1
|
Okabe T, Aoi R, Yokota A, Tamiya-Ishitsuka H, Jiang Y, Sasaki A, Tsuneda S, Noda N. Arg-73 of the RNA endonuclease MazF in Salmonella enterica subsp. arizonae contributes to guanine and uracil recognition in the cleavage sequence. J Biol Chem 2024; 300:105636. [PMID: 38199572 PMCID: PMC10864209 DOI: 10.1016/j.jbc.2024.105636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 12/14/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024] Open
Abstract
The sequence-specific endoribonuclease MazF is widely conserved among prokaryotes. Approximately 20 different MazF cleavage sequences have been discovered, varying from three to seven nucleotides in length. Although MazFs from various prokaryotes were found, the cleavage sequences of most MazFs are unknown. Here, we characterized the conserved MazF of Salmonella enterica subsp. arizonae (MazF-SEA). Using massive parallel sequencing and fluorometric assays, we revealed that MazF-SEA preferentially cleaves the sequences U∧ACG and U∧ACU (∧ represents cleavage sites). In addition, we predicted the 3D structure of MazF-SEA using AlphaFold2 and aligned it with the crystal structure of RNA-bound Bacillus subtilis MazF to evaluate RNA interactions. We found Arg-73 of MazF-SEA interacts with RNAs containing G and U at the third position from the cleavage sites (U∧ACG and U∧ACU). We then obtained the mutated MazF-SEA R73L protein to evaluate the significance of Arg-73 interaction with RNAs containing G and U at this position. We also used fluorometric and kinetic assays and showed the enzymatic activity of MazF-SEA R73L for the sequence UACG and UACU was significantly decreased. These results suggest Arg-73 is essential for recognizing G and U at the third position from the cleavage sites. This is the first study to our knowledge to identify a single residue responsible for RNA recognition by MazF. Owing to its high specificity and ribosome-independence, MazF is useful for RNA cleavage in vitro. These results will likely contribute to increasing the diversity of MazF specificity and to furthering the application of MazF in RNA engineering.
Collapse
Affiliation(s)
- Takuma Okabe
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan; Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan
| | - Rie Aoi
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan; Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan
| | - Akiko Yokota
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan
| | - Hiroko Tamiya-Ishitsuka
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan
| | - Yunong Jiang
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan; Graduate School of Comprehensive Human Sciences, University of Tsukuba, Ibaraki, Japan
| | - Akira Sasaki
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan
| | - Satoshi Tsuneda
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan.
| | - Naohiro Noda
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan; Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan; School of Integrative and Global Majors, University of Tsukuba, Ibaraki, Japan.
| |
Collapse
|
2
|
Saha LK, Pommier Y. TOP3A coupling with replication forks and repair of TOP3A cleavage complexes. Cell Cycle 2024; 23:115-130. [PMID: 38341866 PMCID: PMC11037291 DOI: 10.1080/15384101.2024.2314440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 01/08/2024] [Indexed: 02/13/2024] Open
Abstract
Humans have two Type IA topoisomerases, topoisomerase IIIα (TOP3A) and topoisomerase IIIβ (TOP3B). In this review, we focus on the role of human TOP3A in DNA replication and highlight the recent progress made in understanding TOP3A in the context of replication. Like other topoisomerases, TOP3A acts by a reversible mechanism of cleavage and rejoining of DNA strands allowing changes in DNA topology. By cleaving and resealing single-stranded DNA, it generates TOP3A-linked single-strand breaks as TOP3A cleavage complexes (TOP3Accs) with a TOP3A molecule covalently bound to the 5´-end of the break. TOP3A is critical for both mitochondrial and for nuclear DNA replication. Here, we discuss the formation and repair of irreversible TOP3Accs, as their presence compromises genome integrity as they form TOP3A DNA-protein crosslinks (TOP3A-DPCs) associated with DNA breaks. We discuss the redundant pathways that repair TOP3A-DPCs, and how their defects are a source of DNA damage leading to neurological diseases and mitochondrial disorders.
Collapse
Affiliation(s)
- Liton Kumar Saha
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| |
Collapse
|
3
|
Saha LK, Saha S, Yang X, Huang SYN, Sun Y, Jo U, Pommier Y. Replication-associated formation and repair of human topoisomerase IIIα cleavage complexes. Nat Commun 2023; 14:1925. [PMID: 37024461 PMCID: PMC10079683 DOI: 10.1038/s41467-023-37498-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 03/08/2023] [Indexed: 04/08/2023] Open
Abstract
Topoisomerase IIIα (TOP3A) belongs to the conserved Type IA family of DNA topoisomerases. Here we report that human TOP3A is associated with DNA replication forks and that a "self-trapping" TOP3A mutant (TOP3A-R364W) generates cellular TOP3A DNA cleavage complexes (TOP3Accs). We show that trapped TOP3Accs that interfere with replication, induce DNA damage and genome instability. To elucidate how TOP3Accs are repaired, we explored the role of Spartan (SPRTN), the metalloprotease associated with DNA replication, which digests proteins forming DNA-protein crosslinks (DPCs). We find that SPRTN-deficient cells show elevated TOP3Accs, whereas overexpression of SPRTN lowers cellular TOP3Accs. SPRTN is deubiquitinated and epistatic with TDP2 in response to TOP3Accs. In addition, we found that MRE11 can excise TOP3Accs, and that cell cycle determines the preference for the SPRTN-TDP2 vs. the ATM-MRE11 pathways, in S vs. G2, respectively. Our study highlights the prevalence of TOP3Accs repair mechanisms to ensure normal DNA replication.
Collapse
Affiliation(s)
- Liton Kumar Saha
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Sourav Saha
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Xi Yang
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Shar-Yin Naomi Huang
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Yilun Sun
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Ukhyun Jo
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Yves Pommier
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA.
| |
Collapse
|
4
|
Ferdous S, Dasgupta T, Annamalai T, Tan K, Tse-Dinh YC. The interaction between transport-segment DNA and topoisomerase IA-crystal structure of MtbTOP1 in complex with both G- and T-segments. Nucleic Acids Res 2022; 51:349-364. [PMID: 36583363 PMCID: PMC9841409 DOI: 10.1093/nar/gkac1205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 11/16/2022] [Accepted: 12/06/2022] [Indexed: 12/31/2022] Open
Abstract
Each catalytic cycle of type IA topoisomerases has been proposed to comprise multistep reactions. The capture of the transport-segment DNA (T-segment) into the central cavity of the N-terminal toroidal structure is an important action, which is preceded by transient gate-segment (G-segment) cleavage and succeeded by G-segment religation for the relaxation of negatively supercoiled DNA and decatenation of DNA. The T-segment passage in and out of the central cavity requires significant domain-domain rearrangements, including the movement of D3 relative to D1 and D4 for the opening and closing of the gate towards the central cavity. Here we report a direct observation of the interaction of a duplex DNA in the central cavity of a type IA topoisomerase and its associated domain-domain conformational changes in a crystal structure of a Mycobacterium tuberculosis topoisomerase I complex that also has a bound G-segment. The duplex DNA within the central cavity illustrates the non-sequence-specific interplay between the T-segment DNA and the enzyme. The rich structural information revealed from the novel topoisomerase-DNA complex, in combination with targeted mutagenesis studies, provides new insights into the mechanism of the topoisomerase IA catalytic cycle.
