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Glukhov A, Marchenkov V, Dzhus U, Krutilina A, Selikhanov G, Gabdulkhakov A. Bacteriophage T5 dUTPase: Combination of Common Enzymatic and Novel Functions. Int J Mol Sci 2024; 25:892. [PMID: 38255966 PMCID: PMC10815766 DOI: 10.3390/ijms25020892] [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: 11/16/2023] [Revised: 12/26/2023] [Accepted: 01/09/2024] [Indexed: 01/24/2024] Open
Abstract
The main function of dUTPases is to regulate the cellular levels of dUTP and dTTP, thereby playing a crucial role in DNA repair mechanisms. Despite the fact that mutant organisms with obliterated dUTPase enzymatic activity remain viable, it is not possible to completely knock out the dut gene due to the lethal consequences of such a mutation for the organism. As a result, it is considered that this class of enzymes performs an additional function that is essential for the organism's survival. In this study, we provide evidence that the dUTPase of bacteriophage T5 fulfills a supplemental function, in addition to its canonical role. We determined the crystal structure of bacteriophage T5 dUTPase with a resolution of 2.0 Å, and we discovered a distinct short loop consisting of six amino acid residues, representing a unique structural feature specific to the T5-like phages dUTPases. The removal of this element did not affect the overall structure of the homotrimer, but it had significant effects on the development of the phage. Furthermore, it was shown that the enzymatic function and the novel function of the bacteriophage T5 dUTPase are unrelated and independent from each other.
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Affiliation(s)
- Anatoly Glukhov
- Institute of Protein Research RAS, 142290 Pushchino, Russia; (A.G.); (V.M.); (U.D.); (G.S.)
| | - Victor Marchenkov
- Institute of Protein Research RAS, 142290 Pushchino, Russia; (A.G.); (V.M.); (U.D.); (G.S.)
| | - Ulyana Dzhus
- Institute of Protein Research RAS, 142290 Pushchino, Russia; (A.G.); (V.M.); (U.D.); (G.S.)
| | - Antonina Krutilina
- Institute of Protein Research RAS, 142290 Pushchino, Russia; (A.G.); (V.M.); (U.D.); (G.S.)
| | - Georgii Selikhanov
- Institute of Protein Research RAS, 142290 Pushchino, Russia; (A.G.); (V.M.); (U.D.); (G.S.)
- International Institute “Solution Chemistry of Advanced Materials and Technologies”, ITMO University, 191002 St. Petersburg, Russia
- Almetyevsk State Petroleum Institute, 423450 Almetyevsk, Russia
| | - Azat Gabdulkhakov
- Institute of Protein Research RAS, 142290 Pushchino, Russia; (A.G.); (V.M.); (U.D.); (G.S.)
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Sanz-Frasquet C, Ciges-Tomas JR, Alite C, Penadés JR, Marina A. The Bacteriophage-Phage-Inducible Chromosomal Island Arms Race Designs an Interkingdom Inhibitor of dUTPases. Microbiol Spectr 2023; 11:e0323222. [PMID: 36622213 PMCID: PMC9927489 DOI: 10.1128/spectrum.03232-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 12/18/2022] [Indexed: 01/10/2023] Open
Abstract
Stl, the master repressor of the Staphylococcus aureus pathogenicity islands (SaPIs), targets phage-encoded proteins to derepress and synchronize the SaPI and the helper phage life cycles. To activate their cycle, some SaPI Stls target both phage dimeric and phage trimeric dUTPases (Duts) as antirepressors, which are structurally unrelated proteins that perform identical functions for the phage. This intimate link between the SaPI's repressor and the phage inducer has imposed an evolutionary optimization of Stl that allows the interaction with Duts from unrelated organisms. In this work, we structurally characterize this sophisticated mechanism of specialization by solving the structure of the prototypical SaPIbov1 Stl in complex with a prokaryotic and a eukaryotic trimeric Dut. The heterocomplexes with Mycobacterium tuberculosis and Homo sapiens Duts show the molecular strategy of Stl to target trimeric Duts from different kingdoms. Our structural results confirm the participation of the five catalytic motifs of trimeric Duts in Stl binding, including the C-terminal flexible motif V that increases the affinity by embracing Stl. In silico and in vitro analyses with a monomeric Dut support the capacity of Stl to recognize this third family of Duts, confirming this protein as a universal Dut inhibitor in the different kingdoms of life. IMPORTANCE Stl, the Staphylococcus aureus pathogenicity island (SaPI) master repressor, targets phage-encoded proteins to derepress and synchronize the SaPI and the helper phage life cycles. This fascinating phage-SaPI arms race is exemplified by the Stl from SaPIbov1 which targets phage dimeric and trimeric dUTPases (Duts), structurally unrelated proteins with identical functions in the phages. By solving the structure of the Stl in complex with a prokaryotic (M. tuberculosis) and a eukaryotic (human) trimeric Dut, we showed that Stl has developed a sophisticated substrate mimicry strategy to target trimeric Duts. Since all these Duts present identical catalytic mechanisms, Stl is able to interact with Duts from different kingdoms. In addition, in silico modeling with monomeric Dut supports the capacity of Stl to recognize this third family of Duts, confirming this protein as a universal Dut inhibitor.
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Affiliation(s)
- Carla Sanz-Frasquet
- Instituto de Biomedicina de Valencia (IBV), CSIC and CIBER de Enfermedades Raras (CIBERER), Valencia, Spain
| | - J. Rafael Ciges-Tomas
- Instituto de Biomedicina de Valencia (IBV), CSIC and CIBER de Enfermedades Raras (CIBERER), Valencia, Spain
| | - Christian Alite
- Instituto de Biomedicina de Valencia (IBV), CSIC and CIBER de Enfermedades Raras (CIBERER), Valencia, Spain
| | - José R. Penadés
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Alberto Marina
- Instituto de Biomedicina de Valencia (IBV), CSIC and CIBER de Enfermedades Raras (CIBERER), Valencia, Spain
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Viral dUTPases: Modulators of Innate Immunity. Biomolecules 2022; 12:biom12020227. [PMID: 35204728 PMCID: PMC8961515 DOI: 10.3390/biom12020227] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/24/2022] [Accepted: 01/26/2022] [Indexed: 11/17/2022] Open
Abstract
Most free-living organisms encode for a deoxyuridine triphosphate nucleotidohydrolase (dUTPase; EC 3.6.1.23). dUTPases represent a family of metalloenzymes that catalyze the hydrolysis of dUTP to dUMP and pyrophosphate, preventing dUTP from being incorporated into DNA by DNA polymerases, maintaining a low dUTP/dTTP pool ratio and providing a necessary precursor for dTTP biosynthesis. Thus, dUTPases are involved in maintaining genomic integrity by preventing the uracilation of DNA. Many DNA-containing viruses, which infect mammals also encode for a dUTPase. This review will summarize studies demonstrating that, in addition to their classical enzymatic activity, some dUTPases possess novel functions that modulate the host innate immune response.
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Zhang Y, Zhang H, Chen Y, Qiao L, Han Y, Lin Y, Si S, Jiang JD. Screening and Identification of a Novel Anti-tuberculosis Compound That Targets Deoxyuridine 5'-Triphosphate Nucleotidohydrolase. Front Microbiol 2021; 12:757914. [PMID: 34707597 PMCID: PMC8544286 DOI: 10.3389/fmicb.2021.757914] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 09/10/2021] [Indexed: 01/08/2023] Open
Abstract
Tuberculosis (TB) is still a threat to humans worldwide. The rise of drug-resistant TB strains has escalated the need for developing effective anti-TB agents. Deoxyuridine 5′-triphosphate nucleotidohydrolase (dUTPase) is essential for thymidylate biosynthesis to maintain the DNA integrity. In Mycobacterium tuberculosis, dUTPase provides the sole source for thymidylate biosynthesis, which also has the specific five-residue loop and the binding pockets absent in human dUTPase. Therefore, dUTPase has been regarded as a promising anti-TB drug target. Herein, we used a luminescence-based dUTPase assay to search for the inhibitors target M. tuberculosis dUTPase (Mt-dUTPase) and identified compound F0414 as a potent Mt-dUTPase inhibitor with an IC50 of 0.80 ± 0.09 μM. F0414 exhibited anti-TB activity with low cytotoxicity. Molecular docking model and site-directed mutation experiments revealed that P79 was the key residue in the interaction of Mt-dUTPase and F0414. Moreover, F0414 was shown to have stronger binding with Mt-dUTPase than with Mt-P79A-dUTPase by surface plasmon resonance (SPR) detection. Interestingly, F0414 exhibited insensitivity and weak directly binding on human dUTPase compared with that on Mt-dUTPase. All the results highlight that F0414 is the first compound reported to have anti-TB activity by inhibiting Mt-dUTPase, which indicates the potential application in anti-TB therapy.
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Affiliation(s)
- Yu Zhang
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hongjuan Zhang
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ying Chen
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Luyao Qiao
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yanxing Han
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yuan Lin
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shuyi Si
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jian-Dong Jiang
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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Szabó JE, Nyíri K, Andrási D, Matejka J, Ozohanics O, Vértessy B. Redox status of cysteines does not alter functional properties of human dUTPase but the Y54C mutation involved in monogenic diabetes decreases protein stability. Sci Rep 2021; 11:19197. [PMID: 34584184 PMCID: PMC8478915 DOI: 10.1038/s41598-021-98790-3] [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: 07/02/2021] [Accepted: 09/13/2021] [Indexed: 02/08/2023] Open
Abstract
Recently it was proposed that the redox status of cysteines acts as a redox switch to regulate both the oligomeric status and the activity of human dUTPase. In a separate report, a human dUTPase point mutation, resulting in a tyrosine to cysteine substitution (Y54C) was identified as the monogenic cause of a rare syndrome associated with diabetes and bone marrow failure. These issues prompt a critical investigation about the potential regulatory role of cysteines in the enzyme. Here we show on the one hand that independently of the redox status of wild-type cysteines, human dUTPase retains its characteristic trimeric assembly and its catalytic activity. On the other hand, the Y54C mutation did not compromise the substrate binding and the catalytic properties of the enzyme at room temperature. The thermal stability of the mutant protein was found to be decreased, which resulted in the loss of 67% of its activity after 90 min incubation at the physiological temperature in contrast to the wild-type enzyme. In addition, the presence or absence of reducing agents had no effect on hDUTY54C activity and stability, although it was confirmed that the introduced cysteine contains a solvent accessible thiol group.
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Affiliation(s)
- Judit Eszter Szabó
- Institute of Enzymology, RCNS, Eötvös Loránd Research Network, Budapest, Hungary.
- Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, Hungary.
| | - Kinga Nyíri
- Institute of Enzymology, RCNS, Eötvös Loránd Research Network, Budapest, Hungary
- Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, Hungary
| | - Dániel Andrási
- Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, Hungary
| | - Judit Matejka
- Institute of Enzymology, RCNS, Eötvös Loránd Research Network, Budapest, Hungary
- Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, Hungary
| | - Olivér Ozohanics
- Department of Biochemistry, Institute of Biochemistry and Molecular Biology, Semmelweis University, Budapest, Hungary
| | - Beáta Vértessy
- Institute of Enzymology, RCNS, Eötvös Loránd Research Network, Budapest, Hungary.
- Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, Hungary.
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Patil A, Duggal H, Bagul KT, Kamble S, Lokhande P, Gacche R, Meshram R. Synthesis of New 3-Arylaminophthalides and 3-Indolyl-phthalides using Ammonium Chloride, Evaluation of their Anti-Mycobacterial Potential and Docking Study. Comb Chem High Throughput Screen 2021; 23:723-739. [PMID: 32321396 DOI: 10.2174/1386207323666200422082754] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 12/03/2019] [Accepted: 01/17/2020] [Indexed: 12/12/2022]
Abstract
OBJECTIVE The study aims at the derivatization of "Phthalides" and synthesizes 3- arylaminophthalides & 3-indolyl-phthalides compounds, and evaluates their anti-tubercular and antioxidant activities. The study has also intended to employ the in silico methods for the identification of possible drug targets in Mycobacterium and evaluate the binding affinities of synthesized compounds. METHODS This report briefly explains the synthesis of phthalide derivatives using ammonium chloride. The synthesized compounds were characterized using spectral analysis. Resazurin Microtiter Assay (REMA) plate method was used to demonstrate the anti-mycobacterial activity of the synthesized compounds. An in-silico pharmacophore probing approach was used for target identification in Mycobacterium. The structural level interaction between the identified putative drug target and synthesized phthalides was studied using Lamarckian genetic algorithm-based software. RESULTS AND DISCUSSION In the present study, we report an effective, environmentally benign scheme for the synthesis of phthalide derivatives. Compounds 5c and 5d from the current series appear to possess good anti-mycobacterial activity. dCTP: deaminasedUTPase was identified as a putative drug target in Mycobacterium. The docking results clearly showed the interactive involvement of conserved residues of dCTP with the synthesized phthalide compounds. CONCLUSION On the eve of evolving anti-TB drug resistance, the data on anti-tubercular and allied activities of the compounds in the present study demonstrates the enormous significance of these newly synthesized derivatives as possible candidate leads in the development of novel anti-tubercular agents. The docking results from the current report provide a structural rationale for the promising anti-tubercular activity demonstrated by 3-arylaminophthalides and 3-indolyl-phthalides compounds.
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Affiliation(s)
- Avinash Patil
- Department of Chemistry, Savitribai Phule Pune University, Pune, India
| | - Harleen Duggal
- Bioinformatics Centre, The Department of Biotechnology and Department of Chemistry, Savitribai Phule Pune University, Pune, India
| | - Kamini T Bagul
- Bioinformatics Centre, The Department of Biotechnology and Department of Chemistry, Savitribai Phule Pune University, Pune, India
| | - Sonali Kamble
- Gramin Science (Vocational) College, Vishnupuri, Nanded, India
| | - Pradeep Lokhande
- Department of Chemistry, Savitribai Phule Pune University, Pune, India
| | - Rajesh Gacche
- Department of Biotechnology, Savitribai Phule Pune University, Pune, India
| | - Rohan Meshram
- Bioinformatics Centre, The Department of Biotechnology and Department of Chemistry, Savitribai Phule Pune University, Pune, India
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Pérez-Moreno G, Sánchez-Carrasco P, Ruiz-Pérez LM, Johansson NG, Müller S, Baragaña B, Hampton SE, Gilbert IH, Kaiser M, Sarkar S, Pandurangan T, Kumar V, González-Pacanowska D. Validation of Plasmodium falciparum dUTPase as the target of 5'-tritylated deoxyuridine analogues with anti-malarial activity. Malar J 2019; 18:392. [PMID: 31796083 PMCID: PMC6889535 DOI: 10.1186/s12936-019-3025-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 11/21/2019] [Indexed: 11/24/2022] Open
Abstract
Background Malaria remains as a major global problem, being one of the infectious diseases that engender highest mortality across the world. Due to the appearance of resistance and the lack of an effective vaccine, the search of novel anti-malarials is required. Deoxyuridine 5′-triphosphate nucleotido-hydrolase (dUTPase) is responsible for the hydrolysis of dUTP to dUMP within the parasite and has been proposed as an essential step in pyrimidine metabolism by providing dUMP for thymidylate biosynthesis. In this work, efforts to validate dUTPase as a drug target in Plasmodium falciparum are reported. Methods To investigate the role of PfdUTPase in cell survival different strategies to generate knockout mutants were used. For validation of PfdUTPase as the intracellular target of four inhibitors of the enzyme, mutants overexpressing PfdUTPase and HsdUTPase were created and the IC50 for each cell line with each compound was determined. The effect of these compounds on dUTP and dTTP levels from P. falciparum was measured using a DNA polymerase assay. Detailed localization studies by indirect immunofluorescence microscopy and live cell imaging were also performed using a cell line overexpressing a Pfdut-GFP fusion protein. Results Different attempts of disruption of the dut gene of P. falciparum were unsuccessful while a 3′ replacement construct could recombine correctly in the locus suggesting that the enzyme is essential. The four 5′-tritylated deoxyuridine analogues described are potent inhibitors of the P. falciparum dUTPase and exhibit antiplasmodial activity. Overexpression of the Plasmodium and human enzymes conferred resistance against selective compounds, providing chemical validation of the target and confirming that indeed dUTPase inhibition is involved in anti-malarial activity. In addition, incubation with these inhibitors was associated with a depletion of the dTTP pool corroborating the central role of dUTPase in dTTP synthesis. PfdUTPase is mainly localized in the cytosol. Conclusion These results strongly confirm the pivotal and essential role of dUTPase in pyrimidine biosynthesis of P. falciparum intraerythrocytic stages.
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Affiliation(s)
- Guiomar Pérez-Moreno
- Instituto de Parasitología y Biomedicina López-Neyra. Consejo Superior de Investigaciones Científicas. Parque Tecnológico de Ciencias de la Salud, Avenida del Conocimiento, s/n 18016-Armilla, Granada, Spain
| | - Paula Sánchez-Carrasco
- Instituto de Parasitología y Biomedicina López-Neyra. Consejo Superior de Investigaciones Científicas. Parque Tecnológico de Ciencias de la Salud, Avenida del Conocimiento, s/n 18016-Armilla, Granada, Spain
| | - Luis Miguel Ruiz-Pérez
- Instituto de Parasitología y Biomedicina López-Neyra. Consejo Superior de Investigaciones Científicas. Parque Tecnológico de Ciencias de la Salud, Avenida del Conocimiento, s/n 18016-Armilla, Granada, Spain
| | | | - Sylke Müller
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, 120 University Place, Glasgow, G12 8TA, UK
| | - Beatriz Baragaña
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Shahienaz Emma Hampton
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Ian Hugh Gilbert
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Marcel Kaiser
- Swiss Tropical and Public Health Institute (Swiss TPH), Socinstrasse 57, 4051, Basel, Switzerland.,University of Basel, Petersplatz 1, 4003, Basel, Switzerland
| | - Sandipan Sarkar
- Syngene International Ltd, Biocon Park, SEZ, Bommasandra Industrial Area - Phase-IV Bommasandra-Jigani Link Road, Bangalore, 560 099, India
| | - Thiyagamurthy Pandurangan
- Syngene International Ltd, Biocon Park, SEZ, Bommasandra Industrial Area - Phase-IV Bommasandra-Jigani Link Road, Bangalore, 560 099, India
| | - Vijeesh Kumar
- Syngene International Ltd, Biocon Park, SEZ, Bommasandra Industrial Area - Phase-IV Bommasandra-Jigani Link Road, Bangalore, 560 099, India
| | - Dolores González-Pacanowska
- Instituto de Parasitología y Biomedicina López-Neyra. Consejo Superior de Investigaciones Científicas. Parque Tecnológico de Ciencias de la Salud, Avenida del Conocimiento, s/n 18016-Armilla, Granada, Spain.
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The Role of a Key Amino Acid Position in Species-Specific Proteinaceous dUTPase Inhibition. Biomolecules 2019; 9:biom9060221. [PMID: 31174420 PMCID: PMC6627510 DOI: 10.3390/biom9060221] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 05/27/2019] [Indexed: 02/06/2023] Open
Abstract
Protein inhibitors of key DNA repair enzymes play an important role in deciphering physiological pathways responsible for genome integrity, and may also be exploited in biomedical research. The staphylococcal repressor StlSaPIbov1 protein was described to be an efficient inhibitor of dUTPase homologues showing a certain degree of species-specificity. In order to provide insight into the inhibition mechanism, in the present study we investigated the interaction of StlSaPIbov1 and Escherichia coli dUTPase. Although we observed a strong interaction of these proteins, unexpectedly the E. coli dUTPase was not inhibited. Seeking a structural explanation for this phenomenon, we identified a key amino acid position where specific mutations sensitized E. coli dUTPase to StlSaPIbov1 inhibition. We solved the three-dimensional (3D) crystal structure of such a mutant in complex with the substrate analogue dUPNPP and surprisingly found that the C-terminal arm of the enzyme, containing the P-loop-like motif was ordered in the structure. This segment was never localized before in any other E. coli dUTPase crystal structures. The 3D structure in agreement with solution phase experiments suggested that ordering of the flexible C-terminal segment upon substrate binding is a major factor in defining the sensitivity of E. coli dUTPase for StlSaPIbov1 inhibition.
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Minias A, Brzostek A, Dziadek J. Targeting DNA Repair Systems in Antitubercular Drug Development. Curr Med Chem 2019; 26:1494-1505. [DOI: 10.2174/0929867325666180129093546] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 11/01/2017] [Accepted: 11/01/2017] [Indexed: 11/22/2022]
Abstract
Infections with Mycobacterium tuberculosis, the causative agent of tuberculosis, are difficult to treat using currently available chemotherapeutics. Clinicians agree on the urgent need for novel drugs to treat tuberculosis. In this mini review, we summarize data that prompts the consideration of DNA repair-associated proteins as targets for the development of new antitubercular compounds. We discuss data, including gene expression data, that highlight the importance of DNA repair genes during the pathogenic cycle as well as after exposure to antimicrobials currently in use. Specifically, we report experiments on determining the essentiality of DNA repair-related genes. We report the availability of protein crystal structures and summarize discovered protein inhibitors. Further, we describe phenotypes of available gene mutants of M. tuberculosis and model organisms Mycobacterium bovis and Mycobacterium smegmatis. We summarize experiments regarding the role of DNA repair-related proteins in pathogenesis and virulence performed both in vitro and in vivo during the infection of macrophages and animals. We detail the role of DNA repair genes in acquiring mutations, which influence the rate of drug resistance acquisition.
