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Ruseva N, Atanasova M, Sbirkova-Dimitrova H, Marković A, Šmelcerović Ž, Šmelcerović A, Cherneva E, Bakalova A. Chloro-substituted pyridine squaramates as new DNase I inhibitors: Synthesis, structural characterization, in vitro evaluation and molecular docking studies. Chem Biol Interact 2023; 386:110772. [PMID: 37898285 DOI: 10.1016/j.cbi.2023.110772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 10/08/2023] [Accepted: 10/16/2023] [Indexed: 10/30/2023]
Abstract
Having continued our recent study on the synthesis and DNase I inhibition of several monosquaramides, two new chloro-substituted pyridine squaramates were synthesized and their structure was identified by X-ray. Their inhibitory properties towards deoxyribonuclease I (DNase I) and xanthine oxidase (XO) were evaluated in vitro. 3-(((6-Chloropyridin-3-yl)methyl)amino)-4-ethoxycyclobut-3-ene-1,2-dione (compound 3a) inhibited DNase I with an IC50 value of 43.82 ± 6.51 μM, thus standing out as one of the most potent small organic DNase I inhibitors tested to date. No cytotoxicity to human tumor cell lines (HL-60, MDA-MB-231 and MCF-7) was observed for the tested compounds. In order to investigate the drug-likeness of the squaramates, the ADME profile and pharmacokinetic properties were evaluated. Molecular docking was performed to reveal the binding mode of the studied compounds on DNase I.
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Affiliation(s)
- Nina Ruseva
- Department of Chemistry, Faculty of Pharmacy, Medical University of Sofia, 2 Dunav Str., 1000, Sofia, Bulgaria
| | - Mariyana Atanasova
- Department of Chemistry, Faculty of Pharmacy, Medical University of Sofia, 2 Dunav Str., 1000, Sofia, Bulgaria
| | - Hristina Sbirkova-Dimitrova
- Institute of Mineralogy and Crystallography "Akad. Ivan Kostov", Bulgarian Academy of Sciences, Acad. G. Bonchev Bl. 107, 1113, Sofia, Bulgaria
| | - Ana Marković
- Department of Pharmacy, Faculty of Medicine, University of Niš, Bulevar Zorana Ðindića 81, 18000, Niš, Serbia
| | - Žaklina Šmelcerović
- Center for Biomedicinal Science, Faculty of Medicine, University of Niš, Bulevar Zorana Ðindića 81, 18000, Niš, Serbia
| | - Andrija Šmelcerović
- Department of Chemistry, Faculty of Medicine, University of Niš, Bulevar Zorana Ðindića 81, 18000, Niš, Serbia.
| | - Emiliya Cherneva
- Department of Chemistry, Faculty of Pharmacy, Medical University of Sofia, 2 Dunav Str., 1000, Sofia, Bulgaria; Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Build. 9, 1113, Sofia, Bulgaria
| | - Adriana Bakalova
- Department of Chemistry, Faculty of Pharmacy, Medical University of Sofia, 2 Dunav Str., 1000, Sofia, Bulgaria.
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Ruseva N, Sbirkova-Dimitrova H, Atanasova M, Marković A, Šmelcerović Ž, Šmelcerović A, Bakalova A, Cherneva E. Synthesis and DNase I Inhibitory Properties of New Squaramides. Molecules 2023; 28:molecules28020538. [PMID: 36677597 PMCID: PMC9863136 DOI: 10.3390/molecules28020538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/19/2022] [Accepted: 12/25/2022] [Indexed: 01/09/2023] Open
Abstract
Three new monosquaramides (3a-c) were synthesized, characterized by IR, NMR and X-ray, and evaluated for inhibitory activity against deoxyribonuclease I (DNase I) and xanthine oxidase (XO) in vitro. The target compounds inhibited DNase I with IC50 values below 100 μM, being at the same time more potent DNase I inhibitors than crystal violet, used as a positive control. 3-Ethoxy-4-((1-(pyridin-3-yl)propan-2-yl)amino)cyclobut-3-ene-1,2-dione (3c) stood out as the most potent compound, exhibiting a slightly better IC50 value (48.04 ± 7.98 μM) compared to the other two compounds. In order to analyze potential binding sites for the studied compounds with DNase I, a molecular docking study was performed. Compounds 3a-c are among the most potent small organic DNase I inhibitors tested to date.
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Affiliation(s)
- Nina Ruseva
- Department of Chemistry, Faculty of Pharmacy, Medical University of Sofia, 2 Dunav Str., 1000 Sofia, Bulgaria
| | - Hristina Sbirkova-Dimitrova
- Institute of Mineralogy and Crystallography “Akad. Ivan Kostov”, Bulgarian Academy of Sciences, Acad. G. Bonchev Bl. 107, 1113 Sofia, Bulgaria
| | - Mariyana Atanasova
- Department of Chemistry, Faculty of Pharmacy, Medical University of Sofia, 2 Dunav Str., 1000 Sofia, Bulgaria
| | - Ana Marković
- Department of Pharmacy, Faculty of Medicine, University of Niš, Bulevar Zorana Đinđića 81, 18000 Niš, Serbia
| | - Žaklina Šmelcerović
- Center for Biomedicinal Science, Faculty of Medicine, University of Niš, Bulevar Zorana Đinđića 81, 18000 Niš, Serbia
| | - Andrija Šmelcerović
- Department of Chemistry, Faculty of Medicine, University of Niš, Bulevar Zorana Đinđića 81, 18000 Niš, Serbia
- Correspondence: (A.Š.); (E.C.)
| | - Adriana Bakalova
- Department of Chemistry, Faculty of Pharmacy, Medical University of Sofia, 2 Dunav Str., 1000 Sofia, Bulgaria
| | - Emiliya Cherneva
- Department of Chemistry, Faculty of Pharmacy, Medical University of Sofia, 2 Dunav Str., 1000 Sofia, Bulgaria
- Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Build. 9, 1113 Sofia, Bulgaria
- Correspondence: (A.Š.); (E.C.)
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McCord JJ, Engavale M, Masoumzadeh E, Villarreal J, Mapp B, Latham MP, Keyel PA, Sutton RB. Structural features of Dnase1L3 responsible for serum antigen clearance. Commun Biol 2022; 5:825. [PMID: 35974043 PMCID: PMC9381713 DOI: 10.1038/s42003-022-03755-5] [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: 11/09/2021] [Accepted: 07/22/2022] [Indexed: 11/09/2022] Open
Abstract
Autoimmunity develops when extracellular DNA released from dying cells is not cleared from serum. While serum DNA is primarily digested by Dnase1 and Dnase1L3, Dnase1 cannot rescue autoimmunity arising from Dnase1L3 deficiencies. Dnase1L3 uniquely degrades antigenic forms of cell-free DNA, including DNA complexed with lipids and proteins. The distinct activity of Dnase1L3 relies on its unique C-terminal Domain (CTD), but the mechanism is unknown. We used multiple biophysical techniques and functional assays to study the interplay between the core catalytic domain and the CTD. While the core domain resembles Dnase1, there are key structural differences between the two enzymes. First, Dnase1L3 is not inhibited by actin due to multiple differences in the actin recognition site. Second, the CTD augments the ability of the core to bind DNA, thereby facilitating the degradation of complexed DNA. Together, these structural insights will inform the development of Dnase1L3-based therapies for autoimmunity.
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Affiliation(s)
- Jon J McCord
- Texas Tech University Health Sciences Center, Dept of Cell Physiology and Molecular Biophysics, Lubbock, TX, USA
| | - Minal Engavale
- Texas Tech University, Dept. of Biological Sciences, Lubbock, TX, USA
| | - Elahe Masoumzadeh
- Texas Tech University, Dept. of Chemistry & Biochemistry, Lubbock, TX, USA
| | - Johanna Villarreal
- Texas Tech University Health Sciences Center, Dept of Cell Physiology and Molecular Biophysics, Lubbock, TX, USA
| | - Britney Mapp
- Texas Tech University, Dept. of Biological Sciences, Lubbock, TX, USA
| | - Michael P Latham
- Texas Tech University, Dept. of Chemistry & Biochemistry, Lubbock, TX, USA
| | - Peter A Keyel
- Texas Tech University, Dept. of Biological Sciences, Lubbock, TX, USA
| | - R Bryan Sutton
- Texas Tech University Health Sciences Center, Dept of Cell Physiology and Molecular Biophysics, Lubbock, TX, USA.
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Verhülsdonk L, Mannherz HG, Napirei M. Comparison of the secretory murine DNase1 family members expressed in Pichia pastoris. PLoS One 2021; 16:e0253476. [PMID: 34329318 PMCID: PMC8323900 DOI: 10.1371/journal.pone.0253476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 06/07/2021] [Indexed: 11/18/2022] Open
Abstract
Soluble nucleases of the deoxyribonuclease 1 (DNase1) family facilitate DNA and chromatin disposal (chromatinolysis) during certain forms of cell differentiation and death and participate in the suppression of anti-nuclear autoimmunity as well as thrombotic microangiopathies caused by aggregated neutrophil extracellular traps. Since a systematic and direct comparison of the specific activities and properties of the secretory DNase1 family members is still missing, we expressed and purified recombinant murine DNase1 (rmDNase1), DNase1-like 2 (rmDNase1L2) and DNase1-like 3 (rmDNase1L3) using Pichia pastoris. Employing different strategies for optimizing culture and purification conditions, we achieved yields of pure protein between ~3 mg/l (rmDNase1L2 and rmDNase1L3) and ~9 mg/l (rmDNase1) expression medium. Furthermore, we established a procedure for post-expressional maturation of pre-mature DNase still bound to an unprocessed tri-N-glycosylated pro-peptide of the yeast α-mating factor. We analyzed glycosylation profiles and determined specific DNase activities by the hyperchromicity assay. Additionally, we evaluated substrate specificities under various conditions at equimolar DNase isoform concentrations by lambda DNA and chromatin digestion assays in the presence and absence of heparin and monomeric skeletal muscle α-actin. Our results suggest that due to its biochemical properties mDNase1L2 can be regarded as an evolutionary intermediate isoform of mDNase1 and mDNase1L3. Consequently, our data show that the secretory DNase1 family members complement each other to achieve optimal DNA degradation and chromatinolysis under a broad spectrum of biological conditions.
