical reactions in a biological cell need enzymes in order to occur at rates...
s, which are defined as catalytic protein
Protein
Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...
s, were the only known biological catalysts
Catalysis
Catalysis is the change in rate of a chemical reaction due to the participation of a substance called a catalyst. Unlike other reagents that participate in the chemical reaction, a catalyst is not consumed by the reaction itself. A catalyst may participate in multiple chemical transformations....
. In 1967, Carl Woese
Carl Woese
Carl Richard Woese is an American microbiologist and physicist. Woese is famous for defining the Archaea in 1977 by phylogenetic taxonomy of 16S ribosomal RNA, a technique pioneered by Woese and which is now standard practice. He was also the originator of the RNA world hypothesis in 1977,...
, Francis Crick
Francis Crick
Francis Harry Compton Crick OM FRS was an English molecular biologist, biophysicist, and neuroscientist, and most noted for being one of two co-discoverers of the structure of the DNA molecule in 1953, together with James D. Watson...
, and Leslie Orgel
Leslie Orgel
Leslie Eleazer Orgel FRS was a British chemist.Born in London, England, Orgel received his B.A. in chemistry with first class honours from Oxford University in 1949...
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 structure
Secondary structure
In biochemistry and structural biology, secondary structure is the general three-dimensional form of local segments of biopolymers such as proteins and nucleic acids...
s. The first ribozymes were discovered in the 1980s by Thomas R. Cech, who was studying RNA splicing
Splicing (genetics)
In molecular biology and genetics, splicing is a modification of an RNA after transcription, in which introns are removed and exons are joined. This is needed for the typical eukaryotic messenger RNA before it can be used to produce a correct protein through translation...
in the ciliated protozoan Tetrahymena thermophila and Sidney Altman
Sidney Altman
Sidney Altman is a Canadian American molecular biologist, who is currently the Sterling Professor of Molecular, Cellular, and Developmental Biology and Chemistry at Yale University. In 1989 he shared the Nobel Prize in Chemistry with Thomas R...
, who was working on the bacterial RNase P
RNase P
Ribonuclease P is a type of ribonuclease which cleaves RNA. RNase P is unique from other RNases in that it is a ribozyme – a ribonucleic acid that acts as a catalyst in the same way that a protein based enzyme would. Its function is to cleave off an extra, or precursor, sequence of RNA on tRNA...
complex. These ribozymes were found in the intron
Intron
An intron is any nucleotide sequence within a gene that is removed by RNA splicing to generate the final mature RNA product of a gene. The term intron refers to both the DNA sequence within a gene, and the corresponding sequence in RNA transcripts. Sequences that are joined together in the final...
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
Sidney Altman
Sidney Altman is a Canadian American molecular biologist, who is currently the Sterling Professor of Molecular, Cellular, and Developmental Biology and Chemistry at Yale University. In 1989 he shared the Nobel Prize in Chemistry with Thomas R...
won the Nobel Prize
Nobel Prize
The Nobel Prizes are annual international awards bestowed by Scandinavian committees in recognition of cultural and scientific advances. The will of the Swedish chemist Alfred Nobel, the inventor of dynamite, established the prizes in 1895...
in chemistry
Chemistry
Chemistry is the science of matter, especially its chemical reactions, but also its composition, structure and properties. Chemistry is concerned with atoms and their interactions with other atoms, and particularly with the properties of chemical bonds....
for their "discovery of catalytic properties of RNA." The term ribozyme was first introduced by Kelly Kruger et al. in 1982 in a paper published in Cell
Cell (journal)
Cell is a peer-reviewed scientific journal publishing research papers across a broad range of disciplines within the life sciences. Areas covered include molecular biology, cell biology, systems biology, stem cells, developmental biology, genetics and genomics, proteomics, cancer research,...
.
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.
In the 1970s Thomas Cech, at the University of Colorado at Boulder
University of Colorado at Boulder
The University of Colorado Boulder is a public research university located in Boulder, Colorado...