Collapse
Affiliation(s)
| | | | - Thirunavukkarasu Annamalai
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA,Biomolecular Sciences Institute, Florida International University, 11200 SW 8th St, Miami, FL 33199, USA
| | - Kemin Tan
- Correspondence may also be addressed to Kemin Tan. Tel: +1 630 252 3948;
| | | |
Collapse
|
5
|
Yang X, Saha S, Yang W, Neuman KC, Pommier Y. Structural and biochemical basis for DNA and RNA catalysis by human Topoisomerase 3β. Nat Commun 2022; 13:4656. [PMID: 35945419 PMCID: PMC9363430 DOI: 10.1038/s41467-022-32221-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 07/21/2022] [Indexed: 11/09/2022] Open
Abstract
In metazoans, topoisomerase 3β (TOP3B) regulates R-loop dynamics and mRNA translation, which are critical for genome stability, neurodevelopment and normal aging. As a Type IA topoisomerase, TOP3B acts by general acid-base catalysis to break and rejoin single-stranded DNA. Passage of a second DNA strand through the transient break permits dissipation of hypernegative DNA supercoiling and catenation/knotting. Additionally, hsTOP3B was recently demonstrated as the human RNA topoisomerase, required for normal neurodevelopment and proposed to be a potential anti-viral target upon RNA virus infection. Here we elucidate the biochemical mechanisms of human TOP3B. We delineate the roles of divalent metal ions, and of a conserved Lysine residue (K10) in the differential catalysis of DNA and RNA. We also demonstrate that three regulatory factors fine-tune the catalytic performance of TOP3B: the TOP3B C-terminal tail, its protein partner TDRD3, and the sequence of its DNA/RNA substrates.
Collapse
Affiliation(s)
- Xi Yang
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Sourav Saha
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Wei Yang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD, 20892, USA
| | - Keir C Neuman
- Laboratory of Single Molecule Biophysics, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yves Pommier
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA.
| |
Collapse
|
6
|
Leng X, Duxin JP. Targeting DNA-Protein Crosslinks via Post-Translational Modifications. Front Mol Biosci 2022; 9:944775. [PMID: 35860355 PMCID: PMC9289515 DOI: 10.3389/fmolb.2022.944775] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 06/03/2022] [Indexed: 11/13/2022] Open
Abstract
Covalent binding of proteins to DNA forms DNA-protein crosslinks (DPCs), which represent cytotoxic DNA lesions that interfere with essential processes such as DNA replication and transcription. Cells possess different enzymatic activities to counteract DPCs. These include enzymes that degrade the adducted proteins, resolve the crosslinks, or incise the DNA to remove the crosslinked proteins. An important question is how DPCs are sensed and targeted for removal via the most suited pathway. Recent advances have shown the inherent role of DNA replication in triggering DPC removal by proteolysis. However, DPCs are also efficiently sensed and removed in the absence of DNA replication. In either scenario, post-translational modifications (PTMs) on DPCs play essential and versatile roles in orchestrating the repair routes. In this review, we summarize the current knowledge of the mechanisms that trigger DPC removal via PTMs, focusing on ubiquitylation, small ubiquitin-related modifier (SUMO) conjugation (SUMOylation), and poly (ADP-ribosyl)ation (PARylation). We also briefly discuss the current knowledge gaps and emerging hypotheses in the field.
Collapse
|
7
|
Huang SYN, Michaels SA, Mitchell BB, Majdalani N, Vanden Broeck A, Canela A, Tse-Dinh YC, Lamour V, Pommier Y. Exonuclease VII repairs quinolone-induced damage by resolving DNA gyrase cleavage complexes. SCIENCE ADVANCES 2021; 7:7/10/eabe0384. [PMID: 33658195 PMCID: PMC7929499 DOI: 10.1126/sciadv.abe0384] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 01/19/2021] [Indexed: 05/25/2023]
Abstract
The widely used quinolone antibiotics act by trapping prokaryotic type IIA topoisomerases, resulting in irreversible topoisomerase cleavage complexes (TOPcc). Whereas the excision repair pathways of TOPcc in eukaryotes have been extensively studied, it is not known whether equivalent repair pathways for prokaryotic TOPcc exist. By combining genetic, biochemical, and molecular biology approaches, we demonstrate that exonuclease VII (ExoVII) excises quinolone-induced trapped DNA gyrase, an essential prokaryotic type IIA topoisomerase. We show that ExoVII repairs trapped type IIA TOPcc and that ExoVII displays tyrosyl nuclease activity for the tyrosyl-DNA linkage on the 5'-DNA overhangs corresponding to trapped type IIA TOPcc. ExoVII-deficient bacteria fail to remove trapped DNA gyrase, consistent with their hypersensitivity to quinolones. We also identify an ExoVII inhibitor that synergizes with the antimicrobial activity of quinolones, including in quinolone-resistant bacterial strains, further demonstrating the functional importance of ExoVII for the repair of type IIA TOPcc.
Collapse
Affiliation(s)
- Shar-Yin N Huang
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
| | - Stephanie A Michaels
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Brianna B Mitchell
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Nadim Majdalani
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Arnaud Vanden Broeck
- Integrated Structural Biology Department, IGBMC, UMR7104 CNRS, U1258 Inserm, University of Strasbourg, Illkirch 67404, France
| | - Andres Canela
- The Hakubi Center for Advanced Research, Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yuk-Ching Tse-Dinh
- Department of Chemistry and Biochemistry, Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
| | - Valerie Lamour
- Integrated Structural Biology Department, IGBMC, UMR7104 CNRS, U1258 Inserm, University of Strasbourg, Illkirch 67404, France
| | - Yves Pommier
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
| |
Collapse
|
8
|
Seddek A, Annamalai T, Tse-Dinh YC. Type IA Topoisomerases as Targets for Infectious Disease Treatments. Microorganisms 2021; 9:E86. [PMID: 33401386 PMCID: PMC7823277 DOI: 10.3390/microorganisms9010086] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 12/13/2020] [Accepted: 12/17/2020] [Indexed: 12/19/2022] Open
Abstract
Infectious diseases are one of the main causes of death all over the world, with antimicrobial resistance presenting a great challenge. New antibiotics need to be developed to provide therapeutic treatment options, requiring novel drug targets to be identified and pursued. DNA topoisomerases control the topology of DNA via DNA cleavage-rejoining coupled to DNA strand passage. The change in DNA topological features must be controlled in vital processes including DNA replication, transcription, and DNA repair. Type IIA topoisomerases are well established targets for antibiotics. In this review, type IA topoisomerases in bacteria are discussed as potential targets for new antibiotics. In certain bacterial pathogens, topoisomerase I is the only type IA topoisomerase present, which makes it a valuable antibiotic target. This review will summarize recent attempts that have been made to identify inhibitors of bacterial topoisomerase I as potential leads for antibiotics and use of these inhibitors as molecular probes in cellular studies. Crystal structures of inhibitor-enzyme complexes and more in-depth knowledge of their mechanisms of actions will help to establish the structure-activity relationship of potential drug leads and develop potent and selective therapeutics that can aid in combating the drug resistant bacterial infections that threaten public health.