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Affiliation(s)
- Lukas Verhülsdonk
- Department of Anatomy and Molecular Embryology, Medical Faculty, Ruhr-University Bochum, Bochum, Germany
| | - Hans Georg Mannherz
- Department of Anatomy and Molecular Embryology, Medical Faculty, Ruhr-University Bochum, Bochum, Germany.,Molecular and Experimental Cardiology, St. Josef-Hospital, Clinics of the Ruhr University Bochum, Bochum, Germany
| | - Markus Napirei
- Department of Anatomy and Molecular Embryology, Medical Faculty, Ruhr-University Bochum, Bochum, Germany
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Gajić M, Ilić BS, Bondžić BP, Džambaski Z, Kojić VV, Jakimov DS, Kocić G, Šmelcerović A. 1,2,3,4-Tetrahydroisoquinoline Derivatives as a Novel Deoxyribonuclease I Inhibitors. Chem Biodivers 2021; 18:e2100261. [PMID: 34170076 DOI: 10.1002/cbdv.202100261] [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: 04/02/2021] [Accepted: 06/25/2021] [Indexed: 12/11/2022]
Abstract
Herein we report an assessment of 24 1,2,3,4-tetrahydroisoquinoline derivatives for potential DNase I (deoxyribonuclease I) inhibitory properties in vitro. Four of them inhibited DNase I with IC50 values below 200 μM. The most potent was 1-(6,7-dimethoxy-1,2,3,4-tetrahydroisoquinolin-1-yl)propan-2-one (2) (IC50 =134.35±11.38 μM) exhibiting slightly better IC50 value compared to three other active compounds, 2-[2-(4-fluorophenyl)-1,2,3,4-tetrahydroisoquinolin-1-yl]-1-phenylethan-1-one (15) (IC50 =147.51±14.87 μM), 2-[2-(4-fluorophenyl)-1,2,3,4-tetrahydroisoquinolin-1-yl]cyclohexan-1-one (18) (IC50 =149.07±2.98 μM) and 2-[6,7-dimethoxy-2-(p-tolyl)-1,2,3,4-tetrahydroisoquinolin-1-yl]cyclohexan-1-one (22) (IC50 =148.31±2.96 μM). Cytotoxicity assessment of the active DNase I inhibitors revealed a lack of toxic effects on the healthy cell lines MRC-5. Molecular docking and molecular dynamics simulations suggest that interactions with Glu 39, His 134, Asn 170, Tyr 211, Asp 251 and His 252 are an important factor for inhibitors affinity toward the DNase I. Observed interactions would be beneficial for the discovery of new active 1,2,3,4-tetrahydroisoquinoline-based inhibitors of DNase I, but might also encourage researchers to further explore and utilize potential therapeutic application of DNase I inhibitors, based on a versatile role of DNase I during apoptotic cell death.
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Affiliation(s)
- Mihajlo Gajić
- University of Niš, Faculty of Medicine, Department of Pharmacy, Blvd. Dr. Zorana Đinđića 81, 18000, Niš, Serbia
| | - Budimir S Ilić
- University of Niš, Faculty of Medicine, Department of Chemistry, Blvd. Dr. Zorana Đinđića 81, 18000, Niš, Serbia
| | - Bojan P Bondžić
- University of Belgrade, Institute of Chemistry, Technology and Metallurgy, National Institute of the Republic of Serbia, Njegoševa 12, 11000, Belgrade, Serbia
| | - Zdravko Džambaski
- University of Belgrade, Institute of Chemistry, Technology and Metallurgy, National Institute of the Republic of Serbia, Njegoševa 12, 11000, Belgrade, Serbia
| | - Vesna V Kojić
- University of Novi Sad, Faculty of Medicine, Oncology Institute of Vojvodina, Put Dr. Goldmana 4, 21204, Sremska Kamenica, Serbia
| | - Dimitar S Jakimov
- University of Novi Sad, Faculty of Medicine, Oncology Institute of Vojvodina, Put Dr. Goldmana 4, 21204, Sremska Kamenica, Serbia
| | - Gordana Kocić
- University of Niš, Faculty of Medicine, Department of Biochemistry, Blvd. Dr. Zorana Đinđića 81, 18000, Niš, Serbia
| | - Andrija Šmelcerović
- University of Niš, Faculty of Medicine, Department of Chemistry, Blvd. Dr. Zorana Đinđića 81, 18000, Niš, Serbia
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Gajić M, Džambaski Z, Ilić BS, Kocić G, Bondžić BP, Šmelcerović A. Synthesis and analysis of 4-oxothiazolidines as potential dual inhibitors of deoxyribonuclease I and xanthine oxidase. Chem Biol Interact 2021; 345:109536. [PMID: 34058176 DOI: 10.1016/j.cbi.2021.109536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/16/2021] [Accepted: 05/24/2021] [Indexed: 10/21/2022]
Abstract
In this study, seven new 4-oxothiazolidine derivatives were synthesized and assayed, along 7 known derivatives, for inhibitory properties against deoxyribonuclease I (DNase I) and xanthine oxidase (XO) in vitro. Among tested compounds, (5Z)-Ethyl-2-(2-(cyanomethylene)-4-oxothiazolidin-5-yliden)acetate (6) exhibited inhibitory activity against both enzymes (DNase I IC50 = 67.94 ± 5.99 μM; XO IC50 = 98.98 ± 13.47 μM), therefore being the first reported dual inhibitor of DNase I and XO. Observed DNase I inhibition qualifies compound 6 as the most potent small organic DNase I inhibitor reported so far. Derivatives of 2-alkyliden-4-oxothiazolidinone (1) inhibited DNase I below 200 μM, while the other tested 4-oxothiazolidine derivatives remained inactive against both enzymes. The molecular docking and molecular dynamics simulations into the binding sites of DNase I and XO enzyme allowed us to clarify the binding modes of this 4-oxothiazolidine derivative, which might aid future development of dual DNase I and XO.
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Affiliation(s)
- Mihajlo Gajić
- University of Niš, Faculty of Medicine, Department of Pharmacy, Blvd. Dr. Zorana Đinđića 81, 18000, Niš, Serbia
| | - Zdravko Džambaski
- University of Belgrade, Institute of Chemistry, Technology and Metallurgy, National Institute of the Republic of Serbia, Njegoševa 12, 11000, Belgrade, Serbia
| | - Budimir S Ilić
- University of Niš, Faculty of Medicine, Department of Chemistry, Blvd. Dr. Zorana Đinđića 81, 18000, Niš, Serbia
| | - Gordana Kocić
- University of Niš, Faculty of Medicine, Department of Biochemistry, Blvd. Dr. Zorana Đinđića 81, 18000, Niš, Serbia
| | - Bojan P Bondžić
- University of Belgrade, Institute of Chemistry, Technology and Metallurgy, National Institute of the Republic of Serbia, Njegoševa 12, 11000, Belgrade, Serbia.
| | - Andrija Šmelcerović
- University of Niš, Faculty of Medicine, Department of Chemistry, Blvd. Dr. Zorana Đinđića 81, 18000, Niš, Serbia.
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Ilić BS, Gajić M, Bondžić BP, Džambaski Z, Kocić G, Šmelcerović A. Deoxyribonuclease I Inhibitory Properties, Molecular Docking and Molecular Dynamics Simulations of 1‐(Pyrrolidin‐2‐yl)propan‐2‐one Derivatives. Chem Biodivers 2021; 18:e2000996. [DOI: 10.1002/cbdv.202000996] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 02/02/2021] [Indexed: 12/20/2022]
Affiliation(s)
- Budimir S. Ilić
- University of Niš Faculty of Medicine, Department of Chemistry Blvd. Dr. Zorana Đinđića 81 18000 Niš Serbia
| | - Mihajlo Gajić
- University of Niš Faculty of Medicine, Department of Pharmacy Blvd. Dr. Zorana Đinđića 81 18000 Niš Serbia
| | - Bojan P. Bondžić
- University of Belgrade Institute of Chemistry, Technology and Metallurgy Njegoševa 12 11000 Belgrade Serbia
| | - Zdravko Džambaski
- University of Belgrade Institute of Chemistry, Technology and Metallurgy Njegoševa 12 11000 Belgrade Serbia
| | - Gordana Kocić
- University of Niš Faculty of Medicine, Department of Biochemistry Blvd. Dr. Zorana Đinđića 81 18000 Niš Serbia
| | - Andrija Šmelcerović
- University of Niš Faculty of Medicine, Department of Chemistry Blvd. Dr. Zorana Đinđića 81 18000 Niš Serbia
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Deoxyribonucleases and Their Applications in Biomedicine. Biomolecules 2020; 10:biom10071036. [PMID: 32664541 PMCID: PMC7407206 DOI: 10.3390/biom10071036] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/03/2020] [Accepted: 07/08/2020] [Indexed: 12/21/2022] Open
Abstract
Extracellular DNA, also called cell-free DNA, released from dying cells or activated immune cells can be recognized by the immune system as a danger signal causing or enhancing inflammation. The cleavage of extracellular DNA is crucial for limiting the inflammatory response and maintaining homeostasis. Deoxyribonucleases (DNases) as enzymes that degrade DNA are hypothesized to play a key role in this process as a determinant of the variable concentration of extracellular DNA. DNases are divided into two families-DNase I and DNase II, according to their biochemical and biological properties as well as the tissue-specific production. Studies have shown that low DNase activity is both, a biomarker and a pathogenic factor in systemic lupus erythematosus. Interventional experiments proved that administration of exogenous DNase has beneficial effects in inflammatory diseases. Recombinant human DNase reduces mucus viscosity in lungs and is used for the treatment of patients with cystic fibrosis. This review summarizes the currently available published data about DNases, their activity as a potential biomarker and methods used for their assessment. An overview of the experiments with systemic administration of DNase is also included. Whether low-plasma DNase activity is involved in the etiopathogenesis of diseases remains unknown and needs to be elucidated.