, 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
Yale University
Yale University is a private, Ivy League university located in New Haven, Connecticut, United States. Founded in 1701 in the Colony of Connecticut, the university is the third-oldest institution of higher education in the United States...
, 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 ribosomeRibosome
A ribosome is a component of cells that assembles the twenty specific amino acid molecules to form the particular protein molecule determined by the nucleotide sequence of an RNA molecule....
, the molecular machine
Molecular machine
A molecular machine, or nanomachine, is any discrete number of molecular components that produce quasi-mechanical movements in response to specific stimuli . The expression is often more generally applied to molecules that simply mimic functions that occur at the macroscopic level...
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 cofactor
Cofactor (biochemistry)
A cofactor is a non-protein chemical compound that is bound to a protein and is required for the protein's biological activity. These proteins are commonly enzymes, and cofactors can be considered "helper molecules" that assist in biochemical transformations....
s. There is no requirement for divalent
Divalent
In chemistry, a divalent ion or molecule has a valence of two and thus can form two bonds with other ions or molecules. An older term for divalent is bivalent....
cations in a five-nucleotide RNA that can catalyze trans-phenylalanation
Phenylalanine
Phenylalanine is an α-amino acid with the formula C6H5CH2CHCOOH. This essential amino acid is classified as nonpolar because of the hydrophobic nature of the benzyl side chain. L-Phenylalanine is an electrically neutral amino acid, one of the twenty common amino acids used to biochemically form...
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.
RNA can also act as a hereditary molecule, which encouraged Walter Gilbert
Walter Gilbert
Walter Gilbert is an American physicist, biochemist, molecular biology pioneer, and Nobel laureate.-Biography:Gilbert was born in Boston, Massachusetts, on March 21, 1932...
to propose that in the distant past, the cell
Cell (biology)
The cell is the basic structural and functional unit of all known living organisms. It is the smallest unit of life that is classified as a living thing, and is often called the building block of life. The Alberts text discusses how the "cellular building blocks" move to shape developing embryos....
used RNA as both the genetic material and the structural and catalytic molecule, rather than dividing these functions between DNA
DNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...
and protein
Protein
Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...
as they are today. This hypothesis became known as the "RNA world hypothesis
RNA world hypothesis
The RNA world hypothesis proposes that life based on ribonucleic acid pre-dates the current world of life based on deoxyribonucleic acid , RNA and proteins. RNA is able both to store genetic information, like DNA, and to catalyze chemical reactions, like an enzyme protein...
" 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 fossil
Living fossil
Living fossil is an informal term for any living species which appears similar to a species otherwise only known from fossils and which has no close living relatives, or a group of organisms which have long fossil records...
s of a life based primarily on nucleic acids.
A recent test-tube study of prion
Prion
A prion is an infectious agent composed of protein in a misfolded form. This is in contrast to all other known infectious agents which must contain nucleic acids . The word prion, coined in 1982 by Stanley B. Prusiner, is a portmanteau derived from the words protein and infection...
folding
Protein folding
Protein folding is the process by which a protein structure assumes its functional shape or conformation. It is the physical process by which a polypeptide folds into its characteristic and functional three-dimensional structure from random coil....
suggests that an RNA may catalyze the pathological protein conformation in the manner of a chaperone enzyme.
Known ribozymes
Naturally occurring ribozymes include:- Peptidyl transferase 23S rRNARibosomal RNARibosomal ribonucleic acid is the RNA component of the ribosome, the enzyme that is the site of protein synthesis in all living cells. Ribosomal RNA provides a mechanism for decoding mRNA into amino acids and interacts with tRNAs during translation by providing peptidyl transferase activity...
- RNase PRNase PRibonuclease P is a type of ribonuclease which cleaves RNA. RNase P is unique from other RNases in that it is a ribozyme – a ribonucleic acid that acts as a catalyst in the same way that a protein based enzyme would. Its function is to cleave off an extra, or precursor, sequence of RNA on tRNA...
