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Duplex DNA and BLM regulate gate opening by the human TopoIIIα-RMI1-RMI2 complex. Nat Commun 2022; 13:584. [PMID: 35102151 PMCID: PMC8803869 DOI: 10.1038/s41467-022-28082-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 01/10/2022] [Indexed: 12/31/2022] Open
Abstract
Topoisomerase IIIα is a type 1A topoisomerase that forms a complex with RMI1 and RMI2 called TRR in human cells. TRR plays an essential role in resolving DNA replication and recombination intermediates, often alongside the helicase BLM. While the TRR catalytic cycle is known to involve a protein-mediated single-stranded (ss)DNA gate, the detailed mechanism is not fully understood. Here, we probe the catalytic steps of TRR using optical tweezers and fluorescence microscopy. We demonstrate that TRR forms an open gate in ssDNA of 8.5 ± 3.8 nm, and directly visualize binding of a second ssDNA or double-stranded (ds)DNA molecule to the open TRR-ssDNA gate, followed by catenation in each case. Strikingly, dsDNA binding increases the gate size (by ~16%), while BLM alters the mechanical flexibility of the gate. These findings reveal an unexpected plasticity of the TRR-ssDNA gate size and suggest that TRR-mediated transfer of dsDNA may be more relevant in vivo than previously believed. Here the authors probe the cleavage and gate opening of single-stranded DNA by the human topoisomerase TRR using a unique single-molecule strategy to reveal structural plasticity in response to both double-stranded DNA and the helicase BLM.
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2
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Czescik J, Zamolo S, Darbre T, Rigo. R, Sissi C, Pecina A, Riccardi L, De Vivo M, Mancin F, Scrimin P. A Gold Nanoparticle Nanonuclease Relying on a Zn(II) Mononuclear Complex. Angew Chem Int Ed Engl 2021; 60:1423-1432. [PMID: 32985766 PMCID: PMC7839518 DOI: 10.1002/anie.202012513] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Indexed: 12/18/2022]
Abstract
Similarly to enzymes, functionalized gold nanoparticles efficiently catalyze chemical reactions, hence the term nanozymes. Herein, we present our results showing how surface-passivated gold nanoparticles behave as synthetic nanonucleases, able to cleave pBR322 plasmid DNA with the highest efficiency reported so far for catalysts based on a single metal ion mechanism. Experimental and computational data indicate that we have been successful in creating a catalytic site precisely mimicking that suggested for natural metallonucleases relying on a single metal ion for their activity. It comprises one Zn(II) ion to which a phosphate diester of DNA is coordinated. Importantly, as in nucleic acids-processing enzymes, a positively charged arginine plays a key role by assisting with transition state stabilization and by reducing the pKa of the nucleophilic alcohol of a serine. Our results also show how designing a catalyst for a model substrate (bis-p-nitrophenylphosphate) may provide wrong indications as for its efficiency when it is tested against the real target (plasmid DNA).
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Affiliation(s)
- Joanna Czescik
- Department of Chemical SciencesUniversity of Padovavia Marzolo, 135131PadovaItaly
- Current address: School of Life and Health SciencesAston UniversityB4 7ETBirminghamUK
| | - Susanna Zamolo
- Department of Chemistry and BiochemistryUniversity of BernFreiestrasse 3CH-3012BernSwitzerland
| | - Tamis Darbre
- Department of Chemistry and BiochemistryUniversity of BernFreiestrasse 3CH-3012BernSwitzerland
| | - Riccardo Rigo.