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Smelcerovic A, Zivkovic A, Ilic BS, Kolarevic A, Hofmann B, Steinhilber D, Stark H. 4-(4-Chlorophenyl)thiazol-2-amines as pioneers of potential neurodegenerative therapeutics with anti-inflammatory properties based on dual DNase I and 5-LO inhibition. Bioorg Chem 2020; 95:103528. [DOI: 10.1016/j.bioorg.2019.103528] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 12/16/2019] [Accepted: 12/19/2019] [Indexed: 11/25/2022]
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Synthesis and DNase I inhibitory properties of some 5,6,7,8-tetrahydrobenzo[4,5]thieno[2,3-d]pyrimidines. Bioorg Chem 2018; 80:693-705. [DOI: 10.1016/j.bioorg.2018.07.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 07/08/2018] [Accepted: 07/09/2018] [Indexed: 12/11/2022]
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Kolarević A, Ilić BS, Kocić G, Džambaski Z, Šmelcerović A, Bondžić BP. Synthesis and DNase I inhibitory properties of some 4‐thiazolidinone derivatives. J Cell Biochem 2018; 120:264-274. [DOI: 10.1002/jcb.27339] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Accepted: 06/27/2018] [Indexed: 01/10/2023]
Affiliation(s)
- Ana Kolarević
- Department of Pharmacy Faculty of Medicine, University of Niš Niš Serbia
| | - Budimir S. Ilić
- Department of Chemistry Faculty of Medicine, University of Niš Niš Serbia
| | - Gordana Kocić
- Department of Biochemistry, Faculty of Medicine, University of Niš Niš Serbia
| | | | | | - Bojan P. Bondžić
- Center for Chemistry ICTM, University of Belgrade Belgrade Serbia
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12
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Kolarević A, Ilić BS, Anastassova N, Mavrova AT, Yancheva D, Kocić G, Šmelcerović A. Benzimidazoles as novel deoxyribonuclease I inhibitors. J Cell Biochem 2018; 119:8937-8948. [DOI: 10.1002/jcb.27147] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Accepted: 05/18/2018] [Indexed: 11/07/2022]
Affiliation(s)
- Ana Kolarević
- Department of Pharmacy Faculty of Medicine, University of Niš Niš Serbia
| | - Budimir S. Ilić
- Department of Chemistry Faculty of Medicine, University of Niš Niš Serbia
| | - Neda Anastassova
- 3Laboratory of Structural Organic Analysis, Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences Sofia Bulgaria
| | - Anelia Ts. Mavrova
- Department of Organic Synthesis, University of Chemical Technology and Metallurgy Sofia Bulgaria
| | - Denitsa Yancheva
- 3Laboratory of Structural Organic Analysis, Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences Sofia Bulgaria
| | - Gordana Kocić
- Department of Biochemistry, Faculty of Medicine, University of Niš Niš Serbia
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Ilić BS, Kolarević A, Kocić G, Šmelcerović A. Ascorbic acid as DNase I inhibitor in prevention of male infertility. Biochem Biophys Res Commun 2018; 498:1073-1077. [DOI: 10.1016/j.bbrc.2018.03.120] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 03/14/2018] [Indexed: 11/28/2022]
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Streptococcus pyogenes nuclease A (SpnA) mediated virulence does not exclusively depend on nuclease activity. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2017; 53:42-48. [PMID: 29158081 DOI: 10.1016/j.jmii.2017.09.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 08/21/2017] [Accepted: 09/18/2017] [Indexed: 01/25/2023]
Abstract
BACKGROUND Streptococcus pyogenes, or Group A Streptococcus (GAS), is a human pathogen that causes a wide range of diseases, including pharyngitis, necrotizing fasciitis and toxic shock syndrome. The bacterium produces a large arsenal of virulence factors, including the cell wall-anchored Streptococcus pyogenes nuclease A (SpnA), which facilitates immune evasion by degrading the DNA backbone of neutrophil extracellular traps. SpnA consists of a C-terminal endo/exonuclease domain and a N-terminal domain of unknown function. METHODS Recombinant SpnA mutants were generated by alanine conversion of selected residues that were predicted to play a role in the enzymatic activity and tested for their ability to degrade DNA. A GAS spnA deletion mutant was complemented with a plasmid-borne catalytic site mutant and analyzed for virulence in a Galleria mellonella (wax moth) infection model. RESULTS Several predicted residues were experimentally confirmed to play a role in SpnA enzymatic activity. These include Glu592, Arg696, His716, Asp767, Asn769, Asp810 and Asp842. Complementation of a GAS spnA deletion mutant with a spnA H716A mutant gene partially restored virulence in wax moth larvae, whereas complementation with the spnA wt gene completely restored activity. Furthermore, complementation with a secreted form of SpnA showed reduced virulence. CONCLUSION Our results show that abolishing the enzymatic activity of SpnA only partially reduces virulence suggesting that SpnA has an additional virulence function, which might be located on the N-terminal domain. Furthermore, cell wall-anchoring of SpnA results in higher virulence compared to secreted SpnA, probably due to a higher local density of the enzyme.
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Doke M, Fukamachi H, Morisaki H, Arimoto T, Kataoka H, Kuwata H. Nucleases from Prevotella intermedia can degrade neutrophil extracellular traps. Mol Oral Microbiol 2016; 32:288-300. [PMID: 27476978 PMCID: PMC5516193 DOI: 10.1111/omi.12171] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/27/2016] [Indexed: 01/19/2023]
Abstract
Periodontitis is an inflammatory disease caused by periodontal bacteria in subgingival plaque. These bacteria are able to colonize the periodontal region by evading the host immune response. Neutrophils, the host's first line of defense against infection, use various strategies to kill invading pathogens, including neutrophil extracellular traps (NETs). These are extracellular net‐like fibers comprising DNA and antimicrobial components such as histones, LL‐37, defensins, myeloperoxidase, and neutrophil elastase from neutrophils that disarm and kill bacteria extracellularly. Bacterial nuclease degrades the NETs to escape NET killing. It has now been shown that extracellular nucleases enable bacteria to evade this host antimicrobial mechanism, leading to increased pathogenicity. Here, we compared the DNA degradation activity of major Gram‐negative periodontopathogenic bacteria, Porphyromonas gingivalis, Prevotella intermedia, Fusobacterium nucleatum, and Aggregatibacter actinomycetemcomitans. We found that Pr. intermedia showed the highest DNA degradation activity. A genome search of Pr. intermedia revealed the presence of two genes, nucA and nucD, putatively encoding secreted nucleases, although their enzymatic and biological activities are unknown. We cloned nucA‐ and nucD‐encoding nucleases from Pr. intermedia ATCC 25611 and characterized their gene products. Recombinant NucA and NucD digested DNA and RNA, which required both Mg2+ and Ca2+ for optimal activity. In addition, NucA and NucD were able to degrade the DNA matrix comprising NETs.
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Affiliation(s)
- M Doke
- Department of Oral Microbiology and Immunology, Showa University School of Dentistry, Shinagawa, Tokyo, Japan
| | - H Fukamachi
- Department of Oral Microbiology and Immunology, Showa University School of Dentistry, Shinagawa, Tokyo, Japan
| | - H Morisaki
- Department of Oral Microbiology and Immunology, Showa University School of Dentistry, Shinagawa, Tokyo, Japan
| | - T Arimoto
- Department of Oral Microbiology and Immunology, Showa University School of Dentistry, Shinagawa, Tokyo, Japan
| | - H Kataoka
- Department of Oral Microbiology and Immunology, Showa University School of Dentistry, Shinagawa, Tokyo, Japan
| | - H Kuwata
- Department of Oral Microbiology and Immunology, Showa University School of Dentistry, Shinagawa, Tokyo, Japan
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16
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Guerreiro PS, Estácio SG, Antunes F, Fernandes AS, Pinheiro PF, Costa JG, Castro M, Miranda JP, Guedes RC, Oliveira NG. Structure-based virtual screening toward the discovery of novel inhibitors of the DNA repair activity of the human apurinic/apyrimidinic endonuclease 1. Chem Biol Drug Des 2016; 88:915-925. [DOI: 10.1111/cbdd.12826] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 05/10/2016] [Accepted: 07/11/2016] [Indexed: 01/21/2023]
Affiliation(s)
- Patrícia S. Guerreiro
- Research Institute for Medicines (iMed.ULisboa); Faculty of Pharmacy; Universidade de Lisboa; Lisbon Portugal
| | - Sílvia G. Estácio
- BioISI - Biosystems and Integrative Sciences Institute; Faculdade de Ciências; Universidade de Lisboa; Lisbon Portugal
| | - Fernando Antunes
- Departamento de Química e Bioquímica and Centro de Química e Bioquímica; Faculdade de Ciências; Universidade de Lisboa; Lisbon Portugal
| | - Ana S. Fernandes
- Research Institute for Medicines (iMed.ULisboa); Faculty of Pharmacy; Universidade de Lisboa; Lisbon Portugal
- CBIOS; Universidade Lusófona Research Center for Biosciences and Health Technologies; Lisbon Portugal
| | - Pedro F. Pinheiro
- Research Institute for Medicines (iMed.ULisboa); Faculty of Pharmacy; Universidade de Lisboa; Lisbon Portugal
- Centro de Química Estrutural (CQE); Instituto Superior Técnico; Universidade de Lisboa; Lisbon Portugal
| | - João G. Costa
- Research Institute for Medicines (iMed.ULisboa); Faculty of Pharmacy; Universidade de Lisboa; Lisbon Portugal
- CBIOS; Universidade Lusófona Research Center for Biosciences and Health Technologies; Lisbon Portugal
| | - Matilde Castro
- Research Institute for Medicines (iMed.ULisboa); Faculty of Pharmacy; Universidade de Lisboa; Lisbon Portugal
| | - Joana P. Miranda
- Research Institute for Medicines (iMed.ULisboa); Faculty of Pharmacy; Universidade de Lisboa; Lisbon Portugal
| | - Rita C. Guedes
- Research Institute for Medicines (iMed.ULisboa); Faculty of Pharmacy; Universidade de Lisboa; Lisbon Portugal
| | - Nuno G. Oliveira
- Research Institute for Medicines (iMed.ULisboa); Faculty of Pharmacy; Universidade de Lisboa; Lisbon Portugal
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17
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Zhang Y, Liu Y, Guo H, Jiang W, Dong P, Liang X. Site-directed mutagenesis of porcine pepsin: Possible role of Asp32, Thr33, Asp215 and Gly217 in maintaining the nuclease activity of pepsin. Enzyme Microb Technol 2016; 89:69-75. [PMID: 27233129 DOI: 10.1016/j.enzmictec.2016.03.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 03/09/2016] [Accepted: 03/28/2016] [Indexed: 12/01/2022]
Abstract
Site-directed mutagenesis of porcine pepsin was performed to identify its active sites that regulate nucleic acid (NA) digestion activity and to analyze the mechanism pepsin-mediated NA digestion. The mutation sites were distributed at the catalytic center of the enzyme (T33A, G34A, Y75H, T77A, Y189H, V214A, G217A and S219A) and at its active site (D32A and D215A) for protein digestion. Mutation of the active site residues Asp32 and Asp215 led to the inactivation of pepsin (both the NA and protein digestion activity), which demonstrated that the active sites of the pepsin protease activity were also important for its nuclease activity. Analysis of the variants revealed that T33A and G217A mutants showed a complete loss of NA digestion activity. In conclusion, residues Asp32, Thr33, Asp215 and Gly217 were related to the pepsin active sites for NA digestion. Moreover, the Y189H and V214A variants showed a loss of digestion activity on double-strand DNA (dsDNA) but only a decrease in digestion activity on single-strand DNA (ssDNA). On the contrary, the G34A variant showed a loss of digestion activity on ssDNA but only a decrease in digestion activity on dsDNA. Our findings are the first to identify the active sites of pepsin nuclease activity and lay the framework for further study of the mechanism of pepsin nuclease activity.
