topoisomerase in prokaryotes and eukaryotes

Zhou Q., Hernandez M.E.G., Fernandez-Lima F., Tse-Dinh Y.-C. Biochemical Basis of E. coli Topoisomerase I Relaxation Activity Reduction by Nonenzymatic Lysine Acetylation. Topoisomerase inhibitor - Wikipedia Annu Rev Biochem. (B) Structure of the E. coli topoisomerase I covalent complex (PDB 3PX7) showing the positioning of the G-strand by residues interacting with the G-strand backbone and a cytosine base (shown in the space-filling display) at a distance of four nucleotides from the phosphoryl tyrosine (PTR) formed from the cleavage of the G-strand. The main feature of this enzyme is that it generates single-strand breaks during the process. Axolotl Academica Publishing. All tangled up: How cells direct, manage and exploit topoisomerase function. Ahmed W., Bhat A.G., Leelaram M.N., Menon S., Nagaraja V. Carboxyl terminal domain basic amino acids of mycobacterial topoisomerase I bind DNA to promote strand passage. 10.1038/nrm.2016.111 Topoisomerase 3 Is Required for Decatenation and Segregation of Human mtDNA. The guiding of the T-strand in and out of the toroid hole is also not well understood. R01 CA052814/CA/NCI NIH HHS/United States, R21 CA187651/CA/NCI NIH HHS/United States, Z01 BC006161/ImNIH/Intramural NIH HHS/United States, NCI CPTC Antibody Characterization Program. In the crystal structure of M. tuberculosis topoisomerase I [62], one Mg2+ ion is coordinated with the negatively charged carboxylate side chain of Glu24 (corresponding to Glu9 in E. coli topoisomerase I, Figure 3A) and Glu111 directly, and to Glu113 indirectly through a water molecule, in addition to the scissile phosphate. It is responsible for relaxing the stress of the DNA double helix generated due to either over winding or under winding. Resistance to Antibody-Drug Conjugates Targeting HER2 in Breast Cancer: Molecular Landscape and Future Challenges. The proteinprotein interactions with other cellular proteins are relevant for the physiological functions and regulation of type IA topoisomerase activities [38]. Type IIA topoisomerases include the enzymes DNA gyrase, eukaryotic topoisomerase II (topo II), and bacterial topoisomerase IV (topo IV). Would you like email updates of new search results? According to the model for type IA topoisomerase catalysis proposed when the crystal structure of the core domains first showed [44] a toroid enclosed by interactions of D3 with D1 and D4, D3 must move away from D1 and D4 for gate opening. Type IA and type IIA topoisomerases require divalent ions for catalytic activity. (C) When a translating ribosome or a helicase unwinds a duplex region in a viral RNA hairpin, and if the hairpin is bound to an immobile RNP or cellular matrix, the helical torsion will need to be relaxed by TOP3B. 8600 Rockville Pike A type IA topoisomerase may have been present in a last universal common ancestor (LUCA) with an RNA genome. Rani P., Nagaraja V. Genome-wide mapping of Topoisomerase I activity sites reveal its role in chromosome segregation. Perry K., Mondragn A. Biochemical Characterization of an Invariant Histidine Involved inEscherichia coliDNA Topoisomerase I Catalysis. Liu L.F., DePew R.E., Wang J.C. Knotted single-stranded DNA rings: A novel topological isomer of circular single-stranded DNA formed by treatment with Escherichia coli protein. Epub 2021 Sep 6. TOP2 (middle) and TOP3 (bottom) both involve mechanisms of DNA strand transfer. Crystal structure of a covalent intermediate in DNA cleavage and rejoining by Escherichia coli DNA topoisomerase I. Tan K., Zhou Q., Cheng B., Zhang Z., Joachimiak A., Tse-Dinh Y.