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Affiliation(s)
- Alina Minias
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
| | - Anna Brzostek
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
| | - Jarosław Dziadek
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
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10
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Kumar H, Kehrer J, Singer M, Reinig M, Santos JM, Mair GR, Frischknecht F. Functional genetic evaluation of DNA house-cleaning enzymes in the malaria parasite: dUTPase and Ap4AH are essential in Plasmodium berghei but ITPase and NDH are dispensable. Expert Opin Ther Targets 2019; 23:251-261. [PMID: 30700216 DOI: 10.1080/14728222.2019.1575810] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 01/25/2019] [Indexed: 02/06/2023]
Abstract
BACKGROUND Cellular metabolism generates reactive oxygen species. The oxidation and deamination of the deoxynucleoside triphosphate (dNTP) pool results in the formation of non-canonical, toxic dNTPs that can cause mutations, genome instability, and cell death. House-cleaning or sanitation enzymes that break down and detoxify non-canonical nucleotides play major protective roles in nucleotide metabolism and constitute key drug targets for cancer and various pathogens. We hypothesized that owing to their protective roles in nucleotide metabolism, these house-cleaning enzymes are key drug targets in the malaria parasite. METHODS Using the rodent malaria parasite Plasmodium berghei we evaluate here, by gene targeting, a group of conserved proteins with a putative function in the detoxification of non-canonical nucleotides as potential antimalarial drug targets: they are inosine triphosphate pyrophosphatase (ITPase), deoxyuridine triphosphate pyrophosphatase (dUTPase) and two NuDiX hydroxylases, the diadenosine tetraphosphate (Ap4A) hydrolase and the nucleoside triphosphate hydrolase (NDH). RESULTS While all four proteins are expressed constitutively across the intraerythrocytic developmental cycle, neither ITPase nor NDH are required for parasite viability. dutpase and ap4ah null mutants, on the other hand, are not viable suggesting an essential function for these proteins for the malaria parasite. CONCLUSIONS Plasmodium dUTPase and Ap4A could be drug targets in the malaria parasite.
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Affiliation(s)
- Hirdesh Kumar
- a Integrative Parasitology, Department of Infectious Diseases , University of Heidelberg Medical School , Heidelberg , Germany
| | - Jessica Kehrer
- a Integrative Parasitology, Department of Infectious Diseases , University of Heidelberg Medical School , Heidelberg , Germany
| | - Mirko Singer
- a Integrative Parasitology, Department of Infectious Diseases , University of Heidelberg Medical School , Heidelberg , Germany
| | - Miriam Reinig
- a Integrative Parasitology, Department of Infectious Diseases , University of Heidelberg Medical School , Heidelberg , Germany
| | - Jorge M Santos
- b Instituto de Medicina Molecular , Faculdade de Medicina da Universidade de Lisboa , Lisbon , Portugal
| | - Gunnar R Mair
- a Integrative Parasitology, Department of Infectious Diseases , University of Heidelberg Medical School , Heidelberg , Germany
- b Instituto de Medicina Molecular , Faculdade de Medicina da Universidade de Lisboa , Lisbon , Portugal
- c Department of Biomedical Sciences , 2008 College of Veterinary Medicine, Iowa State University , Ames , IA USA
| | - Friedrich Frischknecht
- a Integrative Parasitology, Department of Infectious Diseases , University of Heidelberg Medical School , Heidelberg , Germany
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Abstract
Human deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase), essential for DNA integrity, acts as a survival factor for tumor cells and is a target for cancer chemotherapy. Here we report that the Staphylococcal repressor protein StlSaPIBov1 (Stl) forms strong complex with human dUTPase. Functional analysis reveals that this interaction results in significant reduction of both dUTPase enzymatic activity and DNA binding capability of Stl. We conducted structural studies to understand the mechanism of this mutual inhibition. Small-angle X-ray scattering (SAXS) complemented with hydrogen-deuterium exchange mass spectrometry (HDX-MS) data allowed us to obtain 3D structural models comprising a trimeric dUTPase complexed with separate Stl monomers. These models thus reveal that upon dUTPase-Stl complex formation the functional homodimer of Stl repressor dissociates, which abolishes the DNA binding ability of the protein. Active site forming dUTPase segments were directly identified to be involved in the dUTPase-Stl interaction by HDX-MS, explaining the loss of dUTPase activity upon complexation. Our results provide key novel structural insights that pave the way for further applications of the first potent proteinaceous inhibitor of human dUTPase.
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12
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Lima MNN, Melo-Filho CC, Cassiano GC, Neves BJ, Alves VM, Braga RC, Cravo PVL, Muratov EN, Calit J, Bargieri DY, Costa FTM, Andrade CH. QSAR-Driven Design and Discovery of Novel Compounds With Antiplasmodial and Transmission Blocking Activities. Front Pharmacol 2018; 9:146. [PMID: 29559909 PMCID: PMC5845645 DOI: 10.3389/fphar.2018.00146] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 02/12/2018] [Indexed: 11/13/2022] Open
Abstract
Malaria is a life-threatening infectious disease caused by parasites of the genus Plasmodium, affecting more than 200 million people worldwide every year and leading to about a half million deaths. Malaria parasites of humans have evolved resistance to all current antimalarial drugs, urging for the discovery of new effective compounds. Given that the inhibition of deoxyuridine triphosphatase of Plasmodium falciparum (PfdUTPase) induces wrong insertions in plasmodial DNA and consequently leading the parasite to death, this enzyme is considered an attractive antimalarial drug target. Using a combi-QSAR (quantitative structure-activity relationship) approach followed by virtual screening and in vitro experimental evaluation, we report herein the discovery of novel chemical scaffolds with in vitro potency against asexual blood stages of both P. falciparum multidrug-resistant and sensitive strains and against sporogonic development of P. berghei. We developed 2D- and 3D-QSAR models using a series of nucleosides reported in the literature as PfdUTPase inhibitors. The best models were combined in a consensus approach and used for virtual screening of the ChemBridge database, leading to the identification of five new virtual PfdUTPase inhibitors. Further in vitro testing on P. falciparum multidrug-resistant (W2) and sensitive (3D7) parasites showed that compounds LabMol-144 and LabMol-146 demonstrated fair activity against both strains and presented good selectivity versus mammalian cells. In addition, LabMol-144 showed good in vitro inhibition of P. berghei ookinete formation, demonstrating that hit-to-lead optimization based on this compound may also lead to new antimalarials with transmission blocking activity.
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Affiliation(s)
- Marilia N N Lima
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculty of Pharmacy, Federal University of Goiás, Goiânia, Brazil
| | - Cleber C Melo-Filho
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculty of Pharmacy, Federal University of Goiás, Goiânia, Brazil
| | - Gustavo C Cassiano
- Laboratory of Tropical Diseases - Prof. Dr. Luiz Jacintho da Silva, Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, UNICAMP, Campinas, Brazil
| | - Bruno J Neves
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculty of Pharmacy, Federal University of Goiás, Goiânia, Brazil.,Laboratory of Cheminformatics, PPG-SOMA, University Center of Anápolis/UniEVANGELICA, Anápolis, Brazil
| | - Vinicius M Alves
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculty of Pharmacy, Federal University of Goiás, Goiânia, Brazil
| | - Rodolpho C Braga
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculty of Pharmacy, Federal University of Goiás, Goiânia, Brazil
| | - Pedro V L Cravo
- Global Health and Tropical Medicine Centre, Unidade de Parasitologia Médica, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Eugene N Muratov
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States.,Department of Chemical Technology, Odessa National Polytechnic University, Odessa, Ukraine
| | - Juliana Calit
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Daniel Y Bargieri
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Fabio T M Costa
- Laboratory of Tropical Diseases - Prof. Dr. Luiz Jacintho da Silva, Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, UNICAMP, Campinas, Brazil
| | - Carolina H Andrade
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculty of Pharmacy, Federal University of Goiás, Goiânia, Brazil.,Laboratory of Tropical Diseases - Prof. Dr. Luiz Jacintho da Silva, Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, UNICAMP, Campinas, Brazil
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13
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Benedek A, Pölöskei I, Ozohanics O, Vékey K, Vértessy BG. The Stl repressor from Staphylococcus aureus is an efficient inhibitor of the eukaryotic fruitfly dUTPase. FEBS Open Bio 2017; 8:158-167. [PMID: 29435406 PMCID: PMC5794464 DOI: 10.1002/2211-5463.12302] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 06/25/2017] [Accepted: 06/30/2017] [Indexed: 11/17/2022] Open
Abstract
DNA metabolism and repair is vital for the maintenance of genome integrity. Specific proteinaceous inhibitors of key factors in this process have high potential for deciphering pathways of DNA metabolism and repair. The dUTPase enzyme family is responsible for guarding against erroneous uracil incorporation into DNA. Here, we investigate whether the staphylococcal Stl repressor may interact with not only bacterial but also eukaryotic dUTPase. We provide experimental evidence for the formation of a strong complex between Stl and Drosophila melanogasterdUTPase. We also find that dUTPase activity is strongly diminished in this complex. Our results suggest that the dUTPase protein sequences involved in binding to Stl are at least partially conserved through evolution from bacteria to eukaryotes.