- Department of Pharmaceutical and Pharmacological SciencesUniversity of Padovavia Marzolo 535131PadovaItaly
| | - Claudia Sissi
- Department of Pharmaceutical and Pharmacological SciencesUniversity of Padovavia Marzolo 535131PadovaItaly
| | - Adam Pecina
- Laboratory of Molecular Modeling & Drug DiscoveryIstituto Italiano di Tecnologia (IIT)Via Morego 3016163GenovaItaly
| | - Laura Riccardi
- Laboratory of Molecular Modeling & Drug DiscoveryIstituto Italiano di Tecnologia (IIT)Via Morego 3016163GenovaItaly
| | - Marco De Vivo
- Laboratory of Molecular Modeling & Drug DiscoveryIstituto Italiano di Tecnologia (IIT)Via Morego 3016163GenovaItaly
| | - Fabrizio Mancin
- Department of Chemical SciencesUniversity of Padovavia Marzolo, 135131PadovaItaly
| | - Paolo Scrimin
- Department of Chemical SciencesUniversity of Padovavia Marzolo, 135131PadovaItaly
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3
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Czescik J, Zamolo S, Darbre T, Rigo. R, Sissi C, Pecina A, Riccardi L, De Vivo M, Mancin F, Scrimin P. A Gold Nanoparticle Nanonuclease Relying on a Zn(II) Mononuclear Complex. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202012513] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Joanna Czescik
- Department of Chemical Sciences University of Padova via Marzolo, 1 35131 Padova Italy
- Current address: School of Life and Health Sciences Aston University B4 7ET Birmingham UK
| | - Susanna Zamolo
- Department of Chemistry and Biochemistry University of Bern Freiestrasse 3 CH-3012 Bern Switzerland
| | - Tamis Darbre
- Department of Chemistry and Biochemistry University of Bern Freiestrasse 3 CH-3012 Bern Switzerland
| | - Riccardo Rigo.
- Department of Pharmaceutical and Pharmacological Sciences University of Padova via Marzolo 5 35131 Padova Italy
| | - Claudia Sissi
- Department of Pharmaceutical and Pharmacological Sciences University of Padova via Marzolo 5 35131 Padova Italy
| | - Adam Pecina
- Laboratory of Molecular Modeling & Drug Discovery Istituto Italiano di Tecnologia (IIT) Via Morego 30 16163 Genova Italy
| | - Laura Riccardi
- Laboratory of Molecular Modeling & Drug Discovery Istituto Italiano di Tecnologia (IIT) Via Morego 30 16163 Genova Italy
| | - Marco De Vivo
- Laboratory of Molecular Modeling & Drug Discovery Istituto Italiano di Tecnologia (IIT) Via Morego 30 16163 Genova Italy
| | - Fabrizio Mancin
- Department of Chemical Sciences University of Padova via Marzolo, 1 35131 Padova Italy
| | - Paolo Scrimin
- Department of Chemical Sciences University of Padova via Marzolo, 1 35131 Padova Italy
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4
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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.
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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.
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5
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Synthesis, molecular docking, antimicrobial evaluation, and DNA cleavage assay of new thiadiazole/oxadiazole ciprofloxacin derivatives. MONATSHEFTE FUR CHEMIE 2019. [DOI: 10.1007/s00706-019-02478-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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6
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Mohammed HH, Abuo-Rahma GEDA, Abbas SH, Abdelhafez ESM. Current Trends and Future Directions of Fluoroquinolones. Curr Med Chem 2019; 26:3132-3149. [DOI: 10.2174/0929867325666180214122944] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Revised: 10/16/2017] [Accepted: 02/08/2018] [Indexed: 12/12/2022]
Abstract
Fluoroquinolones represent an interesting synthetic class of antimicrobial agents with broad spectrum and potent activity. Since the discovery of nalidixic acid, the prototype of quinolones, several structural modifications to the quinolone nucleus have been carried out for improvement of potency, spectrum of activity, and to understand their structure activity relationship (SAR). The C-7 substituent was reported to have a major impact on the activity. Accordingly, Substitution at C-7 or its N-4-piperazinyl moiety was found to affect potency, bioavailability, and physicochemical properties. Also, it can increase the affinity towards mammalian topoisomerases that may shift quinolones from antibacterial to anticancer candidates. Moreover, the presence of DNA topoisomerases in both eukaryotic and prokaryotic cells makes them excellent targets for chemotherapeutic intervention in antibacterial and anticancer therapies. Based on this concept, several fluoroquionolones derivatives have been synthesized and biologically evaluated as antibacterial, antituberculosis, antiproliferative, antiviral and antifungal agents. This review is an attempt to focus on the therapeutic prospects of fluoroquinolones with an updated account on their atypical applications such as antitubercular and anticancer activities.