-C. Figure 1 shows some of the potential topological barriers occurring during the life cycle of a positive-sense single-stranded RNA virus that may require the RNA topoisomerase activity of human TOP3B. In mammals The site is secure. Type II DNA topoisomerases: Enzymes that can unknot a topologically knotted DNA molecule via a reversible double-strand break. Tetracysteine motifs that form the zinc ribbon fold [88] can be found in the topoisomerase I gene of a majority of bacterial species. Lee S.K., Xue Y., Shen W., Zhang Y., Joo Y., Ahmad M., Chinen M., Ding Y., Ku W.L., De S., et al. Additional interactions with the ssDNA include hydrogen bonds and cation interactions. TnpB may also be the ancestor of the eukaryotic transposon-encoded Fanzor (Fz) proteins 4,7, raising the possibility that eukaryotes are also equipped with CRISPR-Cas/OMEGA-like programmable RNA . At the active sites of these topoisomerases, divalent ions are coordinated by the TOPRIM motifs (with a conserved glutamate and two conserved aspartates DxD) also seen in many nucleotidyl transferases/hydrolases [78]. Overexpression of the D111N mutant topoisomerase I is toxic to the cells because of deficiency in DNA religation resulting in the accumulation of the cleavage complex on chromosomal DNA. Nat Rev Mol Cell Biol. DNA topoisomerases are enzymes that catalyze changes in the torsional and flexural strain of DNA molecules. Clipboard, Search History, and several other advanced features are temporarily unavailable. Das BB, Ghosh A, Bhattacharjee S, Bhattacharyya A. Mitochondrion. Solution structure of the C-terminal single-stranded DNA-binding domain of Escherichia coli topoisomerase I. Zumstein L., Wang J.C. Probing the structural domains and function in vivo of Escherichia coli DNA topoisomerase I by mutagenesis. FOIA Insights from the Structure of Mycobacterium tuberculosis Topoisomerase I with a Novel Protein Fold. Before replication can start, the DNA . RNA topoisomerase is prevalent in all domains of life and associates with polyribosomes in animals. Humans possess 4 types of topoisomerases, i. e. topoisomerase (topo) I, II, III and V. Topo I, a 100-kDa -, Pommier Y, Sun Y, Huang SN, et al. Please enable it to take advantage of the complete set of features! (2016)]. Human cells encode six topoisomerases (TOP1, TOP1mt, TOP2, TOP2, TOP3 and TOP3), which act on a broad range of DNA and RNA substrates at the nuclear and mitochondrial genomes. The active site tyrosine is part of domain D3 and situated at the interface of domains D1 and D3 and responsible for the transient breakage of the G-strand of DNA along with the subsequent formation of the phosphoryl-tyrosyl covalent complex (Figure 3). The DNA cleavage also became Mg2+ dependent when the first aspartate of the DxD TOPRIM motif was mutated to asparagine without the negatively charged side chain [59,79]. Molecular dissection of Helicobacter pylori Topoisomerase I reveals an additional active site in the carboxyl terminus of the enzyme. 7.2: Semi-Conservative DNA Replication. There is further evidence that the bacterial topoisomerase I C-terminal domains have a specific role for interacting with the T-strand in strand passage for the efficient recognition and relaxation of negatively supercoiled DNA [52,61,86,95]. Mass E., Drolet M. Escherichia coli DNA Topoisomerase I Inhibits R-loop Formation by Relaxing Transcription-induced Negative Supercoiling. Prediction of hub genes and key pathways associated with the radiation response of human hematopoietic stem/progenitor cells using integrated bioinformatics methods. Human topoisomerases and their roles in genome stability and - Nature For type IA enzymes, depicted for TOP3cc, a single strand of negatively supercoiled DNA is cleaved to form a 5 phosphotyrosyl bond, while the 3OH end is held by the enzyme. In these crystal structures, a tyrosine side chain (Tyr177 in E. coli topoisomerase I) wedges between the 4 and 5 DNA bases and creates a kink in the G-strand. Combined techniques of