Topoisomerase
Encyclopedia
Topoisomerases are enzymes that regulate the overwinding or underwinding of DNA. The winding problem of DNA arises due to the intertwined nature of its double helical structure. For example, during DNA replication
, DNA becomes overwound ahead of a replication fork. If left unabated, this tension would eventually grind replication to a halt (a similar event happens during transcription
.)
In order to help overcome these types of topological problems caused by the double helix, topoisomerases bind to either single-stranded or double-stranded DNA and cut the phosphate backbone of the DNA. This intermediate break allows the DNA to be untangled or unwound, and, at the end of these processes, the DNA backbone is resealed again. Since the overall chemical composition and connectivity of the DNA does not change, the tangled and untangled DNAs are chemical isomers, differing only in their global topology, thus their name. Topoisomerases are isomerase
enzymes that act on the topology of DNA
.
proteins if other enzymes are to transcribe
the sequences
that encode
protein
s, or if chromosomes are to be replicated
. In so-called circular DNA
, in which double helical DNA is bent around and joined in a circle
, the two strands are topologically linked, or knotted
. Otherwise identical loops of DNA, having different numbers of twists, are topoisomer
s, and cannot be interconverted by any process that does not involve the breaking of DNA strands. Topoisomerases catalyze and guide the unknotting or unkinking of DNA by creating transient breaks in the DNA using a conserved Tyrosine
as the catalytic residue.
The insertion of viral DNA into chromosomes and other forms of recombination
can also require the action of topoisomerases.
Many drugs operate through interference with the topoisomerases http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=20534341.
The broad-spectrum fluoroquinolone
antibiotic
s act by disrupting the function of bacterial type II topoisomerases. These small molecule inhibitors act as efficient anti-bacterial by hijacking the natural ability of topoisomerase to create breaks in chromosomal DNA.
Some chemotherapy
drugs called topoisomerase inhibitor
s work by interfering with mammalian-type eukaryotic topoisomerases in cancer
cells
. This induces breaks in the DNA that ultimately lead to programmed cell death (apoptosis
). This DNA-damaging effect, outside of its potentially curative properties, may lead to secondary neoplasm
s in the patient.
Topoisomerase I is the antigen
recognized by Anti Scl-70 antibodies in scleroderma
.
, knotting and catenation
. Outside of the essential processes of replication
or transcription
, DNA must be kept as compact as possible, and these three states help this cause. However, when transcription or replication occur, DNA must be free, and these states seriously hinder the processes. In addition, during replication, the newly replicated duplex of DNA and the original duplex of DNA become intertwined and must be completely separated in order to ensure genomic integrity as a cell divides. As a transcription bubble proceeds, DNA ahead of the transcription fork becomes overwound, or positively supercoiled, while DNA behind the transcription bubble becomes underwound, or negatively supercoiled. As replication occurs, DNA ahead of the replication bubble becomes positively supercoiled, while DNA behind the replication fork becomes entangled forming precatenanes. One of the most essential topological problem occurs at the very end of replication, when daughter chromosomes must be fully disentangled before mitosis occurs. Topoisomerase IIA plays an essential role in resolving these topological problems.
Both type I and type II topoisomerases change the linking number
(L) of DNA. Type IA topoisomerases change the linking number by one, type IB and type IC topoisomerases change the linking number by any integer, while type IIA and type IIB topoisomerases change the linking number by two.
DNA replication
DNA replication is a biological process that occurs in all living organisms and copies their DNA; it is the basis for biological inheritance. The process starts with one double-stranded DNA molecule and produces two identical copies of the molecule...
, DNA becomes overwound ahead of a replication fork. If left unabated, this tension would eventually grind replication to a halt (a similar event happens during transcription
Transcription
Transcription may refer to:*Transcription , a business which converts speech into a written or electronic text document*Transcription , software which helps convert speech into text transcript...
.)