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Affiliation(s)
- Hamada H.H. Mohammed
- Department of Medicinal Chemistry, Faculty of Pharmacy, Minia University, Minia 61519, Egypt
| | | | - Samar H. Abbas
- Department of Medicinal Chemistry, Faculty of Pharmacy, Minia University, Minia 61519, Egypt
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7
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Bardell-Cox OA, White AJP, Aragón L, Fuchter MJ. Synthetic studies on the reverse antibiotic natural products, the nybomycins. MEDCHEMCOMM 2019; 10:1438-1444. [PMID: 31534658 PMCID: PMC6748283 DOI: 10.1039/c9md00207c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Accepted: 05/22/2019] [Indexed: 11/21/2022]
Abstract
Antimicrobial resistance (AMR) is a serious issue that could have severe consequences if steps are not taken. The nybomycin natural products have the potential to extend the clinical efficacy of the marketed fluoroquinolone class of antibiotics through a 'reverse antibiotic' approach. However, only very limited structure-activity relationships are known for these fascinating compounds, in part due to challenges with their synthesis. Here we report a new scalable and robust synthetic route to the nybomycin natural products to aid in the development of this series. Through this synthesis, we report the antibiotic activity of novel analogues of this family confirming the selectivity for fluoroquinolone resistant bacteria and potential future opportunities for further optimisation.
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Affiliation(s)
- Oliver A Bardell-Cox
- Department of Chemistry , Imperial College London , Molecular Sciences Research Hub , White City Campus, Wood Lane , London , W12 OBZ , UK .
- Cell Cycle Group , MRC London Institute of Medical Sciences , Du Cane Road , London W12 0NN , UK .
| | - Andrew J P White
- Department of Chemistry , Imperial College London , Molecular Sciences Research Hub , White City Campus, Wood Lane , London , W12 OBZ , UK .
| | - Luis Aragón
- Cell Cycle Group , MRC London Institute of Medical Sciences , Du Cane Road , London W12 0NN , UK .
| | - Matthew J Fuchter
- Department of Chemistry , Imperial College London , Molecular Sciences Research Hub , White City Campus, Wood Lane , London , W12 OBZ , UK .
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8
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Mohammed HH, Abdelhafez ESM, Abbas SH, Moustafa GA, Hauk G, Berger JM, Mitarai S, Arai M, Abd El-Baky RM, Abuo-Rahma GEDA. Design, synthesis and molecular docking of new N-4-piperazinyl ciprofloxacin-triazole hybrids with potential antimicrobial activity. Bioorg Chem 2019; 88:102952. [DOI: 10.1016/j.bioorg.2019.102952] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Revised: 04/20/2019] [Accepted: 04/24/2019] [Indexed: 12/20/2022]
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9
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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.
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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
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10
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Wu B, Siglreitmeier M, Debus C, Schwahn D, Cölfen H, Pipich V. Ionic Dependence of Gelatin Hydrogel Architecture Explored Using Small and Very Small Angle Neutron Scattering Technique. Macromol Biosci 2018; 18:e1800018. [PMID: 29736987 DOI: 10.1002/mabi.201800018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 03/14/2018] [Indexed: 11/11/2022]
Abstract
The hierarchical structure of gelatin hydrogels mimics a natural extracellular matrix and provides an optimized microenvironment for the growth of 3D structured tissue analogs. In the presence of metal ions, gelatin hydrogels exhibit various mechanical properties that are correlated with the molecular interactions and the hierarchical structure. The structure and structural response of gelatin hydrogels to variation of gelatin concentration, pH, or addition of metal ions are explored by small and very small angle neutron scattering over broad length scales. The measurements of the hydrogels reveal the existence of a two-level structure of colloid-like large clusters and a 3D cage-like gel network. In the presence of Fe3+ ions the hydrogels show a highly dense and stiff network, while Ca2+ ions have an opposite effect. The results provide important structural insight for improvement of the design of gelatin based hydrogels and are therefore suitable for various applications.