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Affiliation(s)
- Yanfang Zhang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Yu Liu
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China; Innovation and Application Institute, Zhejiang Ocean University, Zhoushan 316022, China
| | - Hui Guo
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Wei Jiang
- Innovation and Application Institute, Zhejiang Ocean University, Zhoushan 316022, China
| | - Ping Dong
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China.
| | - Xingguo Liang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China.
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18
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Systemic lupus erythematosus: Molecular cloning of fourteen recombinant DNase monoclonal kappa light chains with different catalytic properties. Biochim Biophys Acta Gen Subj 2014; 1840:1725-37. [DOI: 10.1016/j.bbagen.2014.01.027] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Revised: 01/15/2014] [Accepted: 01/16/2014] [Indexed: 11/15/2022]
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19
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Kostrikina IA, Odintsova ES, Buneva VN, Nevinsky GA. Systemic lupus erythematosus: molecular cloning and analysis of recombinant DNase monoclonal κ light chain NGK-1. Int Immunol 2014; 26:439-50. [PMID: 24919596 DOI: 10.1093/intimm/dxu047] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Because DNase antibodies are cytotoxic, enter the nucleus and cause DNA fragmentation inducing cell death by apoptosis, they can play an important role in the pathogenesis of different autoimmune pathologies and especially systemic lupus erythematosus (SLE). The interesting goal of catalytic antibodies research is not only to study a possible biological role of such antibodies, but also to develop in future new human and animal therapies that use the advantages offered by abzymes. An immunoglobulin κ light chain library from SLE patients was cloned into a phagemid vector. Phage particles displaying recombinant monoclonal antibody light chains (MLChs) capable of binding DNA were isolated by affinity chromatography on DNA-cellulose. Sixteen of the 46 MLChs efficiently hydrolyzed DNA; one MLCh (approximately 27-28kDa) was expressed in Escherichia coli and purified by metal chelating and gel filtration. MLCh NGK-1 was electrophoretically homogeneous and demonstrated a positive answer with mouse IgGs against light chains of human antibodies after western blotting. SDS-PAGE in a gel containing DNA demonstrated that the MLCh hydrolyzes DNA and is not contaminated by canonical DNases. The DNase MLCh was activated by several metal ions. The protein sequence of the DNase MLCh has homology with mammalian DNases I and shares with them several identical or similar (with the same side chain functionality) important amino acid residues, which are necessary for DNA hydrolysis and binding of Mg(2+) and Ca(2+) ions. The affinity of DNA for this first example of a MLCh (K(M) = 0.3 microM) was 150- to 200-fold higher than for human DNase I.
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Affiliation(s)
- Irina A Kostrikina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Elena S Odintsova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Valentina N Buneva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Novosibirsk 630090, Russia Novosibirsk State University, Novosibirsk 630090, Russia
| | - Georgy A Nevinsky
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Novosibirsk 630090, Russia Novosibirsk State University, Novosibirsk 630090, Russia
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20
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Ueki M, Kimura-Kataoka K, Takeshita H, Fujihara J, Iida R, Sano R, Nakajima T, Kominato Y, Kawai Y, Yasuda T. Evaluation of all non-synonymous single nucleotide polymorphisms (SNPs) in the genes encoding human deoxyribonuclease I and I-like 3 as a functional SNP potentially implicated in autoimmunity. FEBS J 2013; 281:376-90. [DOI: 10.1111/febs.12608] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Revised: 09/26/2013] [Accepted: 11/04/2013] [Indexed: 11/29/2022]
Affiliation(s)
- Misuzu Ueki
- Division of Medical Genetics and Biochemistry; Faculty of Medical Sciences; University of Fukui; Japan
| | | | - Haruo Takeshita
- Department of Legal Medicine; Shimane University School of Medicine; Japan
| | - Junko Fujihara
- Department of Legal Medicine; Shimane University School of Medicine; Japan
| | - Reiko Iida
- Division of Life Sciences; Faculty of Medical Sciences; University of Fukui; Japan
| | - Rie Sano
- Department of Legal Medicine; Gunma University School of Medicine; Japan
| | - Tamiko Nakajima
- Department of Legal Medicine; Gunma University School of Medicine; Japan
| | - Yoshihiko Kominato
- Department of Legal Medicine; Gunma University School of Medicine; Japan
| | - Yasuyuki Kawai
- Department of Cardiology; Kanazawa Medical University; Ishikawa Japan
| | - Toshihiro Yasuda
- Department of Legal Medicine; Shimane University School of Medicine; Japan
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21
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Manvilla BA, Pozharski E, Toth EA, Drohat AC. Structure of human apurinic/apyrimidinic endonuclease 1 with the essential Mg2+ cofactor. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:2555-62. [PMID: 24311596 PMCID: PMC3852660 DOI: 10.1107/s0907444913027042] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2013] [Accepted: 10/01/2013] [Indexed: 11/10/2022]
Abstract
Apurinic/apyrimidinic endonuclease 1 (APE1) mediates the repair of abasic sites and other DNA lesions and is essential for base-excision repair and strand-break repair pathways. APE1 hydrolyzes the phosphodiester bond at abasic sites, producing 5'-deoxyribose phosphate and the 3'-OH primer needed for repair synthesis. It also has additional repair activities, including the removal of 3'-blocking groups. APE1 is a powerful enzyme that absolutely requires Mg2+, but the stoichiometry and catalytic function of the divalent cation remain unresolved for APE1 and for other enzymes in the DNase I superfamily. Previously reported structures of DNA-free APE1 contained either Sm3+ or Pb2+ in the active site. However, these are poor surrogates for Mg2+ because Sm3+ is not a cofactor and Pb2+ inhibits APE1, and their coordination geometry is expected to differ from that of Mg2+. A crystal structure of human APE1 was solved at 1.92 Å resolution with a single Mg2+ ion in the active site. The structure reveals ideal octahedral coordination of Mg2+ via two carboxylate groups and four water molecules. One residue that coordinates Mg2+ directly and two that bind inner-sphere water molecules are strictly conserved in the DNase I superfamily. This structure, together with a recent structure of the enzyme-product complex, inform on the stoichiometry and the role of Mg2+ in APE1-catalyzed reactions.
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Affiliation(s)
- Brittney A. Manvilla
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 North Greene Street, Baltimore, MD 21201, USA
| | - Edwin Pozharski
- Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201, USA
| | - Eric A. Toth
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 North Greene Street, Baltimore, MD 21201, USA
| | - Alexander C. Drohat
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 North Greene Street, Baltimore, MD 21201, USA
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22
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Villalobos X, Rodríguez L, Prévot J, Oleaga C, Ciudad CJ, Noé V. Stability and immunogenicity properties of the gene-silencing polypurine reverse Hoogsteen hairpins. Mol Pharm 2013; 11:254-64. [PMID: 24251728 DOI: 10.1021/mp400431f] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Gene silencing by either small-interference RNAs (siRNA) or antisense oligodeoxynucleotides (aODN) is widely used in biomedical research. However, their use as therapeutic agents is hindered by two important limitations: their low stability and the activation of the innate immune response. Recently, we developed a new type of molecule to decrease gene expression named polypurine reverse Hoogsteen hairpins (PPRHs) that bind to polypyrimidine targets in the DNA. Herein, stability experiments performed in mouse, human, and fetal calf serum and in PC3 cells revealed that the half-life of PPRHs is much longer than that of siRNAs in all cases. Usage of PPRHs with a nicked-circular structure increased the binding affinity to their target sequence and their half-life in FCS when bound to the target. Regarding the innate immune response, we determined that the levels of the transcription factors IRF3 and its phosphorylated form, as well as NF-κB were increased by siRNAs and not by PPRHs; that the expression levels of several proinflammatory cytokines including IL-6, TNF-α, IFN-α, IFN-ß, IL-1ß, and IL-18 were not significantly increased by PPRHs; and that the cleavage and activation of the proteolytic enzyme caspase-1 was not triggered by PPRHs. These determinations indicated that PPRHs, unlike siRNAs, do not activate the innate inflammatory response.