magnetic tweezers and total internal reflection fluorescence microscopy also detected E. coli topoisomerase I conformational change that is necessary for strand passage, but an alternative model of sliding the domains past each other to create a gate for capturing the T-strand of DNA into the interior of the toroid was proposed [112]. In the case of TOP2cc, the G segment of duplex DNA is cleaved by the two active sites of the homodimer, following capture of the T segment by the closure of the N-terminal ATPase domains. Stoll G., Pietilinen O.P.H., Linder B., Suvisaari J., Brosi C., Hennah W., Leppa V., Torniainen M., Ripatti S., Ala-Mello S., et al. The interest in the physiological significance of RNA topoisomerase activity was greatly heightened by the findings that human topoisomerase III (TOP3B) has both DNA and RNA topoisomerase activities [23,24]. Int J Mol Sci. The ability to unknot single-stranded RNA circles was first observed for Escherichia coli topoisomerase III [22]. 7.4: Eukaryotic Replication. Careers. ), 2Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA, 3Biochemistry PhD Program, Florida International University, Miami, FL 33199, USA. Structural studies of type I topoisomerases. Nat Rev Mol Cell Biol. Here, we review the roles of topoisomerases in mediating chromatin dynamics, transcription, replication, DNA damage repair and genomic stability, and discuss how deregulation of topoisomerases can cause neurodegenerative diseases, immune disorders and cancer. 2016;8(3):221231. For each amino acid along the length of the human sequence, the number of other enzymes with the identical . A divalent ion interaction helps to position the 3-hydroxyl group at the precise location required for the cleaved phosphodiester bond to be rejoined following the passage of another nucleic acid strand through the break. Formation of phosphotyrosine linkage between certain DNA topoisomerases and DNA. Liu L.F., Liu C.-C., Alberts B.M. 2002;3(6):43040. The principal drugs acting against type I topoisomerases are the camptothecins, including topotecan and irinotecan. Viard T., De La Tour C.B. P30 CA013148/CA/NCI NIH HHS/United States, P50 CA136393/CA/NCI NIH HHS/United States, R01 CA190423/CA/NCI NIH HHS/United States, NCI CPTC Antibody Characterization Program, Champoux JJ: DNA topoisomerases: structure, function, and mechanism. Topoisomerase I relaxes the supercoil, and topoisomerase II adds negative supercoils. DNA topoisomerase V is a relative of eukaryotic topoisomerase - PubMed Schoeffler A.J., Berger J.M. The DNA relaxation activity and covalent complex accumulation of Mycobacterium tuberculosis topoisomerase I can be assayed in Escherichia coli: Application for identification of potential FRET-dye labeling sites. Ahumada A., Tse-Dinh Y.-C. Key points: DNA replication is semiconservative. The origin of replication is recognized by certain proteins that bind to this site. The PubMed wordmark and PubMed logo are registered trademarks of the U.S. Department of Health and Human Services (HHS). Copyright: 2019 Bjornsti MA and Kaufmann SH. Narula G., Becker J., Cheng B., Dani N., Abrenica M.V., Tse-Dinh Y.-C. DNA replication begins at an origin of replication. To elucidate the mechanism of this recognition, we examined the interaction of topoisomerases with DNA by electron microscopy. The substitution of Tyr177 with serine to abolish the base-stacking interaction resulted in the complete loss of DNA cleavage and relaxation activity [69]. Rudolph M.G., del Duany Y.T., Jungblut S.P., Ganguly A., Klostermeier D. Crystal structures of Thermotoga maritima reverse gyrase: Inferences for the mechanism of positive DNA supercoiling. Xu D., Shen W., Guo R., Xue Y., Peng W., Sima J., Yang J., Sharov A., Srikantan S., Yang J., et al. Ahumada A., Tse-Dinh Y.