[10] In general, knots in DNA are detrimental and need to be removed (by topoisomerases). [4] Biochemistry, electron microscopy, and recent structures of topoisomerase II bound to DNA reveal that type IIA topoisomerases bind at the apices of DNA, supporting this model. This essentially means that it cannot add nucleotides if a free 3'-OH group is not available. The origin of replication is recognized by certain proteins that bind to this site. [29] Since the host E. coli DNA gyrase can partially compensate for the loss of the phage T4 gene products, mutants defective in either genes 39, 52 or 60 do not completely abolish phage DNA replication, but rather delay its initiation. [22][23] Furthermore, compaction of the E. coli genome is achieved in part by negative supercoiling. In E. coli, type I topoisomerase can only relieve negatively supercoiled DNA (negative supercoiling is the end result of newly replicated DNA genome). 2-5 Numerous studies have shown that these enzymes can catalyze DNA strand passage reactions; and are essential to resolve topological . The structure of topo IB bound to DNA has been solved (pdb id = 1A36). One strand is synthesized continuously in the direction of the replication fork; this is called the leading strand. Research on DNA topoisomerases has progressed into development in therapeutics, as our understanding of the biochemistry, molecular biology, and regulation of DNA topoisomerases has been rapidly applied to clinical pharmacology. Although CPT derivatives stabilize a single-strand cleavage complex, subsequent collisions with replication or transcription machinery are thought to generate toxic double-stranded DNA breaks. Helicase opens up the DNA double helix, resulting in the formation of the replication fork. DNA topoisomerases (or topoisomerases) are enzymes that catalyze changes in the topological state of DNA, interconverting relaxed and supercoiled forms, linked (catenated) and unlinked species, and knotted and unknotted DNA. In addition to the detrimental aspects of DNA topology that require resolution, there are also beneficial aspects. Language links are at the top of the page across from the title. 7) are examples of catalytic inhibitors of topo II, i.e. PMID: 25875362; PMCID: PMC4396842, "Crystal structure of the amino-terminal fragment of vaccinia virus DNA topoisomerase I at 1.6 A resolution", "Structure of the N-terminal fragment of topoisomerase V reveals a new family of topoisomerases", "Topoisomerase V relaxes supercoiled DNA by a constrained swiveling mechanism", "Drugging topoisomerases: lessons and challenges", "Epigenetic inactivation of the premature aging Werner syndrome gene in human cancer", "MRE11-deficiency associated with improved long-term disease free survival and overall survival in a subset of stage III colon cancer patients in randomized CALGB 89803 trial", "ATM expression predicts Veliparib and Irinotecan sensitivity in gastric cancer by mediating P53 independent regulation of cell cycle and apoptosis", "Identification of cetrimonium bromide and irinotecan as compounds with synthetic lethality against NDRG1 deficient prostate cancer cells", "mTOR regulates the expression of DNA damage response enzymes in long-lived Snell dwarf, GHRKO, and PAPPA-KO mice", https://en.wikipedia.org/w/index.php?title=Type_I_topoisomerase&oldid=1045901823, Articles to be expanded from February 2021, Creative Commons Attribution-ShareAlike License 4.0. Type IB topoisomerases were originally identified in eukaryotes and in viruses. In the case of gyrase, a substantial amount of the free energy from ATP hydrolysis is transduced into torsional stress in DNA, i.e. The double-helical structure of DNA involves the intertwining of the two polynucleotide strands around each other, which potentially gives rise to topological problems. This strand passage mechanism shares several features with type IIA topoisomerases. The mechanism of DNA cleavage by type IIA topoisomerases has recently been the focus of many biochemical and structural biology studies. Synthetic lethality arises when a combination of deficiencies in the expression of two or more genes leads to cell death, whereas a deficiency in only one of these genes does not. No data suggest that Topo IB "controls" the swiveling insofar as that it has a mechanism in place that triggers religation after a specific number of supercoils removed. 