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Affiliation(s)
- Xenia Villalobos
- Department of Biochemistry and Molecular Biology, School of Pharmacy, University of Barcelona , Av. Diagonal 643, E-08028 Barcelona, Spain
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23
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Shigematsu M, Ogawa T, Tanaka W, Takahashi K, Kitamoto HK, Hidaka M, Masaki H. Evidence for DNA cleavage caused directly by a transfer RNA-targeting toxin. PLoS One 2013; 8:e75512. [PMID: 24069426 PMCID: PMC3775755 DOI: 10.1371/journal.pone.0075512] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Accepted: 08/13/2013] [Indexed: 11/24/2022] Open
Abstract
The killer yeast species Pichiaacaciae produces a heteromeric killer protein, PaT, that causes DNA damage and arrests the cell cycle of sensitive Saccharomyces cerevisiae in the S phase. However, the mechanism by which DNA damage occurs remains elusive. A previous study has indicated that Orf2p, a subunit of PaT, specifically cleaves an anticodon loop of an S. cerevisiae transfer RNA (tRNAGlnmcm5s2UUG). This finding raised a question about whether the DNA damage is a result of the tRNA cleavage or whether Orf2p directly associates with and cleaves the genomic DNA of sensitive yeast cells. We showed that Orf2p cleaves genomic DNA in addition to cleaving tRNA in vitro. This DNA cleavage requires the same Orf2p residue as that needed for tRNA cleavage, His299. The expression of Orf2p, in which His299 was substituted to alanine, abolished the cell cycle arrest of the host cell. Moreover, the translation impairment induced by tRNA cleavage enabled Orf2p to enter the nucleus, thereby inducing histone phosphorylation.
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Affiliation(s)
| | - Tetsuhiro Ogawa
- Department of Biotechnology, The University of Tokyo, Tokyo, Japan
- * E-mail: (HM); (TO)
| | - Wataru Tanaka
- Department of Biotechnology, The University of Tokyo, Tokyo, Japan
| | | | | | - Makoto Hidaka
- Department of Biotechnology, The University of Tokyo, Tokyo, Japan
| | - Haruhiko Masaki
- Department of Biotechnology, The University of Tokyo, Tokyo, Japan
- * E-mail: (HM); (TO)
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24
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Parsiegla G, Noguere C, Santell L, Lazarus RA, Bourne Y. The structure of human DNase I bound to magnesium and phosphate ions points to a catalytic mechanism common to members of the DNase I-like superfamily. Biochemistry 2012; 51:10250-8. [PMID: 23215638 DOI: 10.1021/bi300873f] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Recombinant human DNase I (Pulmozyme, dornase alfa) is used for the treatment of cystic fibrosis where it improves lung function and reduces the number of exacerbations. The physiological mechanism of action is thought to involve the reduction of the viscoelasticity of cystic fibrosis sputum by hydrolyzing high concentrations of DNA into low-molecular mass fragments. Here we describe the 1.95 Å resolution crystal structure of recombinant human DNase I (rhDNase I) in complex with magnesium and phosphate ions, both bound in the active site. Complementary mutagenesis data of rhDNase I coupled to a comprehensive structural analysis of the DNase I-like superfamily argue for the key catalytic role of Asn7, which is invariant among mammalian DNase I enzymes and members of this superfamily, through stabilization of the magnesium ion coordination sphere. Overall, our combined structural and mutagenesis data suggest the occurrence of a magnesium-assisted pentavalent phosphate transition state in human DNase I during catalysis, where Asp168 may play a key role as a general catalytic base.
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Affiliation(s)
- Goetz Parsiegla
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université and CNRS UMR 7257, Parc Scientifique et Technonlogique de Luminy, Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 09, France.
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25
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Comparative biochemical properties of vertebrate deoxyribonuclease I. Comp Biochem Physiol B Biochem Mol Biol 2012; 163:263-73. [DOI: 10.1016/j.cbpb.2012.07.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Revised: 07/26/2012] [Accepted: 07/27/2012] [Indexed: 11/18/2022]
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26
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Chang A, Khemlani A, Kang H, Proft T. Functional analysis of Streptococcus pyogenes nuclease A (SpnA), a novel group A streptococcal virulence factor. Mol Microbiol 2011; 79:1629-42. [PMID: 21231972 DOI: 10.1111/j.1365-2958.2011.07550.x] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Streptococcus pyogenes nuclease A (SpnA) is a recently discovered DNase that plays a role in virulence as shown in a mouse infection model. SpnA is the only cell wall-anchored DNase found in S. pyogenes thus far and shows a unique protein architecture. The C-terminal nuclease domain contains highly conserved catalytic site and Mg(2+) binding site residues. However, expression of the SpnA nuclease domain alone resulted in a soluble, but enzymatically inactive protein. We found that at least two out of three oligonucleotide/oligosaccharide-binding fold motifs found in the N-terminal domain are required for SpnA activity, probably contributing to substrate binding. Using a combination of a spnA deletion mutant and a Lactococcus lactis'gain-of-function' mutant, we have shown that SpnA promotes survival in whole human blood and in neutrophil killing assays and this is, at least in part, achieved by the destruction of neutrophil extracellular traps (NETs). We observed higher frequencies for anti-SpnA antibodies in streptococcal disease patient sera (79%, n = 19) compared with sera from healthy donors (33%, n = 9) suggesting that SpnA is expressed during infection. Detection of anti-SpnA antibodies in patient serum might be useful for the diagnostic of post-streptococcal diseases, such as acute rheumatic fever or glomerulonephritis.
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Affiliation(s)
- Ann Chang
- Department of Molecular Medicine & Pathology, School of Medical Sciences, University of Auckland, Auckland, New Zealand
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27
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Guéroult M, Picot D, Abi-Ghanem J, Hartmann B, Baaden M. How cations can assist DNase I in DNA binding and hydrolysis. PLoS Comput Biol 2010; 6:e1001000. [PMID: 21124947 PMCID: PMC2987838 DOI: 10.1371/journal.pcbi.1001000] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2010] [Accepted: 10/15/2010] [Indexed: 11/27/2022] Open
Abstract
DNase I requires Ca2+ and Mg2+ for hydrolyzing double-stranded DNA. However, the number and the location of DNase I ion-binding sites remain unclear, as well as the role of these counter-ions. Using molecular dynamics simulations, we show that bovine pancreatic (bp) DNase I contains four ion-binding pockets. Two of them strongly bind Ca2+ while the other two sites coordinate Mg2+. These theoretical results are strongly supported by revisiting crystallographic structures that contain bpDNase I. One Ca2+ stabilizes the functional DNase I structure. The presence of Mg2+ in close vicinity to the catalytic pocket of bpDNase I reinforces the idea of a cation-assisted hydrolytic mechanism. Importantly, Poisson-Boltzmann-type electrostatic potential calculations demonstrate that the divalent cations collectively control the electrostatic fit between bpDNase I and DNA. These results improve our understanding of the essential role of cations in the biological function of bpDNase I. The high degree of conservation of the amino acids involved in the identified cation-binding sites across DNase I and DNase I-like proteins from various species suggests that our findings generally apply to all DNase I-DNA interactions. DNase I requires Ca2+ and Mg2+ for hydrolyzing double-stranded DNA. Here, we show that bovine pancreatic (bp) DNase I contains four ion-binding pockets. Two of them, previously observed in the crystallographic structure of free bpDNase I, strongly bind Ca2+. The other two sites bind Mg2+ and are described in detail for the first time. One Ca2+ stabilizes the functional DNase I structure. The presence of Mg2+ in close vicinity to the catalytic pocket of bpDNase I reinforces the idea of a cation-assisted hydrolytic mechanism. Poisson-Boltzmann-type electrostatic potential calculations demonstrate that the divalent cations collectively control the electrostatic fit between bpDNase I and DNA. Thus, this work reveals the link between cation binding and the biological function of bpDNase I. The high degree of conservation of the amino acids involved in the identified cation-binding sites across DNase I and DNase I-like proteins from various species suggests that our findings generally apply to all DNase I-DNA interactions.
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Affiliation(s)
- Marc Guéroult
- CNRS UPR 9080, Institut de Biologie Physico-Chimique, Paris, France
- INTS, INSERM UMR S665, Paris, France
| | - Daniel Picot
- CNRS UMR 7099, Institut de Biologie Physico-Chimique, Paris, France
| | | | | | - Marc Baaden
- CNRS UPR 9080, Institut de Biologie Physico-Chimique, Paris, France
- * E-mail: . (BH); (MB)
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28
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Abstract
Nucleases cleave the phosphodiester bonds of nucleic acids and may be endo or exo, DNase or RNase, topoisomerases, recombinases, ribozymes, or RNA splicing enzymes. In this review, I survey nuclease activities with known structures and catalytic machinery and classify them by reaction mechanism and metal-ion dependence and by their biological function ranging from DNA replication, recombination, repair, RNA maturation, processing, interference, to defense, nutrient regeneration or cell death. Several general principles emerge from this analysis. There is little correlation between catalytic mechanism and biological function. A single catalytic mechanism can be adapted in a variety of reactions and biological pathways. Conversely, a single biological process can often be accomplished by multiple tertiary and quaternary folds and by more than one catalytic mechanism. Two-metal-ion-dependent nucleases comprise the largest number of different tertiary folds and mediate the most diverse set of biological functions. Metal-ion-dependent cleavage is exclusively associated with exonucleases producing mononucleotides and endonucleases that cleave double- or single-stranded substrates in helical and base-stacked conformations. All metal-ion-independent RNases generate 2',3'-cyclic phosphate products, and all metal-ion-independent DNases form phospho-protein intermediates. I also find several previously unnoted relationships between different nucleases and shared catalytic configurations.