-C. These enzymes span all domains of life and are essential for function. Two recent reviews on type IA topoisomerases have discussed the essential functions of bacterial type IA topoisomerase [14] and the many versatile collaborations engaged by eukaryotic TOP3 to carry out different topological transactions [38]. Domain structure of topoisomerase 11 enzymes from prokaryotes and MeSH Kirkegaard K., Wang J.C. Bacterial DNA topoisomerase I can relax positively supercoiled DNA containing a single-stranded loop. TOPcc can also form on damaged DNA during replication and transcription, and engage specific repair pathways, such as those mediated by tyrosyl-DNA phosphodiesterase 1 (TDP1) and TDP2 and by endonucleases (MRE11, XPF-ERCC1 and MUS81). Residues conserved for the specific binding of a cytosine base 4 nucleotides upstream of the scissile phosphate are shown in blue. Site-directed mutagenesis of E. coli topoisomerase at Gly194, Arg195 and Gln197 confirmed that mutations at these residues reduced the relaxation activity significantly [63,64]. Please enable it to take advantage of the complete set of features! The C-terminal domains observed in the topoisomerase I of bacteria and the topoisomerase III of higher eukaryotes have evolved to enhance the interactions with nucleic acid substrates and proteinprotein interactions using the repeated C-terminal domains and basic amino acid residues. A recent report of an additional active site in the C-terminal domains of Helicobacter pylori topoisomerase I [106] further illustrates the diverse properties of type IA topoisomerase C-terminal domains. Here we characterize a prokaryotic counterpart to the eukaryotic topoisomerase I in the hyperthermophilic methanogen Methanopyrus kandleri. The figure is modified from a published version for potential TOP3B action on mRNA in [29]. Active site residues assist in the nucleophilic attack of a phosphodiester bond between two nucleotides to form a covalent intermediate with a 5-phosphotyrosine linkage to the cleaved nucleic acid. On the contrary, most eukaryotes utilize type I topoisomerases, that cut a single strand of DNA, during the movement of the replication fork.Type I Topoisomerases (creates s. Cheng B., Feng J., Gadgil S., Tse-Dinh Y.-C. Topoisomerases constitute a family of highly conserved essential enzymes, which exist in all investigated living pro- and eukaryotic cells. Prokaryotic Contributions to Eukaryote Evolution: Sharing is Caring. Furthermore, mutations in human TOP3B are linked to disorders in neurodevelopment and mental health [23,24,25,26,27]. 1 Supercoiling 2 Positive and Negative Supercoilings 3 Topoisomerase 3.1 Type I topoisomerase 3.2 Type II topoisomerase 4 Nucleosomes 4.1 Histones and Transcription Regulation 4.2 Nucleosome Sliding 4.3 Chromatin Remodeler Supercoiling relaxed DNA molecule negative supercoil (D) Alignment of residues (shown in red) that are strictly conserved in type IA topoisomerases for interacting with the G-strand backbone. Zhu C.-X., Roche C.J., Papanicolaou N., Dipietrantonio A., Tse-Dinh Y.-C. Site-directed Mutagenesis of Conserved Aspartates, Glutamates and Arginines in the Active Site Region ofEscherichia coliDNA Topoisomerase I. Chen S.-J., Wang J.C. Changes in the linkage of DNA strands occur through a mechanism of strand rotation, where the untethered 5 DNA end of the cleaved strand swivels about the noncleaved DNA strand. PMC Bizard A.H., Hickson I.D. 2023 Jan 9;16(1):94. doi: 10.3390/ph16010094. [Google Scholar] Abstract. A R338W mutation introduced at the corresponding arginine residue in human topoisomerase III has been shown to facilitate trapping of the intracellular covalent complex with both DNA and RNA [77], confirming a similar role for this arginine residue in the cleavage and rejoining of the RNA G-strand. Zhang T., Wallis