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Affiliation(s)
- András Benedek
- Institute of Enzymology Research Centre for Natural Sciences Hungarian Academy of Sciences Budapest Hungary.,Department of Applied Biotechnology Budapest University of Technology and Economics Hungary
| | - István Pölöskei
- Department of Applied Biotechnology Budapest University of Technology and Economics Hungary
| | - Olivér Ozohanics
- Institute of Organic Chemistry Research Centre for Natural Sciences Hungarian Academy of Sciences Budapest Hungary
| | - Károly Vékey
- Institute of Organic Chemistry Research Centre for Natural Sciences Hungarian Academy of Sciences Budapest Hungary
| | - Beáta G Vértessy
- Institute of Enzymology Research Centre for Natural Sciences Hungarian Academy of Sciences Budapest Hungary.,Department of Applied Biotechnology Budapest University of Technology and Economics Hungary
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14
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Zang K, Li F, Ma Q. The dUTPase of white spot syndrome virus assembles its active sites in a noncanonical manner. J Biol Chem 2017; 293:1088-1099. [PMID: 29187596 DOI: 10.1074/jbc.m117.815266] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 11/14/2017] [Indexed: 01/04/2023] Open
Abstract
dUTPases are essential enzymes for maintaining genome integrity and have recently been shown to play moonlighting roles when containing extra sequences. Interestingly, the trimeric dUTPase of white spot syndrome virus (wDUT) harbors a sequence insert at the position preceding the C-terminal catalytic motif V (pre-V insert), rarely seen in other dUTPases. However, whether this extra sequence endows wDUT with additional properties is unknown. Herein, we present the crystal structures of wDUT in both ligand-free and ligand-bound forms. We observed that the pre-V insert in wDUT forms an unusual β-hairpin structure in the domain-swapping region and thereby facilitates a unique orientation of the adjacent C-terminal segment, positioning the catalytic motif V onto the active site of its own subunit instead of a third subunit. Consequently, wDUT employs two-subunit active sites, unlike the widely accepted paradigm that the active site of trimeric dUTPase is contributed by all three subunits. According to results from local structural comparisons, the active-site configuration of wDUT is similar to that of known dUTPases. However, we also found that residues in the second-shell region of the active site are reconfigured in wDUT as an adaption to its unique C-terminal orientation. We also show that deletion of the pre-V insert significantly reduces wDUT's enzymatic activity and thermal stability. We hypothesize that this rare structural arrangement confers additional functionality to wDUT. In conclusion, our study expands the structural diversity in the conserved dUTPase family and illustrates how sequence insertion and amino acid substitution drive protein evolution cooperatively.
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Affiliation(s)
- Kun Zang
- From the Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Nanhai Road 7, Qingdao 266071, China.,the Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China, and.,the University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fuhua Li
- From the Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Nanhai Road 7, Qingdao 266071, China.,the Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China, and
| | - Qingjun Ma
- From the Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Nanhai Road 7, Qingdao 266071, China, .,the Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China, and
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15
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Hirmondo R, Lopata A, Suranyi EV, Vertessy BG, Toth J. Differential control of dNTP biosynthesis and genome integrity maintenance by the dUTPase superfamily enzymes. Sci Rep 2017; 7:6043. [PMID: 28729658 PMCID: PMC5519681 DOI: 10.1038/s41598-017-06206-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 06/12/2017] [Indexed: 01/22/2023] Open
Abstract
dUTPase superfamily enzymes generate dUMP, the obligate precursor for de novo dTTP biosynthesis, from either dUTP (monofunctional dUTPase, Dut) or dCTP (bifunctional dCTP deaminase/dUTPase, Dcd:dut). In addition, the elimination of dUTP by these enzymes prevents harmful uracil incorporation into DNA. These two beneficial outcomes have been thought to be related. Here we determined the relationship between dTTP biosynthesis (dTTP/dCTP balance) and the prevention of DNA uracilation in a mycobacterial model that encodes both the Dut and Dcd:dut enzymes, and has no other ways to produce dUMP. We show that, in dut mutant mycobacteria, the dTTP/dCTP balance remained unchanged, but the uracil content of DNA increased in parallel with the in vitro activity-loss of Dut accompanied with a considerable increase in the mutation rate. Conversely, dcd:dut inactivation resulted in perturbed dTTP/dCTP balance and two-fold increased mutation rate, but did not increase the uracil content of DNA. Thus, unexpectedly, the regulation of dNTP balance and the prevention of DNA uracilation are decoupled and separately brought about by the Dcd:dut and Dut enzymes, respectively. Available evidence suggests that the discovered functional separation is conserved in humans and other organisms.
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Affiliation(s)
- Rita Hirmondo
- Institute of Enzymology, RCNS, Hungarian Academy of Sciences, Budapest, Hungary
| | - Anna Lopata
- Institute of Enzymology, RCNS, Hungarian Academy of Sciences, Budapest, Hungary
| | - Eva Viola Suranyi
- Institute of Enzymology, RCNS, Hungarian Academy of Sciences, Budapest, Hungary
- Department of Applied Biotechnology, Budapest University of Technology and Economics, Budapest, Hungary
| | - Beata G Vertessy
- Institute of Enzymology, RCNS, Hungarian Academy of Sciences, Budapest, Hungary
- Department of Applied Biotechnology, Budapest University of Technology and Economics, Budapest, Hungary
| | - Judit Toth
- Institute of Enzymology, RCNS, Hungarian Academy of Sciences, Budapest, Hungary.
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16
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Kerepesi C, Szabó JE, Papp-Kádár V, Dobay O, Szabó D, Grolmusz V, Vértessy BG. Life without dUTPase. Front Microbiol 2016; 7:1768. [PMID: 27933035 PMCID: PMC5122711 DOI: 10.3389/fmicb.2016.01768] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 10/21/2016] [Indexed: 11/22/2022] Open
Abstract
Fine-tuned regulation of the cellular nucleotide pools is indispensable for faithful replication of Deoxyribonucleic Acid (DNA). The genetic information is also safeguarded by DNA damage recognition and repair processes. Uracil is one of the most frequently occurring erroneous bases in DNA; it can arise from cytosine deamination or thymine-replacing incorporation. Two enzyme activities are primarily involved in keeping DNA uracil-free: dUTPase (dUTP pyrophosphatase) activity that prevent thymine-replacing incorporation and uracil-DNA glycosylase activity that excise uracil from DNA and initiate uracil-excision repair. Both dUTPase and the most efficient uracil-DNA glycosylase (UNG) is thought to be ubiquitous in free-living organisms. In the present work, we have systematically investigated the genotype of deposited fully sequenced bacterial and Archaeal genomes. We have performed bioinformatic searches in these genomes using the already well described dUTPase and UNG gene sequences. For dUTPases, we have included the trimeric all-beta and the dimeric all-alpha families and also, the bifunctional dCTP (deoxycytidine triphosphate) deaminase-dUTPase sequences. Surprisingly, we have found that in contrast to the generally held opinion, a wide number of bacterial and Archaeal species lack all of the previously described dUTPase gene(s). The dut– genotype is present in diverse bacterial phyla indicating that loss of this (or these) gene(s) has occurred multiple times during evolution. We discuss potential survival strategies in lack of dUTPases, such as simultaneous lack or inhibition of UNG and possession of exogenous or alternate metabolic enzymes involved in uracil-DNA metabolism. The potential that genes previously not associated with dUTPase activity may still encode enzymes capable of hydrolyzing dUTP is also discussed. Our data indicate that several unicellular microorganisms may efficiently cope with a dut– genotype lacking all of the previously described dUTPase genes, and potentially leading to an unusual uracil-enrichment in their genomic DNA.
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Affiliation(s)
- Csaba Kerepesi
- PIT Bioinformatics Group, Institute of Mathematics, Eötvös Loránd University Budapest, Hungary
| | - Judit E Szabó
- Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and EconomicsBudapest, Hungary; Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of SciencesBudapest, Hungary
| | - Veronika Papp-Kádár
- Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and EconomicsBudapest, Hungary; Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of SciencesBudapest, Hungary
| | - Orsolya Dobay
- Institute of Medical Microbiology, Semmelweis University Budapest, Hungary
| | - Dóra Szabó
- Institute of Medical Microbiology, Semmelweis University Budapest, Hungary
| | - Vince Grolmusz
- PIT Bioinformatics Group, Institute of Mathematics, Eötvös Loránd UniversityBudapest, Hungary; Uratim Ltd.,Budapest, Hungary
| | - Beáta G Vértessy
- Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and EconomicsBudapest, Hungary; Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of SciencesBudapest, Hungary
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17
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Nagy GN, Suardíaz R, Lopata A, Ozohanics O, Vékey K, Brooks BR, Leveles I, Tóth J, Vértessy BG, Rosta E. Structural Characterization of Arginine Fingers: Identification of an Arginine Finger for the Pyrophosphatase dUTPases. J Am Chem Soc 2016; 138:15035-15045. [PMID: 27740761 DOI: 10.1021/jacs.6b09012] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Arginine finger is a highly conserved and essential residue in many GTPase and AAA+ ATPase enzymes that completes the active site from a distinct protomer, forming contacts with the γ-phosphate of the nucleotide. To date, no pyrophosphatase has been identified that employs an arginine finger fulfilling all of the above properties; all essential arginine fingers are used to catalyze the cleavage of the γ-phosphate. Here, we identify and unveil the role of a conserved arginine residue in trimeric dUTPases that meets all the criteria established for arginine fingers. We found that the conserved arginine adjacent to the P-loop-like motif enables structural organization of the active site for efficient catalysis via its nucleotide coordination, while its direct electrostatic role in transition state stabilization is secondary. An exhaustive structure-based comparison of analogous, conserved arginines from nucleotide hydrolases and transferases revealed a consensus amino acid location and orientation for contacting the γ-phosphate of the substrate nucleotide. Despite the structurally equivalent position, functional differences between arginine fingers of dUTPases and NTPases are explained on the basis of the unique chemistry performed by the pyrophosphatase dUTPases.
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Affiliation(s)
- Gergely N Nagy
- Department of Biotechnology and Food Sciences, Budapest University of Technology and Economics , Budapest 1111, Hungary.,Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences , Budapest 1117, Hungary
| | - Reynier Suardíaz
- Department of Chemistry, King's College London , London SE1 1DB, United Kingdom
| | - Anna Lopata
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences , Budapest 1117, Hungary
| | - Olivér Ozohanics
- MS Proteomics Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences , Budapest 1117, Hungary
| | - Károly Vékey
- Core Technologies Centre, Research Centre for Natural Sciences, Hungarian Academy of Sciences , Budapest 1117, Hungary
| | - Bernard R Brooks
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health , Rockville, Maryland 10892-9314, United States
| | - Ibolya Leveles
- Department of Biotechnology and Food Sciences, Budapest University of Technology and Economics , Budapest 1111, Hungary.,Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences , Budapest 1117, Hungary
| | - Judit Tóth
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences , Budapest 1117, Hungary
| | - Beata G Vértessy
- Department of Biotechnology and Food Sciences, Budapest University of Technology and Economics , Budapest 1111, Hungary.,Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences , Budapest 1117, Hungary
| | - Edina Rosta
- Department of Chemistry, King's College London , London SE1 1DB, United Kingdom
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18
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Lopata A, Leveles I, Bendes ÁÁ, Viskolcz B, Vértessy BG, Jójárt B, Tóth J. A Hidden Active Site in the Potential Drug Target Mycobacterium tuberculosis dUTPase Is Accessible through Small Amplitude Protein Conformational Changes. J Biol Chem 2016; 291:26320-26331. [PMID: 27815500 DOI: 10.1074/jbc.m116.734012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 11/04/2016] [Indexed: 11/06/2022] Open
Abstract
dUTPases catalyze the hydrolysis of dUTP into dUMP and pyrophosphate to maintain the proper nucleotide pool for DNA metabolism. Recent evidence suggests that dUTPases may also represent a selective drug target in mycobacteria because of the crucial role of these enzymes in maintaining DNA integrity. Nucleotide-hydrolyzing enzymes typically harbor a buried ligand-binding pocket at interdomain or intersubunit clefts, facilitating proper solvent shielding for the catalyzed reaction. The mechanism by which substrate binds this hidden pocket and product is released in dUTPases is unresolved because of conflicting crystallographic and spectroscopic data. We sought to resolve this conflict by using a combination of random acceleration molecular dynamics (RAMD) methodology and structural and biochemical methods to study the dUTPase from Mycobacterium tuberculosis In particular, the RAMD approach used in this study provided invaluable insights into the nucleotide dissociation process that reconciles all previous experimental observations. Specifically, our data suggest that nucleotide binding takes place as a small stretch of amino acids transiently slides away and partially uncovers the active site. The in silico data further revealed a new dUTPase conformation on the pathway to a relatively open active site. To probe this model, we developed the Trp21 reporter and collected crystallographic, spectroscopic, and kinetic data that confirmed the interaction of Trp21 with the active site shielding C-terminal arm, suggesting that the RAMD method is effective. In summary, our computational simulations and spectroscopic results support the idea that small loop movements in dUTPase allow the shuttlingof the nucleotides between the binding pocket and the solvent.