Collapse
Affiliation(s)
- Ahmed Seddek
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA; (A.S.); (T.A.)
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
| | - Thirunavukkarasu Annamalai
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA; (A.S.); (T.A.)
| | - Yuk-Ching Tse-Dinh
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA; (A.S.); (T.A.)
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
| |
Collapse
|
9
|
Saha S, Sun Y, Huang SYN, Baechler SA, Pongor LS, Agama K, Jo U, Zhang H, Tse-Dinh YC, Pommier Y. DNA and RNA Cleavage Complexes and Repair Pathway for TOP3B RNA- and DNA-Protein Crosslinks. Cell Rep 2020; 33:108569. [PMID: 33378676 PMCID: PMC7859927 DOI: 10.1016/j.celrep.2020.108569] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 11/20/2020] [Accepted: 12/07/2020] [Indexed: 12/31/2022] Open
Abstract
The present study demonstrates that topoisomerase 3B (TOP3B) forms both RNA and DNA cleavage complexes (TOP3Bccs) in vivo and reveals a pathway for repairing TOP3Bccs. For inducing and detecting cellular TOP3Bccs, we engineer a “self-trapping” mutant of TOP3B (R338W-TOP3B). Transfection with R338W-TOP3B induces R-loops, genomic damage, and growth defect, which highlights the importance of TOP3Bcc repair mechanisms. To determine how cells repair TOP3Bccs, we deplete tyrosyl-DNA phosphodiesterases (TDP1 and TDP2). TDP2-deficient cells show elevated TOP3Bccs both in DNA and RNA. Conversely, overexpression of TDP2 lowers cellular TOP3Bccs. Using recombinant human TDP2, we demonstrate that TDP2 can process both denatured and proteolyzed TOP3Bccs. We also show that cellular TOP3Bccs are ubiquitinated by the E3 ligase TRIM41 before undergoing proteasomal processing and excision by TDP2. Saha et al. introduce an approach to generate and detect the catalytic intermediates of TOP3B in DNA and RNA by engineering a self-poisoning enzyme, R338W-TOP3B. They reveal the cellular consequences of abortive TOP3Bcc formation and a repair pathway involving TRIM41, the proteasome, and TDP2 for processing of TOP3Bcc.
Collapse
Affiliation(s)
- Sourav Saha
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Yilun Sun
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Shar-Yin Naomi Huang
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Simone Andrea Baechler
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Lorinc Sandor Pongor
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Keli Agama
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Ukhyun Jo
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Hongliang Zhang
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Yuk-Ching Tse-Dinh
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA; Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
| | - Yves Pommier
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
| |
Collapse
|
10
|
Dasgupta T, Ferdous S, Tse-Dinh YC. Mechanism of Type IA Topoisomerases. Molecules 2020; 25:E4769. [PMID: 33080770 PMCID: PMC7587558 DOI: 10.3390/molecules25204769] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/12/2020] [Accepted: 10/15/2020] [Indexed: 11/16/2022] Open
Abstract
Topoisomerases in the type IA subfamily can catalyze change in topology for both DNA and RNA substrates. A type IA topoisomerase may have been present in a last universal common ancestor (LUCA) with an RNA genome. 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. 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. 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. 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. In addition to type IA topoisomerase structures observed by X-ray crystallography, we now have evidence from biophysical studies for the dynamic conformations that are required for type IA topoisomerases to catalyze the change in the topology of the nucleic acid substrates.
Collapse
Affiliation(s)
- Tumpa Dasgupta
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA; (T.D.); (S.F.)
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
- Biochemistry PhD Program, Florida International University, Miami, FL 33199, USA
| | - Shomita Ferdous
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA; (T.D.); (S.F.)
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
- Biochemistry PhD Program, Florida International University, Miami, FL 33199, USA
| | - Yuk-Ching Tse-Dinh
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA; (T.D.); (S.F.)
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
| |
Collapse
|
11
|
Kondekar SM, Gunjal GV, Pablo Radicella J, Rao DN. Molecular dissection of Helicobacter pylori Topoisomerase I reveals an additional active site in the carboxyl terminus of the enzyme. DNA Repair (Amst) 2020; 91-92:102853. [PMID: 32447233 DOI: 10.1016/j.dnarep.2020.102853] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 03/07/2020] [Accepted: 04/05/2020] [Indexed: 12/15/2022]
Abstract
DNA topoisomerases play a crucial role in maintaining DNA superhelicity, thereby regulating various cellular processes. Unlike most other species, the human pathogen Helicobacter pylori has only two topoisomerases, Topoisomerase I and DNA gyrase, the physiological roles of which remain to be explored. Interestingly, there is enormous variability among the C-terminal domains (CTDs) of Topoisomerase I across bacteria. H. pylori Topoisomerase I (HpTopoI) CTD harbors four zinc finger motifs (ZFs). We show here that sequential deletion of the third and/or fourth ZFs had only a marginal effect on the HpTopoI activity, while deletion of the second, third and fourth ZFs severely reduced DNA relaxation activity. Deletion of all ZFs drastically hampered DNA binding and thus abolished DNA relaxation. Surprisingly, mutagenesis of the annotated active site tyrosine residue (Y297 F) did not abrogate the enzyme activity and HpTopoI CTD alone (spanning the four ZFs) showed DNA relaxation activity. Additionally, a covalent linkage between the DNA and HpTopoI CTD was identified. The capacity of HpTopoI CTD to complement Escherichia coli topA mutant strains further supported the in vitro observations. Collectively these results imply that not all ZFs are dispensable for HpTopoI activity and unveil the presence of additional non-canonical catalytic site(s) within the enzyme.