M., Petrovic V., Challis J., Kalitsis P., Hudson D.F. The deoxyribose and bases of the G-strand interact with other polar, positively charged and aromatic residues that extend from the interface of core domains D1 and D3 into D4 (Figure 3B). The Implication of Topoisomerase II Inhibitors in Synthetic Lethality for Cancer Therapy. Brochu J., Breton E.V., Drolet M. Supercoiling, R-Loops, Replication and the Functions of Bacterial Type 1A Topoisomerases. Deletion of TOP3B Is Associated with Cognitive Impairment and Facial Dysmorphism. Here, based on available structural and biochemical data, we discuss how a type IA topoisomerase may recognize and bind single-stranded DNA or RNA to initiate its required catalytic function. Direct Interaction between Escherichia coli RNA Polymerase and the Zinc Ribbon Domains of DNA Topoisomerase I. Ahmed W., Sala C., Hegde S.R., Jha R.K., Cole S.T., Nagaraja V. Transcription facilitated genome-wide recruitment of topoisomerase I and DNA gyrase. Liu D., Shao Y., Chen G., Tse-Dinh Y.-C., Piccirilli J.A., Weizmann Y. Synthesizing topological structures containing RNA. Sequence comparisons of eukaryotic type I topoisomerases. Biochemistry, DNA Replication - StatPearls - NCBI Bookshelf Reverse gyrase, which occurs in thermophilic archaea, comprises a type IA topo coupled to a helicase, and is the only known enzyme that can introduce positive supercoils into DNA. [1] Structural studies are needed to determine the exact folding of these C-terminal motifs in eukaryotic topoisomerase III enzymes. Zhang Z., Cheng B., Tse-Dinh Y.-C. Copyright notice. The flexibility of this glycine may facilitate this conformational change required for G-strand binding [63]. PMC If the supercoiling is not relieved, it will physically prevent the movement of helicase. The acetylation of lysine residues can also influence the topoisomerase activity of E. coli topoisomerase I [98,99]. Huang L., Wang Z., Narayanan N., Yang Y. Arginine methylation of the C-terminus RGG motif promotes TOP3B topoisomerase activity and stress granule localization. Accessibility 1.6: DNA Supercoiling and Topoisomerases - Biology LibreTexts The positive charge of Mg2+ can help to position the 3-OH of the cleaved G-strand for a nucleophilic attack on the phosphotyrosine linkage and stabilize the transition state for DNA rejoining. (C) Alignment of residues strictly conserved at the active site and type IA topoisomerases including bacterial topoisomerase I, reverse gyrase (RG) and topoisomerase III from prokaryotes and eukaryotes. The Zn(II) Binding Motifs of E. coli DNA Topoisomerase I Is Part of a High-Affinity DNA Binding Domain. This mutation was utilized to obtain the crystal structure of the covalent complex formed between E. coli topoisomerase I core domains and cleaved DNA (PDB 3PX7) [60]. In contrast, the rapid closing of the DNA gate formed by E. coli topoisomerase I observed in the single-molecule assays would allow a fast rate of relaxation of negatively supercoiled DNA [110]. DNA topoisomerases: structure, function, and mechanism. 2021 Sep;60:234-244. doi: 10.1016/j.mito.2021.08.017. Wang J.C. Cellular roles of DNA topoisomerases: A molecular perspective. Vos S.M., Tretter E.M., Schmidt B.H., Berger J.M. There is only one origin in prokaryotes (in E. coli, oriC) and it is characterized by arrays of repeated sequences. -, Seol Y, Neuman KC: The Dynamic Interplay Between DNA Topoisomerases and DNA Topology. Distinct actions of topoisomerase poisons. Rani P., Kalladi S., Bansia H., Rao S., Jha R.K., Jain P., Bhaduri T., Nagaraja V. A Type IA DNA/RNA topoisomerase with RNA hydrolysis activity participates in ribosomal RNA processing. Disclaimer. Galdieria sulphuraria has acquired many genes from bacteria and archaea.

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