3; Table 2). More recently, several structures of the DNA-bound structure have been solved in an attempt to understand both the chemical mechanism for DNA cleavage and the structural basis for inhibition of topoisomerase by antibacterial poisons. Recent single molecule experiments have confirmed what bulk-plasmid relaxation experiments have proposed earlier, which is that uncoiling of the DNA is torque-driven and proceeds until religation occurs. The first type II topoisomerase to be discovered was DNA gyrase from bacteria, by Martin Gellert and coworkers in 1976,[5] and also characterized by Nicholas Cozzarelli and co-workers. Rodriguez and Stock have done further work to identify a "latch" that is involved in communicating the hydrolysis of ATP to the introduction of positive supercoils. Reverse gyrase is particularly interesting because an ATPase domain, which resembles the helicase-like domain of the Rho transcription factor, is attached (the structure of reverse gyrase was solved by Rodriguez and Stock, EMBO J 2002). Mitoxantrone is a synthetic anthracenedione that is chemically and functionally similar to anthracyclines. Type IIA topoisomerases consist of several key motifs: Eukaryotic type II topoisomerases are homodimers (A2), while prokaryotic type II topoisomerases are heterotetramers (A2B2). We also show that Fz can be reprogrammed for human genome engineering applications . [20], Type IIA topoisomerase operates through a "two-gate" mechanism (though this is a historical notation), a mechanism supported by biochemistry[21] as well as by structural work.[22]. As the DNA-binding gate separates, the T-segment is transferred through the G-segment. true or false 7. DNA gyrase conforms to the same double-strand passage mechanism as other type II enzymes but has unique features connected with its ability to introduce negative supercoils into DNA. 14.4: DNA Replication in Prokaryotes - Biology LibreTexts One strand, which is complementary to the 3' to 5' parental DNA strand, is synthesized continuously towards the replication fork because the polymerase can add nucleotides in this direction. The LibreTexts libraries arePowered by NICE CXone Expertand are supported by the Department of Education Open Textbook Pilot Project, the UC Davis Office of the Provost, the UC Davis Library, the California State University Affordable Learning Solutions Program, and Merlot. [33], Merbarone is a thiobarbituric acid derivative, and dexrazoxane (ICRF-187), one of several related bisdioxopiperazine derivatives, (Fig. Single-strand binding proteins bind to the single-stranded DNA to prevent the helix from re-forming. Type IIB topoisomerases are found in archaea and some higher plants. DNA replication and repair - Knowledge @ AMBOSS Structure and Function of Cellular Genomes | Microbiology - Lumen Learning Answered: Topoisomerase and SSB proteins are | bartleby The . See the article TOP1 for further details on this well-studied type 1B topoisomerase. Type IIA topoisomerases form double-stranded breaks with four-base pair overhangs, while type IIB topoisomerases form double-stranded breaks with two base overhangs. In human patients the deficient DNA repair genes include WRN[13] and MRE11. 11.2 DNA Replication - Microbiology | OpenStax DNA unwinds at the origin of replication. The enzyme first wraps around DNA and creates a single, 3' phosphotyrosine intermediate. Type IB topoisomerases change the linking number by multiples of 1 (n). [citation needed], The bacteriophage (phage) T4 gyrase (type II topoismerase) is a multisubunit protein consisting of the products of genes 39, 52 and probably 60. Examples of type IIA topoisomerases include eukaryotic topo II and topo II, in addition to bacterial gyrase and topo IV. Cellular roles of DNA topoisomerases: a molecular perspective Topoisomerases bind to DNA in a noncovalent fashion followed by the formation of transient cleavage complexes. Members of this subclass include topo I, topo III (which contain additional Zinc-binding motifs), and reverse gyrase. Primase synthesizes RNA primers complementary to the DNA strand. One gene, termed topo VI-B (since it resembles gyrB), contains the ATPase domain, a transducer domain (Pfam PF09239), and a C-terminal Ig-fold-like H2TH domain (Pfam PF18000). [19] showing that the HTH and Toprim fold had a novel conformation compared with that of topo IIA. Analysis of sequence and mutagenesis data indicates that the type Ia topoisomerases (those found in prokaryotes, and the example given here) may be related to the major family of type II topoisomerases (found in all life apart from some archaea). Due to their frequent presence in proliferating eukaryotic cells, inhibitors of type II topoisomerases have been extensively studied and used as anti-cancer medications. Type IA topoisomerases have since evolved to catalyze the resolution of topological barriers encountered by genomes that require the passing of nucleic acid strand (s) through a break on a single DNA or RNA strand. [46] These are typically used in conjunction with other chemotherapy drugs to treat cancers including testicular tumors, small-cell lung cancer, and leukemia. DNA topology refers to the crossing of the two DNA strands that alters the twist of the double helix and gives rise to tertiary conformations of DNA, such as supercoils, knots and catenanes. DNA Topoisomerase - an overview | ScienceDirect Topics Accessibility StatementFor more information contact us atinfo@libretexts.org. E. coli topA mutants were also found to suppress the production of anucleate cells caused by mutations in the muk . Small molecules that target type II topoisomerase are divided into two classes: inhibitors and poisons. Quinolone antibacterial compounds