Collapse
Affiliation(s)
- Sumedha M Kondekar
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Gaurav V Gunjal
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Juan Pablo Radicella
- Institute of Cellular and Molecular Radiobiology, Institut de Biologie François Jacob, CEA, F-92265 Fontenay aux Roses, France; Université de Paris and Université Paris-Saclay, F-92265 Fontenay aux Roses, France
| | - Desirazu N Rao
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India.
| |
Collapse
|
12
|
Cao N, Tan K, Zuo X, Annamalai T, Tse-Dinh YC. Mechanistic insights from structure of Mycobacterium smegmatis topoisomerase I with ssDNA bound to both N- and C-terminal domains. Nucleic Acids Res 2020; 48:4448-4462. [PMID: 32232337 PMCID: PMC7192597 DOI: 10.1093/nar/gkaa201] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 02/20/2020] [Accepted: 03/18/2020] [Indexed: 12/17/2022] Open
Abstract
Type IA topoisomerases interact with G-strand and T-strand ssDNA to regulate DNA topology. However, simultaneous binding of two ssDNA segments to a type IA topoisomerase has not been observed previously. We report here the crystal structure of a type IA topoisomerase with ssDNA segments bound in opposite polarity to the N- and C-terminal domains. Titration of small ssDNA oligonucleotides to Mycobacterium smegmatis topoisomerase I with progressive C-terminal deletions showed that the C-terminal region has higher affinity for ssDNA than the N-terminal active site. This allows the C-terminal domains to capture one strand of underwound negatively supercoiled DNA substrate first and position the N-terminal domains to bind and cleave the opposite strand in the relaxation reaction. Efficiency of negative supercoiling relaxation increases with the number of domains that bind ssDNA primarily with conserved aromatic residues and possibly with assistance from polar/basic residues. A comparison of bacterial topoisomerase I structures showed that a conserved transesterification unit (N-terminal toroid structure) for cutting and rejoining of a ssDNA strand can be combined with two different types of C-terminal ssDNA binding domains to form diverse bacterial topoisomerase I enzymes that are highly efficient in their physiological role of preventing excess negative supercoiling in the genome.
Collapse
Affiliation(s)
- Nan Cao
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
- Biomolecular Sciences Institute, Florida International University, 11200 SW 8 St, Miami, FL 33199, USA
| | - Kemin Tan
- Structural Biology Center, X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, 9700 S. Cass Avenue, Lemont, IL 60439, USA
| | - Xiaobing Zuo
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, 9700 S. Cass Avenue, Lemont, IL 60439, USA
| | - Thirunavukkarasu Annamalai
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
- Biomolecular Sciences Institute, Florida International University, 11200 SW 8 St, Miami, FL 33199, USA
| | - Yuk-Ching Tse-Dinh
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
- Biomolecular Sciences Institute, Florida International University, 11200 SW 8 St, Miami, FL 33199, USA
| |
Collapse
|
13
|
Tiwari PB, Chapagain PP, Seddek A, Annamalai T, Üren A, Tse-Dinh YC. Covalent Complex of DNA and Bacterial Topoisomerase: Implications in Antibacterial Drug Development. ChemMedChem 2020; 15:623-631. [PMID: 32043806 PMCID: PMC7133791 DOI: 10.1002/cmdc.201900721] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Indexed: 12/11/2022]
Abstract
A topoisomerase-DNA transient covalent complex can be a druggable target for novel topoisomerase poison inhibitors that represent a new class of antibacterial or anticancer drugs. Herein, we have investigated molecular features of the functionally important Escherichia coli topoisomerase I (EctopoI)-DNA covalent complex (EctopoIcc) for molecular simulations, which is very useful in the development of new antibacterial drugs. To demonstrate the usefulness of our approach, we used a model small molecule (SM), NSC76027, obtained from virtual screening. We examined the direct binding of NSC76027 to EctopoI as well as inhibition of EctopoI relaxation activity of this SM via experimental techniques. We then performed molecular dynamics (MD) simulations to investigate the dynamics and stability of EctopoIcc and EctopoI-NSC76027-DNA ternary complex. Our simulation results show that NSC76027 forms a stable ternary complex with EctopoIcc. EctopoI investigated here also serves as a model system for investigating a complex of topoisomerase and DNA in which DNA is covalently attached to the protein.
Collapse
Affiliation(s)
| | - Prem P Chapagain
- Department of Physics, Florida International University, Miami, FL 33199, USA
- Biomolecular sciences institute, Florida International University, Miami, FL 33199, USA
| | - Ahmed Seddek
- Biomolecular sciences institute, Florida International University, Miami, FL 33199, USA
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
| | - Thirunavukkarasu Annamalai
- Biomolecular sciences institute, Florida International University, Miami, FL 33199, USA
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
| | - Aykut Üren
- Department of Oncology, Georgetown University, Washington, DC 20057, USA
| | - Yuk-Ching Tse-Dinh
- Biomolecular sciences institute, Florida International University, Miami, FL 33199, USA
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
| |
Collapse
|
14
|
Cao N, Tan K, Annamalai T, Joachimiak A, Tse-Dinh YC. Investigating mycobacterial topoisomerase I mechanism from the analysis of metal and DNA substrate interactions at the active site. Nucleic Acids Res 2019; 46:7296-7308. [PMID: 29905859 PMCID: PMC6101483 DOI: 10.1093/nar/gky492] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 05/25/2018] [Indexed: 12/18/2022] Open
Abstract
We have obtained new crystal structures of Mycobacterium tuberculosis topoisomerase I, including structures with ssDNA substrate bound to the active site, with and without Mg2+ ion present. Significant enzyme conformational changes upon DNA binding place the catalytic tyrosine in a pre-transition state position for cleavage of a specific phosphodiester linkage. Meanwhile, the enzyme/DNA complex with bound Mg2+ ion may represent the post-transition state for religation in the enzyme's multiple-step DNA relaxation catalytic cycle. The first observation of Mg2+ ion coordinated with the TOPRIM residues and DNA phosphate in a type IA topoisomerase active site allows assignment of likely catalytic role for the metal and draws a comparison to the proposed mechanism for type IIA topoisomerases. The critical function of a strictly conserved glutamic acid in the DNA cleavage step was assessed through site-directed mutagenesis. The functions assigned to the observed Mg2+ ion can account for the metal requirement for DNA rejoining but not DNA cleavage by type IA topoisomerases. This work provides new structural insights into a more stringent requirement for DNA rejoining versus cleavage in the catalytic cycle of this essential enzyme, and further establishes the potential for selective interference of DNA rejoining by this validated TB drug target.