In order to help overcome these types of topological problems caused by the double helix, topoisomerases bind to either single-stranded or double-stranded DNA and cut the phosphate backbone of the DNA. This intermediate break allows the DNA to be untangled or unwound, and, at the end of these processes, the DNA backbone is resealed again. Since the overall chemical composition and connectivity of the DNA does not change, the tangled and untangled DNAs are chemical isomers, differing only in their global topology, thus their name. Topoisomerases are isomerase
Isomerase
In biochemistry, an isomerase is an enzyme that catalyzes the structural rearrangement of isomers. Isomerases thus catalyze reactions of the formwhere B is an isomer of A.-Nomenclature:...
enzymes that act on the topology of 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...
.
Function
The double-helical configuration that DNA strands naturally reside makes them difficult to separate, and yet they must be separated by helicaseHelicase
Helicases are a class of enzymes vital to all living organisms. They are motor proteins that move directionally along a nucleic acid phosphodiester backbone, separating two annealed nucleic acid strands using energy derived from ATP hydrolysis.-Function:Many cellular processes Helicases are a...
proteins if other enzymes are to transcribe
Transcription (genetics)
Transcription is the process of creating a complementary RNA copy of a sequence of DNA. Both RNA and DNA are nucleic acids, which use base pairs of nucleotides as a complementary language that can be converted back and forth from DNA to RNA by the action of the correct enzymes...
the sequences
DNA sequence
The sequence or primary structure of a nucleic acid is the composition of atoms that make up the nucleic acid and the chemical bonds that bond those atoms. Because nucleic acids, such as DNA and RNA, are unbranched polymers, this specification is equivalent to specifying the sequence of...
that encode
Genetic code
The genetic code is the set of rules by which information encoded in genetic material is translated into proteins by living cells....
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, or if chromosomes are to be replicated
DNA replication
DNA replication is a biological process that occurs in all living organisms and copies their DNA; it is the basis for biological inheritance. The process starts with one double-stranded DNA molecule and produces two identical copies of the molecule...
. In so-called circular DNA
Circular DNA
Circular DNA is a form of DNA that is found in viruses, bacteria and archaea as well as in eukaryotic cells in the form of either mitochondrial DNA or plastid DNA....
, in which double helical DNA is bent around and joined in a circle
Circle
A circle is a simple shape of Euclidean geometry consisting of those points in a plane that are a given distance from a given point, the centre. The distance between any of the points and the centre is called the radius....
, the two strands are topologically linked, or knotted
Knot theory
In topology, knot theory is the study of mathematical knots. While inspired by knots which appear in daily life in shoelaces and rope, a mathematician's knot differs in that the ends are joined together so that it cannot be undone. In precise mathematical language, a knot is an embedding of a...
. Otherwise identical loops of DNA, having different numbers of twists, are topoisomer
Topoisomer
Topoisomers or topological isomers are molecules with the same chemical formula and stereochemical bond connectivities but different topologies. Examples of molecules for which there exist topoisomers include DNA, which can form knots, and catenanes...
s, and cannot be interconverted by any process that does not involve the breaking of DNA strands. Topoisomerases catalyze and guide the unknotting or unkinking of DNA by creating transient breaks in the DNA using a conserved Tyrosine
Tyrosine
Tyrosine or 4-hydroxyphenylalanine, is one of the 22 amino acids that are used by cells to synthesize proteins. Its codons are UAC and UAU. It is a non-essential amino acid with a polar side group...
as the catalytic residue.
The insertion of viral DNA into chromosomes and other forms of recombination
Genetic recombination
Genetic recombination is a process by which a molecule of nucleic acid is broken and then joined to a different one. Recombination can occur between similar molecules of DNA, as in homologous recombination, or dissimilar molecules, as in non-homologous end joining. Recombination is a common method...
can also require the action of topoisomerases.
Clinical significance
- See also topoisomerase inhibitorTopoisomerase inhibitorTopoisomerase inhibitors are agents designed to interfere with the action of topoisomerase enzymes , which are enzymes that control the changes in DNA structure by catalyzing the breaking and rejoining of the phosphodiester backbone of DNA strands during the normal cell cycle.In recent years,...