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Affiliation(s)
- Anna Lopata
- From the Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary H1117
| | - Ibolya Leveles
- From the Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary H1117
| | - Ábris Ádám Bendes
- From the Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary H1117
| | - Béla Viskolcz
- the Institute of Chemistry, University of Miskolc, Miskolc, Hungary H3529
| | - Beáta G Vértessy
- From the Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary H1117.,the Department of Applied Biotechnology, Budapest University of Technology and Economics, Budapest, Hungary H1111, and
| | - Balázs Jójárt
- Department of Chemical Informatics, University of Szeged, Szeged, Hungary H6725
| | - Judit Tóth
- From the Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary H1117,
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19
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Abstract
Artificially modified nucleotides, in the form of nucleoside analogues, are widely used in the treatment of cancers and various other diseases, and have become important tools in the laboratory to characterise DNA repair pathways. In contrast, the role of endogenously occurring nucleotide modifications in genome stability is little understood. This is despite the demonstration over three decades ago that the cellular DNA precursor pool is orders of magnitude more susceptible to modification than the DNA molecule itself. More recently, underscoring the importance of this topic, oxidation of the cellular nucleotide pool achieved through targeting the sanitation enzyme MTH1, appears to be a promising anti-cancer strategy. This article reviews our current understanding of modified DNA precursors in genome stability, with a particular focus upon oxidised nucleotides, and outlines some important outstanding questions.
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Affiliation(s)
- Sean G Rudd
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
| | - Nicholas C K Valerie
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Thomas Helleday
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
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20
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Benedek A, Horváth A, Hirmondó R, Ozohanics O, Békési A, Módos K, Révész Á, Vékey K, Nagy GN, Vértessy BG. Potential steps in the evolution of a fused trimeric all-β dUTPase involve a catalytically competent fused dimeric intermediate. FEBS J 2016; 283:3268-86. [PMID: 27380921 DOI: 10.1111/febs.13800] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Revised: 06/08/2016] [Accepted: 07/04/2016] [Indexed: 12/15/2022]
Abstract
Deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase) is essential for genome integrity. Interestingly, this enzyme from Drosophila virilis has an unusual form, as three monomer repeats are merged with short linker sequences, yielding a fused trimer-like dUTPase fold. Unlike homotrimeric dUTPases that are encoded by a single repeat dut gene copy, the three repeats of the D. virilis dut gene are not identical due to several point mutations. We investigated the potential evolutionary pathway that led to the emergence of this extant fused trimeric dUTPase in D. virilis. The herein proposed scenario involves two sequential gene duplications followed by sequence divergence amongst the dut repeats. This pathway thus requires the existence of a transient two-repeat-containing fused dimeric dUTPase intermediate. We identified the corresponding ancestral dUTPase single repeat enzyme together with its tandem repeat evolutionary intermediate and characterized their enzymatic function and structural stability. We additionally engineered and characterized artificial single or tandem repeat constructs from the extant enzyme form to investigate the influence of the emergent residue alterations on the formation of a functional assembly. The observed severely impaired stability and catalytic activity of these latter constructs provide a plausible explanation for evolutionary persistence of the extant fused trimeric D. virilis dUTPase form. For the ancestral homotrimeric and the fused dimeric intermediate forms, we observed strong catalytic and structural competence, verifying viability of the proposed evolutionary pathway. We conclude that the progression along the herein described evolutionary trajectory is determined by the retained potential of the enzyme for its conserved three-fold structural symmetry.
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Affiliation(s)
- András Benedek
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary. .,Department of Applied Biotechnology and Food Science, Budapest University of Technology and Economics, Hungary.
| | - András Horváth
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Rita Hirmondó
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Olivér Ozohanics
- Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Angéla Békési
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Károly Módos
- Institute of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - Ágnes Révész
- Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Károly Vékey
- Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Gergely N Nagy
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary. .,Department of Applied Biotechnology and Food Science, Budapest University of Technology and Economics, Hungary.
| | - Beáta G Vértessy
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary. .,Department of Applied Biotechnology and Food Science, Budapest University of Technology and Economics, Hungary.
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21
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In Vitro Analysis of Predicted DNA-Binding Sites for the Stl Repressor of the Staphylococcus aureus SaPIBov1 Pathogenicity Island. PLoS One 2016; 11:e0158793. [PMID: 27388898 PMCID: PMC4936726 DOI: 10.1371/journal.pone.0158793] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 06/22/2016] [Indexed: 12/27/2022] Open
Abstract
The regulation model of the Staphylococcus aureus pathogenicity island SaPIbov1 transfer was recently reported. The repressor protein Stl obstructs the expression of SaPI proteins Str and Xis, latter which is responsible for mobilization initiation. Upon Φ11 phage infection of S. aureus. phage dUTPase activates the SaPI transfer via Stl-dUTPase complex formation. Our aim was to predict the binding sites for the Stl repressor within the S. aureus pathogenicity island DNA sequence. We found that Stl was capable to bind to three 23-mer oligonucleotides, two of those constituting sequence segments in the stl-str, while the other corresponding to sequence segment within the str-xis intergenic region. Within these oligonucleotides, mutational analysis revealed that the predicted binding site for the Stl protein exists as a palindromic segment in both intergenic locations. The palindromes are built as 6-mer repeat sequences involved in Stl binding. The 6-mer repeats are separated by a 5 oligonucleotides long, nonspecific sequence. Future examination of the interaction between Stl and its binding sites in vivo will provide a molecular explanation for the mechanisms of gene repression and gene activation exerted simultaneously by the Stl protein in regulating transfer of the SaPIbov1 pathogenicity island in S. aureus.
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22
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Nyíri K, Vértessy BG. Perturbation of genome integrity to fight pathogenic microorganisms. Biochim Biophys Acta Gen Subj 2016; 1861:3593-3612. [PMID: 27217086 DOI: 10.1016/j.bbagen.2016.05.024] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 05/05/2016] [Accepted: 05/18/2016] [Indexed: 10/21/2022]
Abstract
BACKGROUND Resistance against antibiotics is unfortunately still a major biomedical challenge for a wide range of pathogens responsible for potentially fatal diseases. SCOPE OF REVIEW In this study, we aim at providing a critical assessment of the recent advances in design and use of drugs targeting genome integrity by perturbation of thymidylate biosynthesis. MAJOR CONCLUSION We find that research efforts from several independent laboratories resulted in chemically highly distinct classes of inhibitors of key enzymes within the routes of thymidylate biosynthesis. The present article covers numerous studies describing perturbation of this metabolic pathway in some of the most challenging pathogens like Mycobacterium tuberculosis, Plasmodium falciparum, and Staphylococcus aureus. GENERAL SIGNIFICANCE Our comparative analysis allows a thorough summary of the current approaches to target thymidylate biosynthesis enzymes and also include an outlook suggesting novel ways of inhibitory strategies. This article is part of a Special Issue entitled "Science for Life" Guest Editor: Dr. Austen Angell, Dr. Salvatore Magazù and Dr. Federica Migliardo.
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Affiliation(s)
- Kinga Nyíri
- Dept. Biotechnology, Budapest University of Technology and Economics, 4 Szent Gellért tér, Budapest HU 1111, Hungary; Institute of Enzymology, RCNS, Hungarian Academy of Sciences, 2 Magyar tudósok körútja, Budapest HU 1117, Hungary.
| | - Beáta G Vértessy
- Dept. Biotechnology, Budapest University of Technology and Economics, 4 Szent Gellért tér, Budapest HU 1111, Hungary; Institute of Enzymology, RCNS, Hungarian Academy of Sciences, 2 Magyar tudósok körútja, Budapest HU 1117, Hungary.
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Maiques E, Quiles-Puchalt N, Donderis J, Ciges-Tomas JR, Alite C, Bowring JZ, Humphrey S, Penadés JR, Marina A. Another look at the mechanism involving trimeric dUTPases in Staphylococcus aureus pathogenicity island induction involves novel players in the party. Nucleic Acids Res 2016; 44:5457-69. [PMID: 27112567 PMCID: PMC4914113 DOI: 10.1093/nar/gkw317] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 04/13/2016] [Indexed: 12/14/2022] Open
Abstract
We have recently proposed that the trimeric staphylococcal phage encoded dUTPases (Duts) are signaling molecules that act analogously to eukaryotic G-proteins, using dUTP as a second messenger. To perform this regulatory role, the Duts require their characteristic extra motif VI, present in all the staphylococcal phage coded trimeric Duts, as well as the strongly conserved Dut motif V. Recently, however, an alternative model involving Duts in the transfer of the staphylococcal islands (SaPIs) has been suggested, questioning the implication of motifs V and VI. Here, using state-of the-art techniques, we have revisited the proposed models. Our results confirm that the mechanism by which the Duts derepress the SaPI cycle depends on dUTP and involves both motifs V and VI, as we have previously proposed. Surprisingly, the conserved Dut motif IV is also implicated in SaPI derepression. However, and in agreement with the proposed alternative model, the dUTP inhibits rather than inducing the process, as we had initially proposed. In summary, our results clarify, validate and establish the mechanism by which the Duts perform regulatory functions.