Collapse
Affiliation(s)
- Nan Cao
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8 St, Miami, FL 33199, USA.,Biomolecular Sciences Institute, Florida International University, 11200 SW 8 St, Miami, FL 33199, USA
| | - Kemin Tan
- Structural Biology Center, Biosciences, Argonne National Laboratory, 9700 S. Cass Avenue, Argonne, IL 60439, USA
| | - Thirunavukkarasu Annamalai
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8 St, Miami, FL 33199, USA.,Biomolecular Sciences Institute, Florida International University, 11200 SW 8 St, Miami, FL 33199, USA
| | - Andrzej Joachimiak
- Structural Biology Center, Biosciences, Argonne National Laboratory, 9700 S. Cass Avenue, Argonne, IL 60439, USA
| | - Yuk-Ching Tse-Dinh
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8 St, Miami, FL 33199, USA.,Biomolecular Sciences Institute, Florida International University, 11200 SW 8 St, Miami, FL 33199, USA
| |
Collapse
|
15
|
PPEF: A bisbenzimdazole potent antimicrobial agent interacts at acidic triad of catalytic domain of E. coli topoisomerase IA. Biochim Biophys Acta Gen Subj 2019; 1863:1524-1535. [PMID: 31145964 DOI: 10.1016/j.bbagen.2019.05.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 05/20/2019] [Accepted: 05/23/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND Topoisomerase is a well known target to develop effective antibacterial agents. In pursuance of searching novel antibacterial agents, we have established a novel bisbenzimidazole (PPEF) as potent E. coli topoisomerase IA poison inhibitor. METHODS In order to gain insights into the mechanism of action of PPEF and understanding protein-ligand interactions, we have produced wild type EcTopo 67 N-terminal domain (catalytic domain) and its six mutant proteins at acidic triad (D111, D113, E115). The DDE motif is replaced by alanine (A) to create three single mutants: D111A, D113A, E115A and three double mutants: D111A-D113A, D113A-E115A and D111A-E115A. RESULTS Calorimetric study of PPEF with single mutants showed 10 fold lower affinity than that of wild type EcTopo 67 (7.32 × 106 M-1for wild type, 0.89 × 106 M-1for D111A) and 100 fold lower binding with double mutant D113A-E115A (0.02 × 106 M-1) was observed. The mutated proteins showed different CD signature as compared to wild type protein. CD and fluorescence titrations were done to study the interaction between EcTopo 67 and ligands. Molecular docking study validated that PPEF has decreased binding affinity towards mutated enzymes as compared to wild type. CONCLUSION The overall study reveals that PPEF binds to D113 and E115 of acidic triad of EcTopo 67. Point mutations decrease binding affinity of PPEF towards DDE motif of topoisomerase. GENERAL SIGNIFICANCE This study concludes PPEF as poison inhibitor of E. coli Topoisomerase IA, which binds to acidic triad of topoisomerase IA, responsible for its function. PPEF can be considered as therapeutic agent against bacteria.
Collapse
|
16
|
Jeanne Dit Fouque K, Garabedian A, Leng F, Tse-Dinh YC, Fernandez-Lima F. Microheterogeneity of Topoisomerase IA/IB and Their DNA-Bound States. ACS OMEGA 2019; 4:3619-3626. [PMID: 30842985 PMCID: PMC6396120 DOI: 10.1021/acsomega.8b02887] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Accepted: 01/11/2019] [Indexed: 05/14/2023]
Abstract
Topoisomerases are important complex enzymes that modulate DNA topology to maintain chromosome superstructure and integrity. These enzymes are involved in many cellular processes that resolve specific DNA superstructures and intermediates. The low abundance combined with the biological heterogeneity of relevant intermediates of topoisomerases makes their structural information not readily accessible using traditional structural biology tools (e.g., NMR and X-ray crystallography). In the present work, a second-generation trapped ion mobility spectrometry-mass spectrometry (TIMS-MS) was used to study Escherichia coli topoisomerase IA (EcTopIA) and variola virus topoisomerase IB (vTopIB) as well as their complexes with a single-stranded DNA and a stem-loop DNA under native conditions. The higher trapping efficiency and extended mass range of the new, convex TIMS geometry allowed for the separation and identification of multiple conformational states for the two topoisomerases and their DNA complexes. Inspection of the conformational space of EcTopIA and vTopIB in complex with DNA showed that upon DNA binding, the number of conformational states is significantly reduced, suggesting that the DNA binding selects for a narrow range of conformers restricted by the interaction with the DNA substrate. The large microheterogeneity observed for the two DNA binding proteins suggests that they can have multiple biological functions. This work highlights the potential of TIMS-MS for the structural investigations of intrinsically disordered proteins (e.g., DNA binding proteins) as a way to gain a better understanding of the mechanisms involved in DNA substrate recognition, binding, and assembly of the catalytically active enzyme-DNA complex.
Collapse
Affiliation(s)
- Kevin Jeanne Dit Fouque
- Department
of Chemistry and Biochemistry and Biomolecular Sciences Institute,Florida International University, 11200 SW 8th St., AHC4-233, Miami, Florida 33199, United States
| | - Alyssa Garabedian
- Department
of Chemistry and Biochemistry and Biomolecular Sciences Institute,Florida International University, 11200 SW 8th St., AHC4-233, Miami, Florida 33199, United States
| | - Fenfei Leng
- Department
of Chemistry and Biochemistry and Biomolecular Sciences Institute,Florida International University, 11200 SW 8th St., AHC4-233, Miami, Florida 33199, United States
| | - Yuk-Ching Tse-Dinh
- Department
of Chemistry and Biochemistry and Biomolecular Sciences Institute,Florida International University, 11200 SW 8th St., AHC4-233, Miami, Florida 33199, United States
| | - Francisco Fernandez-Lima
- Department
of Chemistry and Biochemistry and Biomolecular Sciences Institute,Florida International University, 11200 SW 8th St., AHC4-233, Miami, Florida 33199, United States
| |
Collapse
|
17
|
Abstract
Bacterial Topoisomerase I is a potential target for the identification of novel topoisomerase poison inhibitors that could provide leads for a new class of antibacterial compounds. Here we describe in detail a fluorescence-based cleavage assay that is successfully used in HTS for the discovery of bacterial topoisomerase Ι poisons.
Collapse
|
18
|
Evidence for Inhibition of Topoisomerase 1A by Gold(III) Macrocycles and Chelates Targeting Mycobacterium tuberculosis and Mycobacterium abscessus. Antimicrob Agents Chemother 2018; 62:AAC.01696-17. [PMID: 29483110 DOI: 10.1128/aac.01696-17] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 02/08/2018] [Indexed: 01/15/2023] Open
Abstract
Mycobacterium tuberculosis and the fast-growing species Mycobacterium abscessus are two important human pathogens causing persistent pulmonary infections that are difficult to cure and require long treatment times. The emergence of drug-resistant M. tuberculosis strains and the high level of intrinsic resistance of M. abscessus call for novel drug scaffolds that effectively target both pathogens. In this study, we evaluated the activity of bis(pyrrolide-imine) gold(III) macrocycles and chelates, originally designed as DNA intercalators capable of targeting human topoisomerase types I and II (Topo1 and Topo2), against M. abscessus and M. tuberculosis We identified a total of 5 noncytotoxic compounds active against both mycobacterial pathogens under replicating in vitro conditions. We chose one of these hits, compound 14, for detailed analysis due to its potent bactericidal mode of inhibition and scalable synthesis. The clinical relevance of this compound was demonstrated by its ability to inhibit a panel of diverse M. tuberculosis and M. abscessus clinical isolates. Prompted by previous data suggesting that compound 14 may target topoisomerase/gyrase enzymes, we demonstrated that it lacked cross-resistance with fluoroquinolones, which target the M. tuberculosis gyrase. In vitro enzyme assays confirmed the potent activity of compound 14 against bacterial topoisomerase 1A (Topo1) enzymes but not gyrase. Novel scaffolds like compound 14 with potent, selective bactericidal activity against M. tuberculosis and M. abscessus that act on validated but underexploited targets like Topo1 represent a promising starting point for the development of novel therapeutics for infections by pathogenic mycobacteria.