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29
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Sequence-Dependent DNA Flexibility Mediates DNase I Cleavage. J Mol Biol 2010; 395:123-33. [DOI: 10.1016/j.jmb.2009.10.023] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2009] [Revised: 10/09/2009] [Accepted: 10/12/2009] [Indexed: 11/17/2022]
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30
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2-Nitro-5-Thiosulfobenzoic Acid as a Novel Inhibitor Specific for Deoxyribonuclease I. Protein J 2008; 27:240-6. [DOI: 10.1007/s10930-008-9130-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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31
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Ueki M, Takeshita H, Fujihara J, Ueta G, Nakajima T, Kominato Y, Kishi K, Iida R, Yasuda T. Susceptibility of mammalian deoxyribonucleases I (DNases I) to proteolysis by proteases and its relationships to tissue distribution: Biochemical and molecular analysis of equine DNase I. Comp Biochem Physiol B Biochem Mol Biol 2007; 148:93-102. [PMID: 17544308 DOI: 10.1016/j.cbpb.2007.04.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2007] [Revised: 04/25/2007] [Accepted: 04/26/2007] [Indexed: 10/23/2022]
Abstract
Equine (Equus caballus) deoxyribonuclease I (DNase I) was purified from the parotid gland, and its 1295-bp cDNA was cloned. The mature equine DNase I protein consisted of 260 amino acid residues. The enzymatic properties and structural aspects of the equine enzyme were closely similar to those of other mammalian DNases I. Mammalian DNases I are classified into three types--pancreatic, parotid and pancreatic-parotid-based on their tissue distribution; as equine DNase I showed the highest activity in the parotid gland, it was confirmed to be of the parotid-type. Comparison of the susceptibility of mammalian DNases I to proteolysis by proteases demonstrated a marked correlation between tissue distribution and sensitivity/resistance to proteolysis; pancreatic-type DNase I shared properties of resistance to proteolysis by trypsin and chymotrypsin, whereas parotid-type DNase I did not. In contrast, pancreatic-parotid-type DNase I exhibited resistance to proteolysis by pepsin, whereas the other enzyme types did not. However, site-directed mutagenesis analysis revealed that only a single amino acid substitution could not account for acquisition of proteolysis resistance in the mammalian DNase I family during the course of molecular evolution. These properties are compatible with adaptation of mammalian DNases I for maintaining their activity in vivo.
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Affiliation(s)
- Misuzu Ueki
- Division of Medical Genetics and Biochemistry, Faculty of Medical Sciences, University of Fukui, Eiheiji, Fukui 910-1193, Japan
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32
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Jiang W, Han Y, Pan Q, Shen T, Liu C. Roles of exogenous divalent metals in the nucleolytic activity of Cu,Zn superoxide dismutase. J Inorg Biochem 2007; 101:667-77. [PMID: 17292965 DOI: 10.1016/j.jinorgbio.2006.12.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2006] [Revised: 11/25/2006] [Accepted: 12/14/2006] [Indexed: 10/23/2022]
Abstract
It is well known that the wild type Cu,Zn superoxide dismutase (holo SOD) catalyzes the conversion of superoxide anion to peroxide hydrogen and dioxygen. However, a new function of holo SOD, i.e., nucleolytic activity has been found [W. Jiang, T. Shen, Y. Han, Q. Pan, C. Liu, J. Biol. Inorg. Chem. 11 (2006) 835-848], which is linked to the incorporation of exogenous divalent metals into the enzyme-DNA complex. In this study, the roles of exogenous divalent metals in the nucleolytic activity were explored in detail by a series of biochemical experiments. Based on a non-equivalent multi-site binding model, affinity of a divalent metal for the enzyme-DNA complex was determined by absorption titration, indicating that the complex can provide at least a high and a low affinity site for the metal ion. These mean that the holo SOD may use a "two exogenous metal ion pathway" as a mechanism in which both metal ions are directly involved in the catalytic process of DNA cleavage. In addition, the pH versus DNA cleavage rate profiles can be fitted to two ionizing-group models, indicating the presence of a general acid and a general base in catalysis. A model that requires histidine residues, metal-bound water molecules and two hydrated metal ions to operate in concert could be used to interpret the catalysis of DNA hydrolysis, supported by the dependences of loss of the nucleolytic activity on time and on the concentration of the specific chemical modifier to the histidine residues on the enzyme.
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Affiliation(s)
- Wei Jiang
- Department of Chemistry, Huazhong University of Science and Technology, Wuhan 430074, China
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33
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O’Boyle NM, Holliday GL, Almonacid DE, Mitchell JB. Using reaction mechanism to measure enzyme similarity. J Mol Biol 2007; 368:1484-99. [PMID: 17400244 PMCID: PMC3461574 DOI: 10.1016/j.jmb.2007.02.065] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2006] [Revised: 11/06/2006] [Accepted: 02/19/2007] [Indexed: 11/24/2022]
Abstract
The concept of reaction similarity has been well studied in terms of the overall transformation associated with a reaction, but not in terms of mechanism. We present the first method to give a quantitative measure of the similarity of reactions based upon their explicit mechanisms. Two approaches are presented to measure the similarity between individual steps of mechanisms: a fingerprint-based approach that incorporates relevant information on each mechanistic step; and an approach based only on bond formation, cleavage and changes in order. The overall similarity for two reaction mechanisms is then calculated using the Needleman-Wunsch alignment algorithm. An analysis of MACiE, a database of enzyme mechanisms, using our measure of similarity identifies some examples of convergent evolution of chemical mechanisms. In many cases, mechanism similarity is not reflected by similarity according to the EC system of enzyme classification. In particular, little mechanistic information is conveyed by the class level of the EC system.
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Affiliation(s)
- Noel M. O’Boyle
- Unilever Centre for Molecular Science Informatics, Dept of Chemistry, University of Cambridge, Lensfield Rd, Cambridge CB2 1EW, U.K
| | - Gemma L. Holliday
- Unilever Centre for Molecular Science Informatics, Dept of Chemistry, University of Cambridge, Lensfield Rd, Cambridge CB2 1EW, U.K
- EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, U.K
| | - Daniel E. Almonacid
- Unilever Centre for Molecular Science Informatics, Dept of Chemistry, University of Cambridge, Lensfield Rd, Cambridge CB2 1EW, U.K
| | - John B.O. Mitchell
- Unilever Centre for Molecular Science Informatics, Dept of Chemistry, University of Cambridge, Lensfield Rd, Cambridge CB2 1EW, U.K
- To whom correspondence should be addressed;
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34
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Chen WJ, Lai PJ, Lai YS, Huang PT, Lin CC, Liao TH. Probing the catalytic mechanism of bovine pancreatic deoxyribonuclease I by chemical rescue. Biochem Biophys Res Commun 2006; 352:689-96. [PMID: 17141190 DOI: 10.1016/j.bbrc.2006.11.078] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2006] [Accepted: 11/15/2006] [Indexed: 10/23/2022]
Abstract
Previous structural and mutational studies of bovine pancreatic deoxyribonuclease I (bpDNase I) have demonstrated that the active site His134 and His252 played critical roles in catalysis. In our present study, mutations of these two His residues to Gln, Ala or Gly reduced the DNase activity by a factor of four to five orders of magnitude. When imidazole or primary amines were added exogenously to the Ala or Gly mutants, the residual DNase activities were substantially increased by 60-120-fold. The rescue with imidazole was pH- and concentration-dependent. The pH-activity profiles showed nearly bell-shaped curves, with the maximum activity enhancement for H134A at pH 6.0 and that for H252A at pH 7.5. These findings indicated that the protonated form of imidazole was responsible for the rescue in H134A, and the unprotonated form was for that in H252A, prompting us to assign unambiguously the roles for His134 as a general acid, and His252 as a general base, in bpDNase I catalysis.
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Affiliation(s)
- Wei-Jung Chen
- Institute of Biotechnology, College of Bioresources, National Ilan University, Ilan 26047, Taiwan.
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35
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Hontz JS, Villar-Lecumberri MT, Potter BM, Yoder MD, Dreyfus LA, Laity JH. Differences in crystal and solution structures of the cytolethal distending toxin B subunit: Relevance to nuclear translocation and functional activation. J Biol Chem 2006; 281:25365-72. [PMID: 16809347 DOI: 10.1074/jbc.m603727200] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cytolethal distending toxin (CDT) induces cell cycle arrest and apoptosis in eukaryotic cells, which are mediated by the DNA-damaging CdtB subunit. Here we report the first x-ray structure of an isolated CdtB subunit (Escherichia coli-II CdtB, EcCdtB). In conjunction with previous structural and biochemical observations, active site structural comparisons between free and holotoxin-assembled CdtBs suggested that CDT intoxication is contingent upon holotoxin disassembly. Solution NMR structural and 15N relaxation studies of free EcCdtB revealed disorder in the interface with the CdtA and CdtC subunits (residues Gly233-Asp242). Residues Leu186-Thr209 of EcCdtB, which encompasses tandem arginine residues essential for nuclear translocation and intoxication, were also disordered in solution. In stark contrast, nearly identical well defined alpha-helix and beta-strand secondary structures were observed in this region of the free and holotoxin CdtB crystallographic models, suggesting that distinct changes in structural ordering characterize subunit disassembly and nuclear localization factor binding functions.
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Affiliation(s)
- Jill S Hontz
- Division of Cell Biology and Biophysics, School of Biological Sciences, University of Missouri, Kansas City, Missouri 64110-2499, USA
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36
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Shiokawa D, Shika Y, Saito K, Yamazaki K, Tanuma SI. Physical and biochemical properties of mammalian DNase X proteins: non-AUG translation initiation of porcine and bovine mRNAs for DNase X. Biochem J 2006; 392:511-7. [PMID: 16107205 PMCID: PMC1316290 DOI: 10.1042/bj20051114] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
DNase X is the first human DNase protein identified as being homologous with DNase I. In the present study we describe the isolation of several mammalian DNase X cDNAs and the molecular characterization of their coding proteins. A sequence comparison reveals some conserved characteristics: all the mammalian DNase X proteins have an N-terminal signal peptide, a potential N-linked glycosylation site and a C-terminal hydrophobic domain. Human DNase X, ectopically expressed in HeLa S3 cells, is located in the ER (endoplasmic reticulum) and is modified by an N-linked glycosylation at Asn-243. Gene expression analyses show that the high expression level in muscular tissues, a known feature of human DNASE X, is also observed in mouse DNase X. Interestingly, the translation of porcine and bovine DNase X proteins occurs in the absence of an in-frame AUG initiation codon. We show that their mRNAs utilize a conserved CUG triplet for translation initiation.