- Group IGroup I catalytic intronGroup I introns are large self-splicing ribozymes. They catalyze their own excision from mRNA, tRNA and rRNA precursors in a wide range of organisms. The core secondary structure consists of nine paired regions...
and Group II intronGroup II intronGroup II introns are a large class of self-catalytic ribozymes as well as mobile genetic element found within the genes of all three domains of life. Ribozyme activity can occur under high-salt conditions in vitro. However, assistance from proteins is required for in vivo splicing...
s - GIR1 branching ribozymeGIR1 branching ribozymeThe GIR1 branching ribozyme is a 179 nt ribozyme with a structural resemblance to a group I ribozyme.It is found within a complex type of group I introns also termed twin-ribozyme introns....
- LeadzymeLeadzymeLeadzyme is a small ribozyme that was artificially made using in vitro selection techniques. Leadzyme is able to cleave RNA in the presence of lead. The structure of leadzyme has been determined by X-ray crystallography....
- Although initially created in vitro, natural examples have been found - Hairpin ribozymeHairpin ribozymeThe hairpin ribozyme is a small section of RNA that can act as an enzyme known as a ribozyme. Like the hammerhead ribozyme it is found in RNA satellites of plant viruses...
- Hammerhead ribozymeHammerhead ribozymeHammerhead RNAs are RNAs that self-cleave via a small conserved secondary structural motif termed a hammerhead because of its shape. Most hammerhead RNAs are subsets of two classes of plant pathogenic RNAs: the satellite RNAs of RNA viruses and the viroids. The self-cleavage reactions, first...
- HDV ribozymeHepatitis delta virus ribozymeThe hepatitis delta virus ribozyme is a non-coding RNA that is necessary for viral replication and is thought to be the only catalytic RNA known to be required for viability of a human pathogen. The ribozyme acts to process the RNA transcripts to unit lengths in a self-cleavage reaction...
- Mammalian CPEB3 ribozymeMammalian CPEB3 ribozymeThe mammalian CPEB3 ribozyme is a self cleaving non-coding RNA located in the second intron of the CPEB3 gene which belongs to a family of genes regulating messenger RNA polyadenylation. This ribozyme is highly conserved and...
- VS ribozymeVS ribozymeThe Varkud satellite ribozyme is an RNA enzyme that carries out the cleavage of a phosphodiester bond.-Structure:The VS ribozyme is composed of 5 helices that form an H shape...
- glmS ribozymeGlmS glucosamine-6-phosphate activated ribozymeThe Glucosamine-6-phosphate activated ribozyme is an RNA structure that is both a ribozyme, since it catalyzes a chemical reaction, and a riboswitch, since it regulates genes in response to concentrations of a metabolite....
- CoTC ribozymeBeta-globin co-transcriptional cleavage ribozymeThe Beta-globin co-transcriptional cleavage ribozyme is an RNA enzyme known as a ribozyme.Transcription termination of RNA polymerase II transcripts is proposed to occur by a two stage process. The first stage involves pre-termination cleavage of the nascent transcript downstream of the poly site...
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 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
Polymerase
A polymerase is an enzyme whose central function is associated with polymers of nucleic acids such as RNA and DNA.The primary function of a polymerase is the polymerization of new DNA or RNA against an existing DNA or RNA template in the processes of replication and transcription...
enzymes. The ribozymes are mutated by reverse transcribing them with reverse transcriptase
Reverse transcriptase
In the fields of molecular biology and biochemistry, a reverse transcriptase, also known as RNA-dependent DNA polymerase, is a DNA polymerase enzyme that transcribes single-stranded RNA into single-stranded DNA. It also helps in the formation of a double helix DNA once the RNA has been reverse...
into various cDNA and amplified with mutagenic PCR. The selection parameters in these experiments often differ. One approach for selecting a ligase ribozyme
Ligase ribozyme
The RNA Ligase ribozyme was the first of several types of synthetic ribozymes produced by in vitro evolution and selection techniques. They are an important class of ribozymes because they catalyze the assembly of RNA fragments into phosphodiester RNA polymers, a reaction required of all extant...