Collapse
|
19
|
Zhou Q, Zhou YN, Jin DJ, Tse-Dinh YC. Deacetylation of topoisomerase I is an important physiological function of E. coli CobB. Nucleic Acids Res 2017; 45:5349-5358. [PMID: 28398568 PMCID: PMC5605244 DOI: 10.1093/nar/gkx250] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 04/03/2017] [Indexed: 01/08/2023] Open
Abstract
Escherichia coli topoisomerase I (TopA), a regulator of global and local DNA supercoiling, is modified by Nε-Lysine acetylation. The NAD+-dependent protein deacetylase CobB can reverse both enzymatic and non-enzymatic lysine acetylation modification in E. coli. Here, we show that the absence of CobB in a ΔcobB mutant reduces intracellular TopA catalytic activity and increases negative DNA supercoiling. TopA expression level is elevated as topA transcription responds to the increased negative supercoiling. The slow growth phenotype of the ΔcobB mutant can be partially compensated by further increase of intracellular TopA level via overexpression of recombinant TopA. The relaxation activity of purified TopA is decreased by in vitro non-enzymatic acetyl phosphate mediated lysine acetylation, and the presence of purified CobB protects TopA from inactivation by such non-enzymatic acetylation. The specific activity of TopA expressed from His-tagged fusion construct in the chromosome is inversely proportional to the degree of in vivo lysine acetylation during growth transition and growth arrest. These findings demonstrate that E. coli TopA catalytic activity can be modulated by lysine acetylation–deacetylation, and prevention of TopA inactivation from excess lysine acetylation and consequent increase in negative DNA supercoiling is an important physiological function of the CobB protein deacetylase.
Collapse
Affiliation(s)
- Qingxuan Zhou
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA.,Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
| | - Yan Ning Zhou
- Transcription Control Section, RNA Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Ding Jun Jin
- Transcription Control Section, RNA Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Yuk-Ching Tse-Dinh
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA.,Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
| |
Collapse
|
20
|
Synthesizing topological structures containing RNA. Nat Commun 2017; 8:14936. [PMID: 28361879 PMCID: PMC5381007 DOI: 10.1038/ncomms14936] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 02/15/2017] [Indexed: 12/27/2022] Open
Abstract
Though knotting and entanglement have been observed in DNA and proteins, their existence in RNA remains an enigma. Synthetic RNA topological structures are significant for understanding the physical and biological properties pertaining to RNA topology, and these properties in turn could facilitate identifying naturally occurring topologically nontrivial RNA molecules. Here we show that topological structures containing single-stranded RNA (ssRNA) free of strong base pairing interactions can be created either by configuring RNA-DNA hybrid four-way junctions or by template-directed synthesis with a single-stranded DNA (ssDNA) topological structure. By using a constructed ssRNA knot as a highly sensitive topological probe, we find that Escherichia coli DNA topoisomerase I has low RNA topoisomerase activity and that the R173A point mutation abolishes the unknotting activity for ssRNA, but not for ssDNA. Furthermore, we discover the topological inhibition of reverse transcription (RT) and obtain different RT-PCR patterns for an ssRNA knot and circle of the same sequence.
Collapse
|
21
|
Yu X, Zhang M, Annamalai T, Bansod P, Narula G, Tse-Dinh YC, Sun D. Synthesis, evaluation, and CoMFA study of fluoroquinophenoxazine derivatives as bacterial topoisomerase IA inhibitors. Eur J Med Chem 2016; 125:515-527. [PMID: 27689733 DOI: 10.1016/j.ejmech.2016.09.053] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Revised: 09/16/2016] [Accepted: 09/17/2016] [Indexed: 10/21/2022]
Abstract
New antibacterial agents with novel target and mechanism of action are urgently needed to combat problematic bacterial infections and mounting antibiotic resistances. Topoisomerase IA represents an attractive and underexplored antibacterial target, as such, there is a growing interest in developing selective and potent topoisomerase I inhibitors for antibacterial therapy. Based on our initial biological screening, fluoroquinophenoxazine 1 was discovered as a low micromolar inhibitor against E. coli topoisomerase IA. In the literature, fluoroquinophenoxazine analogs have been investigated as antibacterial and anticancer agents, however, their topoisomerase I inhibition was relatively underexplored and there is little structure-activity relationship (SAR) available. The good topoisomerase I inhibitory activity of 1 and the lack of SAR prompted us to design and synthesize a series of fluoroquinophenoxazine analogs to systematically evaluate the SAR and to probe the structural elements of the fluoroquinophenoxazine core toward topoisomerase I enzyme target recognition. In this study, a series of fluoroquinophenoxazine analogs was designed, synthesized, and evaluated as topoisomerase I inhibitors and antibacterial agents. Target-based assays revealed that the fluoroquinophenoxazine derivatives with 9-NH2 and/or 6-substituted amine functionalities generally exhibited good to excellent inhibitory activities against topoisomerase I with IC50s ranging from 0.24 to 3.9 μM. Notably, 11a bearing the 6-methylpiperazinyl and 9-amino motifs was identified as one of the most potent topoisomerase I inhibitors (IC50 = 0.48 μM), and showed broad spectrum antibacterial activity (MICs = 0.78-7.6 μM) against all the bacteria strains tested. Compound 11g with the 6-bipiperidinyl lipophilic side chain exhibited the most potent antituberculosis activity (MIC = 2.5 μM, SI = 9.8). In addition, CoMFA analysis was performed to investigate the 3D-QSAR of this class of fluoroquinophenoxazine derivatives. The constructed CoMFA model produced reasonable statistics (q2 = 0.688 and r2 = 0.806). The predictive power of the developed model was obtained using a test set of 7 compounds, giving a predictive correlation coefficient r2pred of 0.767. Collectively, these promising data demonstrated that fluoroquinophenoxazine derivatives have the potential to be developed as a new chemotype of potent topoisomerase IA inhibitors with antibacterial therapeutic potential.