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Affiliation(s)
- Daisuke Shiokawa
- *Department of Biochemistry, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Yukari Shika
- *Department of Biochemistry, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Kazuki Saito
- *Department of Biochemistry, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Kosuke Yamazaki
- *Department of Biochemistry, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Sei-ichi Tanuma
- *Department of Biochemistry, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
- †Genome and Drug Research Center, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
- To whom correspondence should be addressed (email )
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37
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Napirei M, Wulf S, Eulitz D, Mannherz HG, Kloeckl T. Comparative characterization of rat deoxyribonuclease 1 (Dnase1) and murine deoxyribonuclease 1-like 3 (Dnase1l3). Biochem J 2005; 389:355-64. [PMID: 15796714 PMCID: PMC1175112 DOI: 10.1042/bj20042124] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Deoxyribonuclease 1 (DNASE1, DNase I) and deoxyribonuclease 1-like 3 (DNASE1L3, DNase gamma, DNase Y, LS-DNase) are members of a DNASE1 protein family that is defined by similar biochemical properties such as Ca2+/Mg2+-dependency and an optimal pH of about 7.0 as well as by a high similarity in their nucleic acid and amino acid sequences. In the present study we describe the recombinant expression of rat Dnase1 and murine Dnase1l3 as fusion proteins tagged by their C-terminus to green fluorescent protein in NIH-3T3 fibroblasts and bovine lens epithelial cells. Both enzymes were translocated into the rough endoplasmic reticulum, transported along the entire secretory pathway and finally secreted into the cell culture medium. No nuclear occurrence of the nucleases was detectable. However, deletion of the N-terminal signal peptide of both nucleases resulted in a cytoplasmic and nuclear distribution of both fusion proteins. Dnase1 preferentially hydrolysed 'naked' plasmid DNA, whereas Dnase1l3 cleaved nuclear DNA with high activity. Dnase1l3 was able to cleave chromatin in an internucleosomal manner without proteolytic help. By contrast, Dnase1 was only able to achieve this cleavage pattern in the presence of proteases that hydrolysed chromatin-bound proteins. Detailed analysis of murine sera derived from Dnase1 knockout mice revealed that serum contains, besides the major serum nuclease Dnase1, an additional Dnase1l3-like nucleolytic activity, which, in co-operation with Dnase1, might help to suppress anti-DNA autoimmunity by degrading nuclear chromatin released from dying cells.
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Affiliation(s)
- Markus Napirei
- Abteilung für Anatomie und Embryologie, Medizinische Fakultät, Ruhr-Universität Bochum, Universitätsstrasse 150, D-44780 Bochum, Germany.
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38
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Openshaw AEA, Race PR, Monzó HJ, Vázquez-Boland JA, Banfield MJ. Crystal structure of SmcL, a bacterial neutral sphingomyelinase C from Listeria. J Biol Chem 2005; 280:35011-7. [PMID: 16093240 DOI: 10.1074/jbc.m506800200] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Sphingomyelinases C are enzymes that catalyze the hydrolysis of sphingomyelin in biological membranes to ceramide and phosphorylcholine. Various pathogenic bacteria produce secreted neutral sphingomyelinases C that act as membrane-damaging virulence factors. Mammalian neutral sphingomyelinases C, which display sequence homology to the bacterial enzymes, are involved in sphingolipid metabolism and signaling. This article describes the first structure to be determined for a member of the neutral sphingomyelinase C family, SmcL, from the intracellular bacterial pathogen Listeria ivanovii. The structure has been refined to 1.9-A resolution with phases derived by single isomorphous replacement with anomalous scattering techniques from a single iridium derivative. SmcL adopts a DNase I-like fold, and is the first member of this protein superfamily to have its structure determined that acts as a phospholipase. The structure reveals several unique features that adapt the protein to its phospholipid substrate. These include large hydrophobic beta-hairpin and hydrophobic loops surrounding the active site that may bind and penetrate the lipid bilayer to position sphingomyelin in a catalytically competent position. The structure also provides insight into the proposed general base/acid catalytic mechanism, in which His-325 and His-185 play key roles.
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Affiliation(s)
- Amy E A Openshaw
- Institute for Cell and Molecular Biosciences, University of Newcastle upon Tyne, Framlington Place, Newcastle upon Tyne, NE2 4HH United Kingdom
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39
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Murakami MT, Fernandes-Pedrosa MF, Tambourgi DV, Arni RK. Structural Basis for Metal Ion Coordination and the Catalytic Mechanism of Sphingomyelinases D. J Biol Chem 2005; 280:13658-64. [PMID: 15654080 DOI: 10.1074/jbc.m412437200] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Sphingomyelinases D (SMases D) from Loxosceles spider venom are the principal toxins responsible for the manifestation of dermonecrosis, intravascular hemolysis, and acute renal failure, which can result in death. These enzymes catalyze the hydrolysis of sphingomyelin, resulting in the formation of ceramide 1-phosphate and choline or the hydrolysis of lysophosphatidyl choline, generating the lipid mediator lysophosphatidic acid. This report represents the first crystal structure of a member of the sphingomyelinase D family from Loxosceles laeta (SMase I), which has been determined at 1.75-angstrom resolution using the "quick cryo-soaking" technique and phases obtained from a single iodine derivative and data collected from a conventional rotating anode x-ray source. SMase I folds as an (alpha/beta)8 barrel, the interfacial and catalytic sites encompass hydrophobic loops and a negatively charged surface. Substrate binding and/or the transition state are stabilized by a Mg2+ ion, which is coordinated by Glu32, Asp34, Asp91, and solvent molecules. In the proposed acid base catalytic mechanism, His12 and His47 play key roles and are supported by a network of hydrogen bonds between Asp34, Asp52, Trp230, Asp233, and Asn252.
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Affiliation(s)
- Mário T Murakami
- Department of Physics, Instituto de Biociências, Letras e Ciências Exatas/Universidade Estadual Paulista, São José do Rio Preto, SP 15054-000, Brazil
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40
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Mundle ST, Fattal MH, Melo LF, Coriolan JD, O'Regan NE, Strauss PR. Novel role of tyrosine in catalysis by human AP endonuclease 1. DNA Repair (Amst) 2005; 3:1447-55. [PMID: 15380100 DOI: 10.1016/j.dnarep.2004.06.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2004] [Indexed: 11/17/2022]
Abstract
Apurinic/apyrimidinic endonuclease (AP endo, HAP1) recognizes abasic sites in ds DNA and makes a single nick in the backbone 5' to the abasic site. In this report we examine the roles of three conserved tyrosine residues in close proximity to the active site. We show that Tyr(128) and Tyr(269), which interact upstream and downstream of the abasic site, respectively, are involved in recognition and binding of abasic site-containing double stranded DNA. However, the two residues are not equivalent, as their effects are differentiated by changes in salt concentration. In sharp contrast, Tyr(171) is directly involved in catalysis as well as binding. Y171F, Y171H, and Y171A all show decreased catalytic efficiencies 25,000-50,000-fold from the WT enzyme. Both imidazole and basic pH markedly stimulate the WT enzyme. Imidazole stimulates Tyr(171) mutant enzymes when tyrosine is also present but basic pH eliminates remaining mutant activity. These results underscore the importance of tyrosines in AP endo catalysis. They render the current hypotheses regarding enzyme action unlikely and allow us to consider the possibility that the phenolate of Tyr(171) is the nucleophile that attacks the scissile phosphate.
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Affiliation(s)
- Sophia T Mundle
- Department of Biology, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA
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41
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Yasuda T, Iida R, Ueki M, Kominato Y, Nakajima T, Takeshita H, Kobayashi T, Kishi K. Molecular evolution of shark and other vertebrate DNases I. ACTA ACUST UNITED AC 2004; 271:4428-35. [PMID: 15560784 DOI: 10.1111/j.1432-1033.2004.04381.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We purified pancreatic deoxyribonuclease I (DNase I) from the shark Heterodontus japonicus using three-step column chromatography. Although its enzymatic properties resembled those of other vertebrate DNases I, shark DNase I was unique in being a basic protein. Full-length cDNAs encoding the DNases I of two shark species, H. japonicus and Triakis scyllia, were constructed from their total pancreatic RNAs using RACE. Nucleotide sequence analyses revealed two structural alterations unique to shark enzymes: substitution of two Cys residues at positions 101 and 104 (which are well conserved in all other vertebrate DNases I) and insertion of an additional Thr or Asn residue into an essential Ca(2+)-binding site. Site-directed mutagenesis of shark DNase I indicated that both of these alterations reduced the stability of the enzyme. When the signal sequence region of human DNase I (which has a high alpha-helical structure content) was replaced with its amphibian, fish and shark counterparts (which have low alpha-helical structure contents), the activity expressed by the chimeric mutant constructs in transfected mammalian cells was approximately half that of the wild-type enzyme. In contrast, substitution of the human signal sequence region into the amphibian, fish and shark enzymes produced higher activity compared with the wild-types. The vertebrate DNase I family may have acquired high stability and effective expression of the enzyme protein through structural alterations in both the mature protein and its signal sequence regions during molecular evolution.