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Affiliation(s)
- Elisa Maiques
- Instituto de Biomedicina de Valencia (IBV-CSIC) and CIBER de Enfermedades Raras (CIBERER), 46010 Valencia, Spain
| | - Nuria Quiles-Puchalt
- Departamento de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad CEU Cardenal Herrera, 46113 Moncada, Valencia, Spain Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, UK
| | - Jorge Donderis
- Instituto de Biomedicina de Valencia (IBV-CSIC) and CIBER de Enfermedades Raras (CIBERER), 46010 Valencia, Spain
| | - J Rafael Ciges-Tomas
- Instituto de Biomedicina de Valencia (IBV-CSIC) and CIBER de Enfermedades Raras (CIBERER), 46010 Valencia, Spain
| | - Christian Alite
- Instituto de Biomedicina de Valencia (IBV-CSIC) and CIBER de Enfermedades Raras (CIBERER), 46010 Valencia, Spain
| | - Janine Z Bowring
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, UK
| | - Suzanne Humphrey
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, UK
| | - José R Penadés
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, UK
| | - Alberto Marina
- Instituto de Biomedicina de Valencia (IBV-CSIC) and CIBER de Enfermedades Raras (CIBERER), 46010 Valencia, Spain
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Abstract
The development and application of a highly versatile suite of tools for mycobacterial genetics, coupled with widespread use of "omics" approaches to elucidate the structure, function, and regulation of mycobacterial proteins, has led to spectacular advances in our understanding of the metabolism and physiology of mycobacteria. In this article, we provide an update on nucleotide metabolism and DNA replication in mycobacteria, highlighting key findings from the past 10 to 15 years. In the first section, we focus on nucleotide metabolism, ranging from the biosynthesis, salvage, and interconversion of purine and pyrimidine ribonucleotides to the formation of deoxyribonucleotides. The second part of the article is devoted to DNA replication, with a focus on replication initiation and elongation, as well as DNA unwinding. We provide an overview of replication fidelity and mutation rates in mycobacteria and summarize evidence suggesting that DNA replication occurs during states of low metabolic activity, and conclude by suggesting directions for future research to address key outstanding questions. Although this article focuses primarily on observations from Mycobacterium tuberculosis, it is interspersed, where appropriate, with insights from, and comparisons with, other mycobacterial species as well as better characterized bacterial models such as Escherichia coli. Finally, a common theme underlying almost all studies of mycobacterial metabolism is the potential to identify and validate functions or pathways that can be exploited for tuberculosis drug discovery. In this context, we have specifically highlighted those processes in mycobacterial DNA replication that might satisfy this critical requirement.
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Evidence-Based Structural Model of the Staphylococcal Repressor Protein: Separation of Functions into Different Domains. PLoS One 2015; 10:e0139086. [PMID: 26414067 PMCID: PMC4634304 DOI: 10.1371/journal.pone.0139086] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 09/09/2015] [Indexed: 12/05/2022] Open
Abstract
Horizontal transfer of mobile genetic elements within Staphylococci is of high biomedical significance as such elements are frequently responsible for virulence and toxic effects. Staphylococcus-encoded repressor proteins regulate the replication of these mobile genetic elements that are located within the so-called pathogenicity islands. Here, we report structural and functional characterization of one such repressor protein, namely the Stl protein encoded by the pathogenicity island SaPIbov1. We create a 3D structural model and based on this prediction, we investigate the different functionalities of truncated and point mutant constructs. Results suggest that a helix-turn-helix motif governs the interaction of the Stl protein with its cognate DNA site: point mutations within this motif drastically decrease DNA-binding ability, whereas the interaction with the Stl-binding partner protein dUTPase is unperturbed by these point mutations. The 3D model also suggested the potential independent folding of a carboxy-terminal domain. This suggestion was fully verified by independent experiments revealing that the carboxy-terminal domain does not bind to DNA but is still capable of binding to and inhibiting dUTPase. A general model is proposed, which suggests that among the several structurally different repressor superfamilies Stl-like Staphylococcal repressor proteins belong to the helix-turn-helix transcription factor group and the HTH motif is suggested to reside within N-terminal segment.
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Róna G, Borsos M, Ellis JJ, Mehdi AM, Christie M, Környei Z, Neubrandt M, Tóth J, Bozóky Z, Buday L, Madarász E, Bodén M, Kobe B, Vértessy BG. Dynamics of re-constitution of the human nuclear proteome after cell division is regulated by NLS-adjacent phosphorylation. Cell Cycle 2015; 13:3551-64. [PMID: 25483092 DOI: 10.4161/15384101.2014.960740] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Phosphorylation by the cyclin-dependent kinase 1 (Cdk1) adjacent to nuclear localization signals (NLSs) is an important mechanism of regulation of nucleocytoplasmic transport. However, no systematic survey has yet been performed in human cells to analyze this regulatory process, and the corresponding cell-cycle dynamics have not yet been investigated. Here, we focused on the human proteome and found that numerous proteins, previously not identified in this context, are associated with Cdk1-dependent phosphorylation sites adjacent to their NLSs. Interestingly, these proteins are involved in key regulatory events of DNA repair, epigenetics, or RNA editing and splicing. This finding indicates that cell-cycle dependent events of genome editing and gene expression profiling may be controlled by nucleocytoplasmic trafficking. For in-depth investigations, we selected a number of these proteins and analyzed how point mutations, expected to modify the phosphorylation ability of the NLS segments, perturb nucleocytoplasmic localization. In each case, we found that mutations mimicking hyper-phosphorylation abolish nuclear import processes. To understand the mechanism underlying these phenomena, we performed a video microscopy-based kinetic analysis to obtain information on cell-cycle dynamics on a model protein, dUTPase. We show that the NLS-adjacent phosphorylation by Cdk1 of human dUTPase, an enzyme essential for genomic integrity, results in dynamic cell cycle-dependent distribution of the protein. Non-phosphorylatable mutants have drastically altered protein re-import characteristics into the nucleus during the G1 phase. Our results suggest a dynamic Cdk1-driven mechanism of regulation of the nuclear proteome composition during the cell cycle.
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Key Words
- Cdc28, cyclin-dependent protein kinase (Cdk) encoded by CDC28
- Cdk1, cyclin-dependent kinase 1
- GO, gene ontology
- NES, nuclear export signal
- NLS, nuclear localization signal
- SNP, single nucleotide polymorphisms
- SV40, Simian virus 40
- UBA1, Ubiquitin-activating enzyme E1
- UNG2, Human Uracil-DNA glycosylase 2
- cNLS, classical nuclear localization signal
- cell cycle
- dNTP, deoxyribonucleotide triphosphate
- dTTP, deoxythymidine triphosphate
- dUMP, deoxyuridine monophosphate
- dUTP, deoxyuridine triphosphate
- dUTPase
- importin
- phosphorylation
- trafficking
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Affiliation(s)
- Gergely Róna
- a Institute of Enzymology; RCNS; Hungarian Academy of Sciences ; Budapest , Hungary
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28
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Hirmondó R, Szabó JE, Nyíri K, Tarjányi S, Dobrotka P, Tóth J, Vértessy BG. Cross-species inhibition of dUTPase via the Staphylococcal Stl protein perturbs dNTP pool and colony formation in Mycobacterium. DNA Repair (Amst) 2015; 30:21-7. [PMID: 25841100 DOI: 10.1016/j.dnarep.2015.03.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 03/09/2015] [Accepted: 03/11/2015] [Indexed: 12/11/2022]
Abstract
Proteins responsible for the integrity of the genome are often used targets in drug therapies against various diseases. The inhibitors of these proteins are also important to study the pathways in genome integrity maintenance. A prominent example is Ugi, a well known cross-species inhibitor protein of the enzyme uracil-DNA glycosylase, responsible for uracil excision from DNA. Here, we report that a Staphylococcus pathogenicity island repressor protein called StlSaPIbov1 (Stl) exhibits potent dUTPase inhibition in Mycobacteria. To our knowledge, this is the first indication of a cross-species inhibitor protein for any dUTPase. We demonstrate that the Staphylococcus aureus Stl and the Mycobacterium tuberculosis dUTPase form a stable complex and that in this complex, the enzymatic activity of dUTPase is strongly inhibited. We also found that the expression of the Stl protein in Mycobacterium smegmatis led to highly increased cellular dUTP levels in the mycobacterial cell, this effect being in agreement with its dUTPase inhibitory role. In addition, Stl expression in M. smegmatis drastically decreased colony forming ability, as well, indicating significant perturbation of the phenotype. Therefore, we propose that Stl can be considered to be a cross-species dUTPase inhibitor and may be used as an important reagent in dUTPase inhibition experiments either in vitro/in situ or in vivo.
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Affiliation(s)
- Rita Hirmondó
- Institute of Enzymology, Research Centre for Natural Sciences (RCNS), Hungarian Academy of Sciences, Budapest, Hungary.
| | - Judit E Szabó
- Institute of Enzymology, Research Centre for Natural Sciences (RCNS), Hungarian Academy of Sciences, Budapest, Hungary; Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, Hungary
| | - Kinga Nyíri
- Institute of Enzymology, Research Centre for Natural Sciences (RCNS), Hungarian Academy of Sciences, Budapest, Hungary; Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, Hungary
| | - Szilvia Tarjányi
- Institute of Enzymology, Research Centre for Natural Sciences (RCNS), Hungarian Academy of Sciences, Budapest, Hungary
| | - Paula Dobrotka
- Institute of Enzymology, Research Centre for Natural Sciences (RCNS), Hungarian Academy of Sciences, Budapest, Hungary; Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, Hungary
| | - Judit Tóth
- Institute of Enzymology, Research Centre for Natural Sciences (RCNS), Hungarian Academy of Sciences, Budapest, Hungary
| | - Beáta G Vértessy
- Institute of Enzymology, Research Centre for Natural Sciences (RCNS), Hungarian Academy of Sciences, Budapest, Hungary; Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, Hungary.
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Nagy GN, Leveles I, Vértessy BG. Preventive DNA repair by sanitizing the cellular (deoxy)nucleoside triphosphate pool. FEBS J 2014; 281:4207-23. [PMID: 25052017 DOI: 10.1111/febs.12941] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2014] [Revised: 07/01/2014] [Accepted: 07/16/2014] [Indexed: 01/24/2023]
Abstract
The occurrence of modified bases in DNA is attributed to some major factors: incorporation of altered nucleotide building blocks and chemical reactions or radiation effects on bases within the DNA structure. Several enzyme families are involved in preventing the incorporation of noncanonical bases playing a 'sanitizing' role. The catalytic mechanism of action of these enzymes has been revealed for a number of representatives in clear structural and kinetic detail. In this review, we focus in detail on those examples where clear evidence has been produced using high-resolution structural studies. Comparing the protein fold and architecture of the enzyme active sites, two main classes of sanitizing deoxyribonucleoside triphosphate pyrophosphatases can be assigned that are distinguished by the site of nucleophilic attack. In enzymes associated with attack at the α-phosphorus, it is shown that coordination of the γ-phosphate group is also ensured by multiple interactions. By contrast, enzymes catalyzing attack at the β-phosphorus atom mainly coordinate the α- and the β-phosphate only. Characteristic differences are also observed with respect to the role of the metal ion cofactor (Mg(2+) ) and the coordination of nucleophilic water. Using different catalytic mechanisms embedded in different protein folds, these enzymes present a clear example of convergent evolution.