Collapse
Affiliation(s)
- Xufen Yu
- Department of Pharmaceutical Sciences, The Daniel K. Inouye College of Pharmacy, University of Hawaii at Hilo, 34 Rainbow Drive, Hilo, HI 96720, USA
| | - Mingming Zhang
- Department of Pharmaceutical Sciences, The Daniel K. Inouye College of Pharmacy, University of Hawaii at Hilo, 34 Rainbow Drive, Hilo, HI 96720, USA
| | | | - Priyanka Bansod
- Department of Chemistry & Biochemistry, Florida International University, Miami, FL 33199, USA
| | - Gagandeep Narula
- Department of Chemistry & Biochemistry, Florida International University, Miami, FL 33199, USA
| | - Yuk-Ching Tse-Dinh
- Department of Chemistry & Biochemistry, Florida International University, Miami, FL 33199, USA; Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
| | - Dianqing Sun
- Department of Pharmaceutical Sciences, The Daniel K. Inouye College of Pharmacy, University of Hawaii at Hilo, 34 Rainbow Drive, Hilo, HI 96720, USA.
| |
Collapse
|
22
|
Small-Molecule Inhibitors Targeting Topoisomerase I as Novel Antituberculosis Agents. Antimicrob Agents Chemother 2016; 60:4028-36. [PMID: 27114277 DOI: 10.1128/aac.00288-16] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 04/15/2016] [Indexed: 01/30/2023] Open
Abstract
Bacterial topoisomerase functions are required for regulation of DNA supercoiling and overcoming the DNA topological barriers that are encountered during many vital cellular processes. DNA gyrase and topoisomerase IV of the type IIA bacterial topoisomerase family are important clinical targets for antibacterial therapy. Topoisomerase I, belonging to the type IA topoisomerase family, has recently been validated as a potential antitubercular target. The topoisomerase I activity has been shown to be essential for bacterial viability and infection in a murine model of tuberculosis. Mixture-based combinatorial libraries were screened in this study to identify novel bacterial topoisomerase I inhibitors. Using positional-scanning deconvolution, selective small-molecule inhibitors of bacterial topoisomerase I were identified starting from a polyamine scaffold. Antibacterial assays demonstrated that four of these small-molecule inhibitors of bacterial topoisomerase I are bactericidal against Mycobacterium smegmatis and Mycobacterium tuberculosis The MICs for growth inhibition of M. smegmatis increased with overexpression of recombinant M. tuberculosis topoisomerase I, consistent with inhibition of intracellular topoisomerase I activity being involved in the antimycobacterial mode of action.
Collapse
|
23
|
Ahmad M, Xue Y, Lee SK, Martindale JL, Shen W, Li W, Zou S, Ciaramella M, Debat H, Nadal M, Leng F, Zhang H, Wang Q, Siaw GEL, Niu H, Pommier Y, Gorospe M, Hsieh TS, Tse-Dinh YC, Xu D, Wang W. RNA topoisomerase is prevalent in all domains of life and associates with polyribosomes in animals. Nucleic Acids Res 2016; 44:6335-49. [PMID: 27257063 PMCID: PMC4994864 DOI: 10.1093/nar/gkw508] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 05/25/2016] [Indexed: 12/14/2022] Open
Abstract
DNA Topoisomerases are essential to resolve topological problems during DNA metabolism in all species. However, the prevalence and function of RNA topoisomerases remain uncertain. Here, we show that RNA topoisomerase activity is prevalent in Type IA topoisomerases from bacteria, archaea, and eukarya. Moreover, this activity always requires the conserved Type IA core domains and the same catalytic residue used in DNA topoisomerase reaction; however, it does not absolutely require the non-conserved carboxyl-terminal domain (CTD), which is necessary for relaxation reactions of supercoiled DNA. The RNA topoisomerase activity of human Top3β differs from that of Escherichia coli topoisomerase I in that the former but not the latter requires the CTD, indicating that topoisomerases have developed distinct mechanisms during evolution to catalyze RNA topoisomerase reactions. Notably, Top3β proteins from several animals associate with polyribosomes, which are units of mRNA translation, whereas the Top3 homologs from E. coli and yeast lack the association. The Top3β-polyribosome association requires TDRD3, which directly interacts with Top3β and is present in animals but not bacteria or yeast. We propose that RNA topoisomerases arose in the early RNA world, and that they are retained through all domains of DNA-based life, where they mediate mRNA translation as part of polyribosomes in animals.
Collapse
Affiliation(s)
- Muzammil Ahmad
- Genome Instability and Chromatin Remodeling Section, Lab of Genetics, National Institute on Aging, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD 21224, USA
| | - Yutong Xue
- Genome Instability and Chromatin Remodeling Section, Lab of Genetics, National Institute on Aging, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD 21224, USA
| | - Seung Kyu Lee
- Genome Instability and Chromatin Remodeling Section, Lab of Genetics, National Institute on Aging, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD 21224, USA
| | - Jennifer L Martindale
- RNA Regulation Section, Lab of Genetics, National Institute on Aging, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD 21224, USA
| | - Weiping Shen
- Genome Instability and Chromatin Remodeling Section, Lab of Genetics, National Institute on Aging, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD 21224, USA
| | - Wen Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, PeKing University, Beijing 1000871, China
| | - Sige Zou
- Translational Gerontology Branch, National Institute on Aging, National Institute of Health, 251 Bayview Boulevard, Baltimore, MD 21224, USA
| | - Maria Ciaramella
- Institute of Biosciences and Bioresources, National Research Council of Italy, Naples 80131, Italy
| | - Hélène Debat
- Institut Jacques Monod, CNRS-Université Paris Diderot-UMR7592, 15 rue Hélène Brion, 75205 Paris Cedex, France
| | - Marc Nadal
- Institut Jacques Monod, CNRS-Université Paris Diderot-UMR7592, 15 rue Hélène Brion, 75205 Paris Cedex, France
| | - Fenfei Leng
- Department of Chemistry & Biochemistry, Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
| | - Hongliang Zhang
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Quan Wang
- Molecular and Cellular Biochemistry Department, Indiana University, 212 South Hawthorne Drive, Bloomington, IN 47405, USA
| | - Grace Ee-Lu Siaw
- Institute of Cellular Organistic Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Hengyao Niu
- Molecular and Cellular Biochemistry Department, Indiana University, 212 South Hawthorne Drive, Bloomington, IN 47405, USA
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Myriam Gorospe
- RNA Regulation Section, Lab of Genetics, National Institute on Aging, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD 21224, USA
| | - Tao-Shih Hsieh
- Institute of Cellular Organistic Biology, Academia Sinica, Taipei 11529, Taiwan Department of Biochemistry, Duke University Medical Center, Durham, NC 73532, USA
| | - Yuk-Ching Tse-Dinh
- Department of Chemistry & Biochemistry, Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
| | - Dongyi Xu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, PeKing University, Beijing 1000871, China
| | - Weidong Wang
- Genome Instability and Chromatin Remodeling Section, Lab of Genetics, National Institute on Aging, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD 21224, USA
| |
Collapse
|
24
|
Targeting bacterial topoisomerase I to meet the challenge of finding new antibiotics. Future Med Chem 2016; 7:459-71. [PMID: 25875873 DOI: 10.4155/fmc.14.157] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Resistance of bacterial pathogens to current antibiotics has grown to be an urgent crisis. Approaches to overcome this challenge include identification of novel targets for discovery of new antibiotics. Bacterial topoisomerase I is present in all bacterial pathogens as a potential target for bactericidal topoisomerase poison inhibitors. Recent efforts have identified inhibitors of bacterial topoisomerase I with antibacterial activity. Additional research on the mode of action and binding site of these inhibitors would provide further validation of the target and establish that bacterial topoisomerase I is druggable. Bacterial topoisomerase I is a potentially high value target for discovery of new antibiotics. Demonstration of topoisomerase I as the cellular target of an antibacterial compound would provide proof-of-concept validation.