were first developed in the 1960s and have been in clinical use since the 1980s. This is consistent with footprinting data that shows that gyrase has a 140-base-pair footprint. Helicase opens up the DNA-forming replication forks; these are extended bidirectionally. Left unresolved, links between replicated DNA will impede cell division. PLoS One. Supercoiling is a vernacular term for DNA with a non-zero linking difference, more correctly referred to as specific linking difference ( = Lk/Lk0, where Lk0 is the mean linking number of the relaxed DNA circle). The consequences of topological perturbations in DNA are exemplified by DNA replication during which the strands of the duplex are separated; this separation leads to the formation of positive supercoils (DNA overwinding or overtwisting) ahead of the replication fork and intertwining of the daughter strands (precatenanes) behind[10][19] (Fig. The organization of type IIB topoisomerases are similar to that of type IIAs, except that all type IIBs have two genes and form heterotetramers. DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. [18] It closely resembles that of the GHKL domain of topo II and MutL and shows that the nucleotide state (ADP versus ATP) effects the orientation of the transducer domain ( and 1MX0). RNA polymerase II frequently has a pausing site that is about 3060 nucleotides downstream of This inhibition appears to be an adaptation to subtly modulate host topoisomerase I activity during infection to ensure optimal phage yield. The capping lobe and catalytic lobe wrap around the DNA. Aminocoumarins (Fig. Extrachromosomal DNA in eukaryotes includes the chromosomes found within organelles of prokaryotic origin (mitochondria and chloroplasts) that evolved by . [64][65] The pausing of RNA polymerase II at these sites and the controlled release of the pausing is thought to have a regulatory role in gene transcription. These DSBs allow rapid up-regulation of expression of such signal responsive genes in a number of systems (see Table below). On the contrary, single-molecule experiments suggest that religation is a random process and has some probability of occurring each time the swiveling 5'-OH end comes in close proximity with the attachment site of the enzyme-linked 3'-end. The structure of type IA topoisomerase resembles a lock, with Domains I, III and IV lying on the bottom of the structure. Last updated on September 19, 2022 by Excedr Topoisomerase: Overview Topoisomerase (DNA topoisomerases) is an enzyme that catalyzes the changes in the intertwined state of two DNA strands. [31], For the non-specialist perhaps the most important aspect of topoisomerases is their role as drug targets both for antibacterial and anti-cancer chemotherapy; several topoisomerase-targeted antibacterial and anti-cancer drugs are listed among the 2019 World Health Organization Model List of essential Medicines. The majority of topo-targeted drugs act in this way, i.e. However, CPT derivatives suffer from limitations associated with toxicity and limited therapeutic half-lives due to chemical instability. The strand-passage reaction can be intra- or intermolecular (Fig. These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. It also requires a free 3'-OH group to which it can add nucleotides by forming a phosphodiester bond between the 3'-OH end and the 5' phosphate of the next nucleotide. [52], Topo II and PARP-1 were found to be constitutively present at a moderate level near the transcription start site of a promoter of a signal-responsive gene. Human cells encode six topoisomerases (TOP1, TOP1mt,. [7][8][9] Topo EC-codes are as follows: ATP-independent (type I), EC 5.6.2.1; ATP-dependent (type II): EC 5.6.2.2. Because this sequence primes the DNA synthesis, it is appropriately called the primer. they prevent completion of the catalytic cycle of topo II but do not stabilize the DNA cleavage complex. Reactions can occur on both single- and double-stranded DNA substrates and can proceed via a 'swivel' or 'strand-passage' mechanism (Fig. [2] Indeed, these enzymes are of interest for a wide range of effects. 14.4.1: DNA Replication in Prokaryotes - Biology LibreTexts Some organisms have two isoforms of topoisomerase II: alpha and beta. [16] The nucleoprotein complex was captured with a long DNA duplex and gepotidacin, a novel bacterial topoisomerase inhibitor. Functionally, these subclasses perform very specialized functions. . The first part of this assay summarizes the known mechanisms by which drugs target topoisomerases, complementing and updating more detailed reviews. Therefore it is the sole type I topoisomerase classified as EC 5.6.2.2 (Table 1). Historically, type IA topoisomerases are referred to as prokaryotic topo I, while type IB topoisomerases are referred to as eukaryotic topoisomerase. [52][53][54][55] Topo II, with other associated enzymes,[54] appears to be important for the release of paused RNA polymerase at highly transcribed or long genes. These compounds are used as first or second line therapies to treat cancers