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Affiliation(s)
- Gergely N Nagy
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary; Department of Applied Biotechnology and Food Science, Budapest University of Technology and Economics, Hungary
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Voronin N, Herzig E, Hizi A. The dUTPase-related gene of bovine immunodeficiency virus is critical for viral replication, despite the lack of dUTPase activity of the encoded protein. Retrovirology 2014; 11:60. [PMID: 25117862 PMCID: PMC4261571 DOI: 10.1186/1742-4690-11-60] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Accepted: 07/09/2014] [Indexed: 01/03/2023] Open
Abstract
Background Deoxyuridine 5′-triphosphate nucleotide-hydrolases (dUTPases) are essential for maintaining low intra-cellular dUTP/dTTP ratios. Therefore, many viruses encode this enzyme to prevent dUTP incorporation into their genomes instead of dTTP. Among the lentiviruses, the non-primate viruses express dUTPases. In bovine immunodeficiency virus (BIV), the putative dUTPase protein is only 74 residues-long, compared to ~130 residues in other lentiviruses. Results In this study, the recombinant BIV dUTPase, as well as infectious wild-type (WT) BIV virions, were shown to lack any detectable dUTPase activity. Controls of recombinant dUTPase from equine infectious anemia virus (EIAV) or of EIAV virions showed substantial dUTPase activities. To assess the importance of the dUTPase to BIV replication, we have generated virions of WT BIV or BIV with mutations in the dUTPase gene. The two mutant viral dUTPases were the double mutant D48E/N57S (in the putative enzyme active site and its vicinity) and a deletion of 36 residues. In dividing Cf2Th cells and under conditions where the WT virus was infectious and generated progeny virions, both mutant viruses were defective, as no progeny viruses were generated. Analyses of the integrated viral cDNA showed that cells infected with the mutant virions carry in their genomic DNA levels of integrated BIV DNA that are comparable to those in WT BIV-infected cells. Conclusions The herby presented results show that the two BIV mutants with the modified dUTPase gene could infect cells, as viral cDNA was synthesized and integrated into the host cell DNA. However, no virions were generated by cells infected by these mutants. The most likely explanation is that either the integrated cDNA of the mutants is defective (due to potential multiple mutations, introduced during reverse-transcription) or that the original dUTPase mutations have led to severe blocks in viral replication at steps post integration. These results emphasize the importance of the dUTPase-related sequence to BIV replication, despite the lack of any detectable catalytic activity. Electronic supplementary material The online version of this article (doi:10.1186/1742-4690-11-60) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | - Amnon Hizi
- Department of Cell and Developmental Biology, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
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Reply. Retina 2014; 34:e21-2. [DOI: 10.1097/iae.0000000000000303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Qiu J, Ma Y, Owusu L, Jiang T, Xin Y. Functional analysis of serine acetyltransferase from Mycobacterium smegmatis. J Basic Microbiol 2014; 54:670-7. [PMID: 24652708 DOI: 10.1002/jobm.201300858] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Accepted: 02/07/2014] [Indexed: 11/08/2022]
Abstract
Serine acetyltransferase (CysE) is involved in L-cysteine biosynthesis in Mycobacterium, and it is important for the self-defense mechanism of the bacteria. Mycobacterium tuberculosis CysE (Rv2335) has been identified as a serine acetyltransferase, and it is orthologous to Mycobacterium smegmatis MSMEG_5947. In this study, the MSMEG_5947 gene was cloned, expressed, and identified as a serine acetyltransferase. To investigate the function of M. smegmatis CysE, a MSMEG_5947 knockout mutant strain (M. sm-ΔM_5947) was generated through homologous recombination. The growth and morphological characteristics of this strain were studied using growth curves and electron microscopy, respectively. M. sm-ΔM_5947 grew slower than M. smegmatis mc(2) 155. Electron microscopy revealed that the lack of the M. smegmatis CysE protein caused drastic morphological changes. Therefore, deletion of the serine acetyltransferase retards the growth of the Mycobacterium, but serine acetyltransferase expression is not essential for the survival of the bacteria.
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Affiliation(s)
- Juanjuan Qiu
- Centralab, the First Affiliated Hospital of Dalian Medical University, Dalian, China
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Migliardo F, Salmeron C, Bayan N. Mobility and temperature resistance of trehalose mycolates as key characteristics of the outer membrane ofMycobacterium tuberculosis. J Biomol Struct Dyn 2014; 33:447-59. [DOI: 10.1080/07391102.2014.887032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Barabás O, Németh V, Bodor A, Perczel A, Rosta E, Kele Z, Zagyva I, Szabadka Z, Grolmusz VI, Wilmanns M, Vértessy BG. Catalytic mechanism of α-phosphate attack in dUTPase is revealed by X-ray crystallographic snapshots of distinct intermediates, 31P-NMR spectroscopy and reaction path modelling. Nucleic Acids Res 2013; 41:10542-55. [PMID: 23982515 PMCID: PMC3905902 DOI: 10.1093/nar/gkt756] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2013] [Revised: 07/29/2013] [Accepted: 07/31/2013] [Indexed: 12/26/2022] Open
Abstract
Enzymatic synthesis and hydrolysis of nucleoside phosphate compounds play a key role in various biological pathways, like signal transduction, DNA synthesis and metabolism. Although these processes have been studied extensively, numerous key issues regarding the chemical pathway and atomic movements remain open for many enzymatic reactions. Here, using the Mason-Pfizer monkey retrovirus dUTPase, we study the dUTPase-catalyzed hydrolysis of dUTP, an incorrect DNA building block, to elaborate the mechanistic details at high resolution. Combining mass spectrometry analysis of the dUTPase-catalyzed reaction carried out in and quantum mechanics/molecular mechanics (QM/MM) simulation, we show that the nucleophilic attack occurs at the α-phosphate site. Phosphorus-31 NMR spectroscopy ((31)P-NMR) analysis confirms the site of attack and shows the capability of dUTPase to cleave the dUTP analogue α,β-imido-dUTP, containing the imido linkage usually regarded to be non-hydrolyzable. We present numerous X-ray crystal structures of distinct dUTPase and nucleoside phosphate complexes, which report on the progress of the chemical reaction along the reaction coordinate. The presently used combination of diverse structural methods reveals details of the nucleophilic attack and identifies a novel enzyme-product complex structure.
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Affiliation(s)
- Orsolya Barabás
- Laboratory of Genome Metabolism, Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest H-1113, Hungary, Laboratory of Molecular Biology, NIDDK, NIH, Bethesda, MD 20892, USA, Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg D-69117, Germany, Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Budapest H-1117, Hungary, Protein Modelling Group MTA-ELTE, Institute of Chemistry, Eötvös Loránd University, Budapest H-1117, Hungary, Department of Chemistry, King's College London, London, SE1 1UL, UK, Department of Medical Chemistry, University of Szeged, Hungary, Department of Computer Science, Eötvös Loránd University, Budapest, Hungary, European Molecular Biology Laboratory, Hamburg Outstation, Hamburg D-22603, Germany and Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, Hungary
| | - Veronika Németh
- Laboratory of Genome Metabolism, Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest H-1113, Hungary, Laboratory of Molecular Biology, NIDDK, NIH, Bethesda, MD 20892, USA, Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg D-69117, Germany, Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Budapest H-1117, Hungary, Protein Modelling Group MTA-ELTE, Institute of Chemistry, Eötvös Loránd University, Budapest H-1117, Hungary, Department of Chemistry, King's College London, London, SE1 1UL, UK, Department of Medical Chemistry, University of Szeged, Hungary, Department of Computer Science, Eötvös Loránd University, Budapest, Hungary, European Molecular Biology Laboratory, Hamburg Outstation, Hamburg D-22603, Germany and Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, Hungary
| | - Andrea Bodor
- Laboratory of Genome Metabolism, Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest H-1113, Hungary, Laboratory of Molecular Biology, NIDDK, NIH, Bethesda, MD 20892, USA, Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg D-69117, Germany, Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Budapest H-1117, Hungary, Protein Modelling Group MTA-ELTE, Institute of Chemistry, Eötvös Loránd University, Budapest H-1117, Hungary, Department of Chemistry, King's College London, London, SE1 1UL, UK, Department of Medical Chemistry, University of Szeged, Hungary, Department of Computer Science, Eötvös Loránd University, Budapest, Hungary, European Molecular Biology Laboratory, Hamburg Outstation, Hamburg D-22603, Germany and Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, Hungary
| | - András Perczel
- Laboratory of Genome Metabolism, Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest H-1113, Hungary, Laboratory of Molecular Biology, NIDDK, NIH, Bethesda, MD 20892, USA, Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg D-69117, Germany, Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Budapest H-1117, Hungary, Protein Modelling Group MTA-ELTE, Institute of Chemistry, Eötvös Loránd University, Budapest H-1117, Hungary, Department of Chemistry, King's College London, London, SE1 1UL, UK, Department of Medical Chemistry, University of Szeged, Hungary, Department of Computer Science, Eötvös Loránd University, Budapest, Hungary, European Molecular Biology Laboratory, Hamburg Outstation, Hamburg D-22603, Germany and Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, Hungary
| | - Edina Rosta
- Laboratory of Genome Metabolism, Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest H-1113, Hungary, Laboratory of Molecular Biology, NIDDK, NIH, Bethesda, MD 20892, USA, Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg D-69117, Germany, Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Budapest H-1117, Hungary, Protein Modelling Group MTA-ELTE, Institute of Chemistry, Eötvös Loránd University, Budapest H-1117, Hungary, Department of Chemistry, King's College London, London, SE1 1UL, UK, Department of Medical Chemistry, University of Szeged, Hungary, Department of Computer Science, Eötvös Loránd University, Budapest, Hungary, European Molecular Biology Laboratory, Hamburg Outstation, Hamburg D-22603, Germany and Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, Hungary
| | - Zoltán Kele
- Laboratory of Genome Metabolism, Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest H-1113, Hungary, Laboratory of Molecular Biology, NIDDK, NIH, Bethesda, MD 20892, USA, Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg D-69117, Germany, Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Budapest H-1117, Hungary, Protein Modelling Group MTA-ELTE, Institute of Chemistry, Eötvös Loránd University, Budapest H-1117, Hungary, Department of Chemistry, King's College London, London, SE1 1UL, UK, Department of Medical Chemistry, University of Szeged, Hungary, Department of Computer Science, Eötvös Loránd University, Budapest, Hungary, European Molecular Biology Laboratory, Hamburg Outstation, Hamburg D-22603, Germany and Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, Hungary
| | - Imre Zagyva