Collapse
|
25
|
Hanaoka K, Shoji M, Kondo D, Sato A, Yang MY, Kamiya K, Shiraishi K. Substrate-mediated proton relay mechanism for the religation reaction in topoisomerase II. J Biomol Struct Dyn 2013; 32:1759-65. [PMID: 24047515 DOI: 10.1080/07391102.2013.834848] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The DNA religation reaction of yeast type II topoisomerase (topo II) was investigated to elucidate its metal-dependent general acid/base catalysis. Quantum mechanical/molecular mechanical calculations were performed for the topo II religation reaction, and the proton transfer pathway was examined. We found a substrate-mediated proton transfer of the topo II religation reaction, which involves the 3' OH nucleophile, the reactive phosphate, water, Arg781, and Tyr782. Metal A stabilizes the transition states, which is consistent with a two-metal mechanism in topo II. This pathway may be required for the cleavage/religation reaction of topo IA and II and will provide a general explanation for the catalytic mechanism in the topo IA and II.
Collapse
Affiliation(s)
- Kyohei Hanaoka
- a Graduate School of Pure and Applied Sciences, University of Tsukuba , Tennodai 1-1-1, Tsukuba , 305-8571 , Japan
| | | | | | | | | | | | | |
Collapse
|
26
|
Cheng B, Cao S, Vasquez V, Annamalai T, Tamayo-Castillo G, Clardy J, Tse-Dinh YC. Identification of anziaic acid, a lichen depside from Hypotrachyna sp., as a new topoisomerase poison inhibitor. PLoS One 2013; 8:e60770. [PMID: 23593306 PMCID: PMC3620467 DOI: 10.1371/journal.pone.0060770] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Accepted: 03/02/2013] [Indexed: 11/18/2022] Open
Abstract
Topoisomerase inhibitors are effective for antibacterial and anticancer therapy because they can lead to the accumulation of the intermediate DNA cleavage complex formed by the topoisomerase enzymes, which trigger cell death. Here we report the application of a novel enzyme-based high-throughput screening assay to identify natural product extracts that can lead to increased accumulation of the DNA cleavage complex formed by recombinant Yersinia pestis topoisomerase I as part of a larger effort to identify new antibacterial compounds. Further characterization and fractionation of the screening positives from the primary assay led to the discovery of a depside, anziaic acid, from the lichen Hypotrachyna sp. as an inhibitor for both Y. pestis and Escherichia coli topoisomerase I. In in vitro assays, anziaic acid exhibits antibacterial activity against Bacillus subtilis and a membrane permeable strain of E. coli. Anziaic acid was also found to act as an inhibitor of human topoisomerase II but had little effect on human topoisomerase I. This is the first report of a depside with activity as a topoisomerase poison inhibitor and demonstrates the potential of this class of natural products as a source for new antibacterial and anticancer compounds.
Collapse
Affiliation(s)
- Bokun Cheng
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, New York, United States of America
| | - Shugeng Cao
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Victor Vasquez
- Unidad Estrategica de Bioprospeccion, Instituto Nacional de Biodiversidad (INBio) and Escuela de Química, Universidad de Costa Rica, San José, Costa Rica
| | - Thirunavukkarasu Annamalai
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, New York, United States of America
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, United States of America
| | - Giselle Tamayo-Castillo
- Unidad Estrategica de Bioprospeccion, Instituto Nacional de Biodiversidad (INBio) and Escuela de Química, Universidad de Costa Rica, San José, Costa Rica
| | - Jon Clardy
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Yuk-Ching Tse-Dinh
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, New York, United States of America
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, United States of America
- * E-mail:
| |
Collapse
|
27
|
Godbole AA, Leelaram MN, Bhat AG, Jain P, Nagaraja V. Characterization of DNA topoisomerase I from Mycobacterium tuberculosis: DNA cleavage and religation properties and inhibition of its activity. Arch Biochem Biophys 2012; 528:197-203. [DOI: 10.1016/j.abb.2012.10.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Revised: 10/02/2012] [Accepted: 10/09/2012] [Indexed: 11/30/2022]
|
28
|
Narula G, Tse-Dinh YC. Residues of E. coli topoisomerase I conserved for interaction with a specific cytosine base to facilitate DNA cleavage. Nucleic Acids Res 2012; 40:9233-43. [PMID: 22833607 PMCID: PMC3467081 DOI: 10.1093/nar/gks688] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Bacterial and archaeal topoisomerase I display selectivity for a cytosine base 4 nt upstream from the DNA cleavage site. Recently, the solved crystal structure of Escherichia coli topoisomerase I covalently linked to a single-stranded oligonucleotide revealed that R169 and R173 interact with the cytosine base at the −4 position via hydrogen bonds while the phenol ring of Y177 wedges between the bases at the −4 and the −5 position. Substituting R169 to alanine changed the selectivity of the enzyme for the base at the −4 position from a cytosine to an adenine. The R173A mutant displayed similar sequence selectivity as the wild-type enzyme, but weaker cleavage and relaxation activity. Mutation of Y177 to serine or alanine rendered the enzyme inactive. Although mutation of each of these residues led to different outcomes, R169, R173 and Y177 work together to interact with a cytosine base at the −4 position to facilitate DNA cleavage. These strictly conserved residues might act after initial substrate binding as a Molecular Ruler to form a protein–DNA complex with the scissile phosphate positioned at the active site for optimal DNA cleavage by the tyrosine hydroxyl nucleophile to facilitate DNA cleavage in the reaction pathway.
Collapse
Affiliation(s)
- Gagandeep Narula
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA
| | | |
Collapse
|