Many drugs operate through interference with the topoisomerases http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=20534341.
The broad-spectrum fluoroquinolone
Quinolone
The quinolones are a family of synthetic broad-spectrum antibiotics. The term quinolone refers to potent synthetic chemotherapeutic antibacterials....
antibiotic
Antibiotic
An antibacterial is a compound or substance that kills or slows down the growth of bacteria.The term is often used synonymously with the term antibiotic; today, however, with increased knowledge of the causative agents of various infectious diseases, antibiotic has come to denote a broader range of...
s act by disrupting the function of bacterial type II topoisomerases. These small molecule inhibitors act as efficient anti-bacterial by hijacking the natural ability of topoisomerase to create breaks in chromosomal DNA.
Some chemotherapy
Chemotherapy
Chemotherapy is the treatment of cancer with an antineoplastic drug or with a combination of such drugs into a standardized treatment regimen....
drugs called topoisomerase inhibitor
Topoisomerase inhibitor
Topoisomerase inhibitors are agents designed to interfere with the action of topoisomerase enzymes , which are enzymes that control the changes in DNA structure by catalyzing the breaking and rejoining of the phosphodiester backbone of DNA strands during the normal cell cycle.In recent years,...
s work by interfering with mammalian-type eukaryotic topoisomerases in cancer
Cancer
Cancer , known medically as a malignant neoplasm, is a large group of different diseases, all involving unregulated cell growth. In cancer, cells divide and grow uncontrollably, forming malignant tumors, and invade nearby parts of the body. The cancer may also spread to more distant parts of the...
cells
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....
. This induces breaks in the DNA that ultimately lead to programmed cell death (apoptosis
Apoptosis
Apoptosis is the process of programmed cell death that may occur in multicellular organisms. Biochemical events lead to characteristic cell changes and death. These changes include blebbing, cell shrinkage, nuclear fragmentation, chromatin condensation, and chromosomal DNA fragmentation...
). This DNA-damaging effect, outside of its potentially curative properties, may lead to secondary neoplasm
Secondary neoplasm
A secondary neoplasm refers to any of a class of cancerous tumors that are either metastatic offshoots of a primary tumor, or apparently unrelated tumors that increase in frequency following certain cancer treatments, including chemotherapy or radiotherapy....
s in the patient.
Topoisomerase I is the antigen
Antigen
An antigen is a foreign molecule that, when introduced into the body, triggers the production of an antibody by the immune system. The immune system will then kill or neutralize the antigen that is recognized as a foreign and potentially harmful invader. These invaders can be molecules such as...
recognized by Anti Scl-70 antibodies in scleroderma
Scleroderma
Systemic sclerosis or systemic scleroderma is a systemic autoimmune disease or systemic connective tissue disease that is a subtype of scleroderma.-Skin symptoms:...
.
Topological problems
There are three main types of topology: supercoilingDNA supercoil
DNA supercoiling refers to the over- or under-winding of a DNA strand, and is an expression of the strain on the polymer. Supercoiling is important in a number of biological processes, such as compacting DNA. Additionally, certain enzymes such as topoisomerases are able to change DNA topology to...
, knotting and catenation
Catenation
Catenation is the ability of a chemical element to form a long chain-like structure via a series of covalent bonds. Catenation occurs most readily in carbon, which forms covalent bonds with other carbon atoms. Catenation is the reason for the presence of a large number of organic compounds in nature...
. Outside of the essential processes of replication
DNA replication
DNA replication is a biological process that occurs in all living organisms and copies their DNA; it is the basis for biological inheritance. The process starts with one double-stranded DNA molecule and produces two identical copies of the molecule...
or transcription
Transcription (genetics)
Transcription is the process of creating a complementary RNA copy of a sequence of DNA. Both RNA and DNA are nucleic acids, which use base pairs of nucleotides as a complementary language that can be converted back and forth from DNA to RNA by the action of the correct enzymes...