including colorectal, ovarian, lung, breast, and cervical. Single-strand binding proteins bind to the single-stranded DNA near the replication fork to keep the fork open. These interfacial inhibitors are stabilized by stacking interactions with the nicked DNA and hydrogen bonding to the enzyme. Further details may exist on the, Mattenberger Y, Silva F, Belin D. 55.2, a phage T4 ORFan gene, encodes an inhibitor of Escherichia coli topoisomerase I and increases phage fitness. It was the type I topoisomerase. They are indispensable for the control of DNA topology. Topoisomerase and SSB proteins are important components of the replication process in prokaryotes, and there are similar proteins that are also found in eukaryotes. While the original topoisomerase II structure shows a situation where the WHDs are separated by a large distance, the structure of gyrase shows a closed conformation, where the WHD close. 5). The range of reactions includes: DNA supercoil relaxation, unknotting of single-stranded circles, and decatenation, provided at least one partner has a single-stranded region. In the case of the archaeal enzyme, reverse gyrase, positive supercoiling of DNA is possible. Both Pfam signatures are found in the single-chain eukayotic topoisomerase. This strand passage mechanism shares several features with type IIA topoisomerases. RNA primers are removed by exonuclease activity. A polypeptide B. If the positive supercoils are not relaxed, progression of the replication fork is impeded, whereas failure to unlink the daughter strands prevents genome segregation, which is required for cell division. 1). Type IC topoisomerases form a covalent 3'-phosphotyrosine intermediate. This domain is thought to communicate the nucleotide state of the ATPase domain to the rest of the protein. Structural studies of type I topoisomerases - PMC - National Center for It is noteworthy that type IB topoisomerases are found in some bacteria . Then how does it add the first nucleotide? Elongation of both the lagging and the leading strand continues. 5). The leading strand can be extended by one primer alone, whereas the lagging strand needs a new primer for each of the short Okazaki fragments. As pointed out by Singh et al.,[58] "about 80% of highly expressed genes in HeLa cells are paused". The first structure of a C-terminal domain of gyrase was solved by Corbett et al. Type IIB topoisomerases are structurally and biochemically distinct, and comprise a single family member, topoisomerase VI (topo VI). Type IIA topoisomerases catalyze transient double-stranded breaks in DNA through the formation of tyrosyl-phosphate bonds between tyrosines in the enzyme (one on each subunit) and 5-phosphates staggered by 4 bases in opposite DNA strands. 4). Both gyrase and topoisomerase IV CTDs bend DNA, but only gyrase introduces negative supercoils. This strand is known as the lagging strand. These differences include the lack of one of the protein 'gates' (the C gate) (Fig. they stabilize the enzyme-DNA covalent cleavage intermediate.[32][33][34]. The first DNA topoisomerase was discovered in bacteria by James Wang in 1971 and was initially named (omega) protein;[3] it is now called Escherichia coli (E. coli) topoisomerase I (topo I) and is a representative of the type IA family of enzymes. DNA supercoiling restricts the transcriptional bursting of - PubMed This function is believed to be performed by topoisomerase II in eukaryotes and by topoisomerase IV in prokaryotes. DNA topoisomerases are enzymes that have evolved to resolve topological problems in DNA (Table 2). Replication in prokaryotes starts from a sequence found on the chromosome called . Human DNA-Topoisomerases - Diagnostic and Therapeutic - PubMed There are two subclasses of type II topoisomerases, type IIA and IIB. Type IB topoisomerases catalyze reactions involving transient single-stranded breaks in DNA through the formation of a tyrosyl-phosphate bond between a tyrosine in the enzyme and a 3-phosphate in the DNA. Involved in RNA processing, Removes (-), but not (+) supercoils, introduces positive supercoils, Removes (+) and (-) supercoils; supports fork movement during replication and transcription. The enzyme uses the hydrolysis of ATP to introduce positive supercoils and overwinds DNA, a feature attractive in hyperthermophiles, in which reverse gyrase is known to exist. [8] The crystal structure of topo V was solved. 202530 and it shows no apparent sequence or structural similarities to the analogous region of eukaryotic type IB topoisomerases. DNA replication employs a large number of proteins and enzymes, each of which plays a critical role during the process. This last structure showed that the Toprim domain and the WHD formed a cleavage complex very similar to that of the type IA topoisomerases and indicated how DNA-binding and cleavage could be uncoupled, and the structure showed that DNA was bent by ~150 degrees through an invariant isoleucine (in topoisomerase II it is I833 and in gyrase it is I172).

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