involves using biotin
Biotin
Biotin, also known as Vitamin H or Coenzyme R, is a water-soluble B-complex vitamin discovered by Bateman in 1916. It is composed of a ureido ring fused with a tetrahydrothiophene ring. A valeric acid substituent is attached to one of the carbon atoms of the tetrahydrothiophene ring...
tags, which are covalently
Covalent bond
A covalent bond is a form of chemical bonding that is characterized by the sharing of pairs of electrons between atoms. The stable balance of attractive and repulsive forces between atoms when they share electrons is known as covalent bonding....
linked to the substrate. If a molecule possesses the desired ligase
Ligase
In biochemistry, ligase is an enzyme that can catalyse the joining of two large molecules by forming a new chemical bond, usually with accompanying hydrolysis of a small chemical group dependent to one of the larger molecules...
activity, a streptavidin
Streptavidin
Streptavidin is a 60000 dalton protein purified from the bacterium Streptomyces avidinii. Streptavidin homo-tetramers have an extraordinarily high affinity for biotin . With a dissociation constant on the order of ≈10-14 mol/L, the binding of biotin to streptavidin is one of the strongest...
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
In vitro
In vitro refers to studies in experimental biology that are conducted using components of an organism that have been isolated from their usual biological context in order to permit a more detailed or more convenient analysis than can be done with whole organisms. Colloquially, these experiments...
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.
Applications
A type of synthetic ribozyme directed against HIVHIV
Human immunodeficiency virus is a lentivirus that causes acquired immunodeficiency syndrome , a condition in humans in which progressive failure of the immune system allows life-threatening opportunistic infections and cancers to thrive...
RNA called gene shears has been developed and has entered clinical testing for HIV infection.
See also
- DeoxyribozymeDeoxyribozymeDeoxyribozymes or DNA enzymes or catalytic DNA, or DNAzymes are DNA molecules with catalytic action. In contrast to the RNA ribozyme that has many catalytic capabilities, DNA is only associated with gene replication and nothing else...
- Spiegelman MonsterSpiegelman MonsterSpiegelman Monster is the name given to an RNA chain of only 218 nucleotides that is able to be reproduced by an RNA replication enzyme. It is named after its creator, Sol Spiegelman, of the University of Illinois at Urbana-Champaign.-Description:...
- CatalysisCatalysisCatalysis is the change in rate of a chemical reaction due to the participation of a substance called a catalyst. Unlike other reagents that participate in the chemical reaction, a catalyst is not consumed by the reaction itself. A catalyst may participate in multiple chemical transformations....
- EnzymeEnzymeEnzymes are proteins that catalyze chemical reactions. In enzymatic reactions, the molecules at the beginning of the process, called substrates, are converted into different molecules, called products. Almost all chemical reactions in a biological cell need enzymes in order to occur at rates...
- RNA world hypothesisRNA world hypothesisThe RNA world hypothesis proposes that life based on ribonucleic acid pre-dates the current world of life based on deoxyribonucleic acid , RNA and proteins. RNA is able both to store genetic information, like DNA, and to catalyze chemical reactions, like an enzyme protein...
- Peptide nucleic acid
- Nucleic acid analoguesNucleic acid analoguesNucleic acid analogues are compounds structurally similar to naturally occurring RNA and DNA, used in medicine and in molecular biology research....
- PAH world hypothesisPAH world hypothesisThe PAH world hypothesis is a speculative hypothesis that proposes that polycyclic aromatic hydrocarbons , assumed to be abundant in the primordial soup of the early Earth, played a major role in the origin of life by mediating the synthesis of RNA molecules, leading into the RNA world...
- SELEXSystematic Evolution of Ligands by Exponential EnrichmentSELEX , also referred to as in vitro selection or in vitro evolution, is a combinatorial chemistry technique in molecular biology for producing oligonucleotides of either single-stranded DNA or RNA that specifically bind to a target ligand or ligands....
- OLE RNAOLE RNAOLE RNA is a conserved RNA structure present in certain bacteria. The RNA averages roughly 610 nucleotides in length. The only known RNAs that are longer than OLE RNA are ribozymes such as the group II intron and ribosomal RNAs...