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Affiliation(s)
- Baohu Wu
- Jülich Centre for Neutron Science (JCNS) at Heinz Maier-Leibnitz Zentrum (MLZ), Forschungszentrum Jülich, Lichtenbergstr. 1, 85748, Garching, Germany.,Department of Chemistry, Physical Chemistry, University of Konstanz, Universitaetsstr 10, Konstanz, 78457, Germany
| | - Maria Siglreitmeier
- Department of Chemistry, Physical Chemistry, University of Konstanz, Universitaetsstr 10, Konstanz, 78457, Germany
| | - Christian Debus
- Department of Chemistry, Physical Chemistry, University of Konstanz, Universitaetsstr 10, Konstanz, 78457, Germany
| | - Dietmar Schwahn
- Forschungs-Neutronenquelle Heinz Maier-Leibnitz (FRM II), Technische Universität München, Lichtenbergstr 1, Garching, 85748, Germany
| | - Helmut Cölfen
- Department of Chemistry, Physical Chemistry, University of Konstanz, Universitaetsstr 10, Konstanz, 78457, Germany
| | - Vitaliy Pipich
- Jülich Centre for Neutron Science (JCNS) at Heinz Maier-Leibnitz Zentrum (MLZ), Forschungszentrum Jülich, Lichtenbergstr. 1, 85748, Garching, Germany
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11
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Redgrave LS, Sutton SB, Webber MA, Piddock LJV. Fluoroquinolone resistance: mechanisms, impact on bacteria, and role in evolutionary success. Trends Microbiol 2014; 22:438-45. [PMID: 24842194 DOI: 10.1016/j.tim.2014.04.007] [Citation(s) in RCA: 584] [Impact Index Per Article: 58.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 04/11/2014] [Accepted: 04/16/2014] [Indexed: 12/12/2022]
Abstract
Quinolone and fluoroquinolone antibiotics are potent, broad-spectrum agents commonly used to treat a range of infections. Resistance to these agents is multifactorial and can be via one or a combination of target-site gene mutations, increased production of multidrug-resistance (MDR) efflux pumps, modifying enzymes, and/or target-protection proteins. Fluoroquinolone-resistant clinical isolates of bacteria have emerged readily and recent data have shown that resistance to this class of antibiotics can have diverse, species-dependent impacts on host-strain fitness. Here we outline the impacts of quinolone-resistance mutations in relation to the fitness and evolutionary success of mutant strains.
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Affiliation(s)
- Liam S Redgrave
- School of Immunity and Infection, Institute of Microbiology and Infection, Biosciences Building, University Road West, University of Birmingham, Birmingham B15 2TT, UK
| | - Sam B Sutton
- School of Immunity and Infection, Institute of Microbiology and Infection, Biosciences Building, University Road West, University of Birmingham, Birmingham B15 2TT, UK
| | - Mark A Webber
- School of Immunity and Infection, Institute of Microbiology and Infection, Biosciences Building, University Road West, University of Birmingham, Birmingham B15 2TT, UK
| | - Laura J V Piddock
- School of Immunity and Infection, Institute of Microbiology and Infection, Biosciences Building, University Road West, University of Birmingham, Birmingham B15 2TT, UK.
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Cheng Z, Tan G, Wang W, Su X, Landry AP, Lu J, Ding H. Iron and zinc binding activity of Escherichia coli topoisomerase I homolog YrdD. Biometals 2014; 27:229-36. [PMID: 24469504 DOI: 10.1007/s10534-013-9698-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Accepted: 12/27/2013] [Indexed: 11/26/2022]
Abstract
YrdD, a homolog of the C-terminal zinc-binding region of Escherichia coli topoisomerase I, is highly conserved among proteobacteria and enterobacteria. However, the function of YrdD remains elusive. Here we report that YrdD purified from E. coli cells grown in LB media contains both zinc and iron. Supplement of exogenous zinc in the medium abolishes the iron binding of YrdD in E. coli cells, indicating that iron and zinc may compete for the same metal binding sites in the protein. While the zinc-bound YrdD is able to bind single-stranded (ss) DNA and protect ssDNA from the DNase I digestion in vitro, the iron-bound YrdD has very little or no binding activity for ssDNA, suggesting that the zinc-bound YrdD may have an important role in DNA repair by interacting with ssDNA in cells.
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Affiliation(s)
- Zishuo Cheng
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA, 70803, USA
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