- Laboratory of Genome Metabolism, Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest H-1113, Hungary, Laboratory of Molecular Biology, NIDDK, NIH, Bethesda, MD 20892, USA, Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg D-69117, Germany, Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Budapest H-1117, Hungary, Protein Modelling Group MTA-ELTE, Institute of Chemistry, Eötvös Loránd University, Budapest H-1117, Hungary, Department of Chemistry, King's College London, London, SE1 1UL, UK, Department of Medical Chemistry, University of Szeged, Hungary, Department of Computer Science, Eötvös Loránd University, Budapest, Hungary, European Molecular Biology Laboratory, Hamburg Outstation, Hamburg D-22603, Germany and Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, Hungary
| | - Zoltán Szabadka
- Laboratory of Genome Metabolism, Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest H-1113, Hungary, Laboratory of Molecular Biology, NIDDK, NIH, Bethesda, MD 20892, USA, Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg D-69117, Germany, Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Budapest H-1117, Hungary, Protein Modelling Group MTA-ELTE, Institute of Chemistry, Eötvös Loránd University, Budapest H-1117, Hungary, Department of Chemistry, King's College London, London, SE1 1UL, UK, Department of Medical Chemistry, University of Szeged, Hungary, Department of Computer Science, Eötvös Loránd University, Budapest, Hungary, European Molecular Biology Laboratory, Hamburg Outstation, Hamburg D-22603, Germany and Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, Hungary
| | - Vince I. Grolmusz
- Laboratory of Genome Metabolism, Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest H-1113, Hungary, Laboratory of Molecular Biology, NIDDK, NIH, Bethesda, MD 20892, USA, Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg D-69117, Germany, Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Budapest H-1117, Hungary, Protein Modelling Group MTA-ELTE, Institute of Chemistry, Eötvös Loránd University, Budapest H-1117, Hungary, Department of Chemistry, King's College London, London, SE1 1UL, UK, Department of Medical Chemistry, University of Szeged, Hungary, Department of Computer Science, Eötvös Loránd University, Budapest, Hungary, European Molecular Biology Laboratory, Hamburg Outstation, Hamburg D-22603, Germany and Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, Hungary
| | - Matthias Wilmanns
- Laboratory of Genome Metabolism, Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest H-1113, Hungary, Laboratory of Molecular Biology, NIDDK, NIH, Bethesda, MD 20892, USA, Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg D-69117, Germany, Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Budapest H-1117, Hungary, Protein Modelling Group MTA-ELTE, Institute of Chemistry, Eötvös Loránd University, Budapest H-1117, Hungary, Department of Chemistry, King's College London, London, SE1 1UL, UK, Department of Medical Chemistry, University of Szeged, Hungary, Department of Computer Science, Eötvös Loránd University, Budapest, Hungary, European Molecular Biology Laboratory, Hamburg Outstation, Hamburg D-22603, Germany and Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, Hungary
| | - Beáta G. Vértessy
- Laboratory of Genome Metabolism, Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest H-1113, Hungary, Laboratory of Molecular Biology, NIDDK, NIH, Bethesda, MD 20892, USA, Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg D-69117, Germany, Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Budapest H-1117, Hungary, Protein Modelling Group MTA-ELTE, Institute of Chemistry, Eötvös Loránd University, Budapest H-1117, Hungary, Department of Chemistry, King's College London, London, SE1 1UL, UK, Department of Medical Chemistry, University of Szeged, Hungary, Department of Computer Science, Eötvös Loránd University, Budapest, Hungary, European Molecular Biology Laboratory, Hamburg Outstation, Hamburg D-22603, Germany and Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, Hungary
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Leveles I, Németh V, Szabó JE, Harmat V, Nyíri K, Bendes ÁÁ, Papp-Kádár V, Zagyva I, Róna G, Ozohanics O, Vékey K, Tóth J, Vértessy BG. Structure and enzymatic mechanism of a moonlighting dUTPase. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:2298-308. [PMID: 24311572 DOI: 10.1107/s0907444913021136] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Accepted: 07/29/2013] [Indexed: 02/08/2023]
Abstract
Genome integrity requires well controlled cellular pools of nucleotides. dUTPases are responsible for regulating cellular dUTP levels and providing dUMP for dTTP biosynthesis. In Staphylococcus, phage dUTPases are also suggested to be involved in a moonlighting function regulating the expression of pathogenicity-island genes. Staphylococcal phage trimeric dUTPase sequences include a specific insertion that is not found in other organisms. Here, a 2.1 Å resolution three-dimensional structure of a ϕ11 phage dUTPase trimer with complete localization of the phage-specific insert, which folds into a small β-pleated mini-domain reaching out from the dUTPase core surface, is presented. The insert mini-domains jointly coordinate a single Mg2+ ion per trimer at the entrance to the threefold inner channel. Structural results provide an explanation for the role of Asp95, which is suggested to have functional significance in the moonlighting activity, as the metal-ion-coordinating moiety potentially involved in correct positioning of the insert. Enzyme-kinetics studies of wild-type and mutant constructs show that the insert has no major role in dUTP binding or cleavage and provide a description of the elementary steps (fast binding of substrate and release of products). In conclusion, the structural and kinetic data allow insights into both the phage-specific characteristics and the generally conserved traits of ϕ11 phage dUTPase.
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Affiliation(s)
- Ibolya Leveles
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, 29 Karolina Street, 1113 Budapest, Hungary
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36
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Róna G, Marfori M, Borsos M, Scheer I, Takács E, Tóth J, Babos F, Magyar A, Erdei A, Bozóky Z, Buday L, Kobe B, Vértessy BG. Phosphorylation adjacent to the nuclear localization signal of human dUTPase abolishes nuclear import: structural and mechanistic insights. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:2495-505. [PMID: 24311590 DOI: 10.1107/s0907444913023354] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Accepted: 08/19/2013] [Indexed: 01/12/2024]
Abstract
Phosphorylation adjacent to nuclear localization signals (NLSs) is involved in the regulation of nucleocytoplasmic transport. The nuclear isoform of human dUTPase, an enzyme that is essential for genomic integrity, has been shown to be phosphorylated on a serine residue (Ser11) in the vicinity of its nuclear localization signal; however, the effect of this phosphorylation is not yet known. To investigate this issue, an integrated set of structural, molecular and cell biological methods were employed. It is shown that NLS-adjacent phosphorylation of dUTPase occurs during the M phase of the cell cycle. Comparison of the cellular distribution of wild-type dUTPase with those of hyperphosphorylation- and hypophosphorylation-mimicking mutants suggests that phosphorylation at Ser11 leads to the exclusion of dUTPase from the nucleus. Isothermal titration microcalorimetry and additional independent biophysical techniques show that the interaction between dUTPase and importin-α, the karyopherin molecule responsible for `classical' NLS binding, is weakened significantly in the case of the S11E hyperphosphorylation-mimicking mutant. The structures of the importin-α-wild-type and the importin-α-hyperphosphorylation-mimicking dUTPase NLS complexes provide structural insights into the molecular details of this regulation. The data indicate that the post-translational modification of dUTPase during the cell cycle may modulate the nuclear availability of this enzyme.
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Affiliation(s)
- Gergely Róna
- Institute of Enzymology, RCNS, Hungarian Academy of Sciences, 1113 Budapest, Hungary
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37
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Migliardo F, Salmeron C, Bayan N. A neutron scattering study on the stability of trehalose mycolates under thermal stress. Chem Phys 2013. [DOI: 10.1016/j.chemphys.2012.12.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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38
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García-Nafría J, Timm J, Harrison C, Turkenburg JP, Wilson KS. Tying down the arm in Bacillus dUTPase: structure and mechanism. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:1367-80. [PMID: 23897460 DOI: 10.1107/s090744491300735x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Accepted: 03/18/2013] [Indexed: 03/07/2023]
Abstract
Homotrimeric dUTPases contain three active sites, each formed by five conserved sequence motifs originating from all three subunits. The essential fifth motif lies in a flexible C-terminal arm which becomes ordered during catalysis and is disordered in most crystal structures. Previously, it has been shown that the two Bacillus subtilis dUTPases, YncF and YosS, differ from their orthologues in the position in the sequence of the essential Phe-lid residue, which stacks against the uracil base, and in the conformation of the general base aspartate, which points away from the active site. Here, three structures of the complex of YncF with dU-PPi-Mg(2+) and the structure of YosS complexed with dUMP are reported. dU-PPi-Mg(2+) triggers the ordering of both the C-terminal arm and a loop (residues 18-26) which is uniquely disordered in the Bacillus dUTPases. The dUMP complex suggests two stages in substrate release. Limited proteolysis experiments allowed those complexes in which C-terminal cleavage is hindered and those in which it can be assumed to be ordered to be identified. The results lead to the suggestion that dUpNHpp is not a perfect substrate mimic, at least for the B. subtilis enzymes, and provide new insights into the mechanism of these two dUTPases in comparison to their orthologues. The enzyme mechanism is reviewed using the present and previous crystal structures as snapshots along the reaction coordinate.
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Affiliation(s)
- Javier García-Nafría
- Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, England
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39
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dUTPases, the unexplored family of signalling molecules. Curr Opin Microbiol 2013; 16:163-70. [PMID: 23541339 DOI: 10.1016/j.mib.2013.02.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Revised: 02/14/2013] [Accepted: 02/23/2013] [Indexed: 11/23/2022]
Abstract
Deciphering the molecular mechanisms that control relevant cellular processes is of utmost importance to understand how viruses, prokaryotic and eukaryotic cells work. The diversity of living organisms suggests that there are novel regulators still to be discovered, which may uncover new regulatory paradigms. dUTPases (Duts) are assumed to be ubiquitous enzymes regulating cellular dUTP levels to prevent misincorporation of uracil into DNA. Recently however, Duts have been involved in the control of several relevant cellular processes, including transfer of mobile genetic elements, regulation of the immune system, autoimmunity or apoptosis, suggesting that they perform regulatory functions. This review aims at investigating the unexplored impact of Duts as novel signalling molecules.
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Tormo-Más M, Donderis J, García-Caballer M, Alt A, Mir-Sanchis I, Marina A, Penadés J. Phage dUTPases Control Transfer of Virulence Genes by a Proto-Oncogenic G Protein-like Mechanism. Mol Cell 2013; 49:947-58. [DOI: 10.1016/j.molcel.2012.12.013] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Revised: 12/05/2012] [Accepted: 12/14/2012] [Indexed: 01/04/2023]
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