, DNA must be kept as compact as possible, and these three states help this cause. However, when transcription or replication occur, DNA must be free, and these states seriously hinder the processes. In addition, during replication, the newly replicated duplex of DNA and the original duplex of DNA become intertwined and must be completely separated in order to ensure genomic integrity as a cell divides. As a transcription bubble proceeds, DNA ahead of the transcription fork becomes overwound, or positively supercoiled, while DNA behind the transcription bubble becomes underwound, or negatively supercoiled. As replication occurs, DNA ahead of the replication bubble becomes positively supercoiled, while DNA behind the replication fork becomes entangled forming precatenanes. One of the most essential topological problem occurs at the very end of replication, when daughter chromosomes must be fully disentangled before mitosis occurs. Topoisomerase IIA plays an essential role in resolving these topological problems.
Classes
Topoisomerases can fix these topological problems and are separated into two types separated by the number of strands cut in one round of action: Both these classes of enzyme utilize a conserved tyrosine. However these enzymes are structurally and mechanistically different. For a video of this process see: http://www.youtube.com/watch?v=EYGrElVyHnU&feature=related.- Type I topoisomeraseType I topoisomeraseType I topoisomerases cut one strand of double-stranded DNA, relax the strand, and reanneal the strands. They are further subdivided into two structurally and mechanistically distinct topoisomerases: type IA and type IB....
cuts one strand of a DNA double helix, relaxation occurs, and then the cut strand is reannealed. Cutting one strand allows the part of the molecule on one side of the cut to rotate around the uncut strand, thereby reducing stress from too much or too little twist in the helix. Such stress is introduced when the DNA strand is "supercoiled" or uncoiled to or from higher orders of coiling. Type I topoisomerases are subdivided into two subclasses: type IA topoisomerases, which share many structural and mechanistic features with the type II topoisomerases, and type IB topoisomerases, which utilize a controlled rotary mechanism. Examples of type IA topoisomerases include topo I and topo III. In the past, type IB topoisomerases were referred to as eukaryotic topo I, but IB topoisomerases are present in all three domains of life. It is interesting to note that type IA topoisomerases form a covalent intermediate with the 5' end of DNA, while the IB topoisomerases form a covalent intermediate with the 3' end of DNA. Recently, a type IC topoisomerase has been identified, called topo V. While it is structurally unique from type IA and IB topoisomerases, it shares a similar mechanism with type IB topoisomerase.
- Type II topoisomeraseType II topoisomeraseType II topoisomerases cut both strands of the DNA helix simultaneously in order to manage DNA tangles and supercoils. They use the hydrolysis of ATP, unlike type I topoisomerase. In this process, these enzymes change the linking number of circular DNA by +/-2....
cuts both strands of one DNA double helix, passes another unbroken DNA helix through it, and then reanneals the cut strand. It is also split into two subclasses: type IIA and type IIB topoisomerases, which share similar structure and mechanisms. Examples of type IIA topoisomerases include eukaryotic topo II, E. coli gyrase, and E. coli topo IV. Examples of type IIB topoisomerase include topo VI. Type II topisomerases utilize ATP hydrolysis.
| Topoisomerase | IA | IB | IIA | IIB |
|---|---|---|---|---|
| Metal Dependence | Yes | No | Yes | Yes |
| ATP Dependence | No | No | Yes | Yes |
| Single- or Double-Stranded cleavage? | SS | SS | DS | DS |
| Cleavage Polarity | 5' | 3' | 5' | 5' |
| Change in L | ±1 | ±N | ±2 | ±2 |
Both type I and type II topoisomerases change the linking number
Linking number
In mathematics, the linking number is a numerical invariant that describes the linking of two closed curves in three-dimensional space. Intuitively, the linking number represents the number of times that each curve winds around the other...
(L) of DNA. Type IA topoisomerases change the linking number by one, type IB and type IC topoisomerases change the linking number by any integer, while type IIA and type IIB topoisomerases change the linking number by two.
Further reading
- James C. Wang (2009) Untangling the Double Helix. DNA Entanglement and the Action of the DNA Topoisomerases, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 2009. 245 pp. ISBN 9780879698799