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Affiliation(s)
- Toshihiro Yasuda
- Division of Medical Genetics and Biochemistry, Faculty of Medical Sciences, University of Fukui, Japan
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42
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Chen WJ, Lee IS, Chen CY, Liao TH. Biological functions of the disulfides in bovine pancreatic deoxyribonuclease. Protein Sci 2004; 13:875-83. [PMID: 15044724 PMCID: PMC2280041 DOI: 10.1110/ps.03438204] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
We characterized the biochemical functions of the small nonessential (C101-C104) and the large essential (C173-C209) disulfides in bovine pancreatic (bp) DNase using alanine mutants [brDNase(C101A)] and [brDNase(C173A) and brDNase(C209A)], respectively. We also characterized the effects of an additional third disulfide [brDNase(F192C/A217C)]. Without the Ca(2+) protection, bpDNase and brDNase(C101A) were readily inactivated by trypsin, whereas brDNase(F192C/A217C) remained active. With Ca(2+), all forms of DNase, except for brDNase(C101A), were protected against trypsin. All forms of DNase, after being dissolved in 6 M guanidine-HCl, were fully reactivated by diluting into a Ca(2+)-containing buffer. However, when diluted into a Ca(2+)-free buffer, bpDNase and brDNase(C101A) remained inactive, but 60% of the bpDNase activity was restored with brDNase(F192C/A217C). When heated, bpDNase was inactivated at a transition temperature of 65 degrees C, brDNase(C101A) at 60 degrees C, and brDNase(F192C/A217C) at 73 degrees C, indicating that the small disulfide, albeit not essential for activity, is important for the structural integrity, and that the introduction of a third disulfide can further stabilize the enzyme. When pellets of brDNase(C173A) and brDNase(C209A) in inclusion bodies were dissolved in 6 M guanidine-HCl and then diluted into a Ca(2+)-containing buffer, 10%-18% of the bpDNase activity was restored, suggesting that the "essential" disulfide is not absolutely crucial for enzymatic catalysis. Owing to the structure-based sequence alignment revealing homology between the "nonessential" disulfide of bpDNase and the active-site motif of thioredoxin, we measured 39% of the thioredoxin-like activity for bpDNase based on the rate of insulin precipitation (DeltaA650nm/min). Thus, the disulfides in bpDNase not only play the role of stabilizing the protein molecule but also may engage in biological functions such as the disulfide/dithiol exchange reaction.
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Affiliation(s)
- Wei-Jung Chen
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, No. 1, Sec. 1, Jen-Ai Road, Taipei 10018, Taiwan.
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43
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Chen WJ, Huang PT, Liu J, Liao TH. Involvement of the N- and C-terminal fragments of bovine pancreatic deoxyribonuclease in active protein folding. Biochemistry 2004; 43:10653-63. [PMID: 15311926 DOI: 10.1021/bi049183i] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The three-dimensional structure of bovine pancreatic (bp) DNase revealed that its N- and C-termini form an antiparallel beta-sheet structure. The involvement of this beta-sheet structure in the active protein folding of bpDNase was thus investigated via a series of deletion and substitution variants. Several substitution variants of N-terminal Leu1 and C-terminal Leu259, and one variant with only the last Thr260 deleted, remained fully active. However, the other deletion variants, in which 2-10 amino acid residues were removed from the C- or N-terminus, all lost the DNase activity. The results indicated that the backbone hydrogen bonding in the antiparallel beta-sheet, rather than the side-chain interactions, is crucial for the correct protein folding. When the deletion variants were complemented with synthetic peptides of the deleted N- or C-terminal sequences, the DNase activity was generated. The highest DNase activity was generated when the C-terminal 10-residue-deleted brDNase(Delta251-260) was admixed with the C-terminal 10-residue peptide (peptide C10) in a molar ratio of 1:400. The noncovalent binding between brDNase(Delta251-260) and peptide C10 exhibited a dissociation constant of 48 microM. Circular dichroism spectra showed that the deletion variants were partially folded with mainly helical structures and that admixture with corresponding peptides facilitated their folding into the nativelike beta-sheet-rich structure. Thermal denaturation profiles also revealed that the transition temperature for brDNase(Delta251-260) was increased from 55 to 63 degrees C after incubation with peptide C10. The folding activation process for the deletion variant occurred in two stages, and Ca(2+) was required.
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Affiliation(s)
- Wei-Jung Chen
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei, Taiwan
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44
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Haghjoo E, Galán JE. Salmonella typhi encodes a functional cytolethal distending toxin that is delivered into host cells by a bacterial-internalization pathway. Proc Natl Acad Sci U S A 2004; 101:4614-9. [PMID: 15070766 PMCID: PMC384795 DOI: 10.1073/pnas.0400932101] [Citation(s) in RCA: 183] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Many bacterial pathogens encode the cytolethal distending toxin (CDT), which causes host cells to arrest during their cell cycle by inflicting DNA damage. CDT is composed of three proteins, CdtA, CdtB, and CdtC. CdtB is the enzymatically active or A subunit, which possesses DNase I-like activity, whereas CdtA and CdtC function as heteromeric B subunits that mediate the delivery of CdtB into host cells. We show here that Salmonella enterica serovar Typhi encodes CDT activity, which depends on the function of a CdtB homologous protein. Remarkably, S. enterica serovar Typhi does not encode apparent homologs of CdtA or CdtC. Instead, we found that toxicity, as well as cdtB expression, requires bacterial internalization into host cells. We propose a pathway of toxin delivery in which bacterial internalization relieves the requirement for the functional equivalent of the B subunit of the CDT toxin.
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Affiliation(s)
- Erik Haghjoo
- Section of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06536, USA
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45
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Nesić D, Hsu Y, Stebbins CE. Assembly and function of a bacterial genotoxin. Nature 2004; 429:429-33. [PMID: 15164065 DOI: 10.1038/nature02532] [Citation(s) in RCA: 221] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2004] [Accepted: 03/30/2004] [Indexed: 12/12/2022]
Abstract
The tripartite cytolethal distending toxin (CDT) induces cell cycle arrest and apoptosis in eukaryotic cells. The subunits CdtA and CdtC associate with the nuclease CdtB to form a holotoxin that translocates CdtB into the host cell, where it acts as a genotoxin by creating DNA lesions. Here we show that the crystal structure of the holotoxin from Haemophilus ducreyi reveals that CDT consists of an enzyme of the DNase-I family, bound to two ricin-like lectin domains. CdtA, CdtB and CdtC form a ternary complex with three interdependent molecular interfaces, characterized by globular, as well as extensive non-globular, interactions. The lectin subunits form a deeply grooved, highly aromatic surface that we show to be critical for toxicity. The holotoxin possesses a steric block of the CdtB active site by means of a non-globular extension of the CdtC subunit, and we identify putative DNA binding residues in CdtB that are essential for toxin activity.
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Affiliation(s)
- Dragana Nesić
- Laboratory of Structural Microbiology, The Rockefeller University, New York 10021, USA
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Yasuda T, Takeshita H, Iida R, Ueki M, Nakajima T, Kaneko Y, Mogi K, Kominato Y, Kishi K. A single amino acid substitution can shift the optimum pH of DNase I for enzyme activity: biochemical and molecular analysis of the piscine DNase I family. Biochim Biophys Acta Gen Subj 2004; 1672:174-83. [PMID: 15182937 DOI: 10.1016/j.bbagen.2004.03.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2004] [Revised: 03/23/2004] [Accepted: 03/31/2004] [Indexed: 11/25/2022]
Abstract
We purified four piscine deoxyribonucleases I (DNases I) from Anguilla japonica, Pagrus major, Cryprus carpio and Oreochromis mossambica. The purified enzymes had an optimum pH for activity of approximately 8.0, significantly higher than those of mammalian enzymes. cDNAs encoding the first three of these piscine DNases I were cloned, and the sequence of the Takifugu rubripes enzyme was obtained from a database search. Nucleotide sequence analyses revealed relatively greater structural variations among the piscine DNase I family than among the other vertebrate DNase I families. From comparison of their catalytic properties, the vertebrate DNases I could be classified into two groups: a low-pH group, such as the mammalian enzymes, with a pH optimum of 6.5-7.0, and a high-pH group, such as the reptile, amphibian and piscine enzymes, with a pH optimum of approximately 8.0. The His residue at position 44 of the former group is replaced by Asp in the latter. Replacement of Asp44 of piscine and amphibian DNases I by His decreased their optimum pH to a value similar to that of the low-pH group. Therefore, Asp44His might be involved in an evolutionarily critical change in the optimum pH for the activity of vertebrate DNases I.
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Affiliation(s)
- T Yasuda
- Division of Medical Genetics and Biochemistry, Faculty of Medical Sciences, University of Fukui, Fukui 910-1193, Japan
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Obama T, Fujii S, Ikezawa H, Ikeda K, Imagawa M, Tsukamoto K. His151 and His296 are the acid-base catalytic residues of Bacillus cereus sphingomyelinase in sphingomyelin hydrolysis. Biol Pharm Bull 2003; 26:920-6. [PMID: 12843611 DOI: 10.1248/bpb.26.920] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Bacillus cereus sphingomyelinase belongs to the Mg(2+)-dependent neutral sphingomyelinase, which hydrolyses sphingomyelin to phosphocholine and ceramide, and acts as an extracellular hemolysin. The triplet residues, His151-Asp195-His296, of the enzyme are highly conserved among bacterial and mammalian Mg(2+)-dependent neutral sphingomyelinases. The triplet residues converge on the active-site pocket of the 3D model of the enzyme. To investigate the function of these residues in the acid-base catalysis, we introduced several mutations for each residue by site-directed mutagenesis. Hemolytic and hydrolytic activities of the enzyme, abolished by the mutations at Asp195 and His296, revealed that these residues are critical for the catalytic function. The effect of the divalent metal cations on the pH dependency of the hydrolytic activities indicates that His296 corresponds to the most acidic ionizable group as a general base. The mutagenesis at His151 was also deleterious; however, the H151A and H151Q mutant enzymes partially retained their activities. The H151A mutation affected the most basic ionizable group, suggesting that His151 may act as a general acid in catalysis. By the structural basis of the 3D model, Asp195 must maintain not only the appropriate spatial arrangement but also pK(a)s of His151 and His296. Taking into consideration all of these, we proposed the acid-base catalytic mechanism of B. cereus sphingomyelinase.
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Affiliation(s)
- Takashi Obama
- Department of Molecular Biology, Graduate School of Pharmaceutical Sciences, Nagoya City University, Aichi, Japan
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Miertzschke M, Greiner-Stöffele T. The xthA gene product of Archaeoglobus fulgidus is an unspecific DNase. EUROPEAN JOURNAL OF BIOCHEMISTRY 2003; 270:1838-49. [PMID: 12694197 DOI: 10.1046/j.1432-1033.2003.03548.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
A thermostable enzyme from the hyperthermophilic sulphate-reducing archaeon, Archaeoglobus fulgidus, was expressed and characterized on the assumption that it is homologous to exonuclease III from Escherichia coli. Sequence similarity database searches were performed based on the amino acid sequence of exonuclease III. The 774 bp long gene was isolated from a culture sample and cloned into different vectors. Expression proved successful by transforming pET28_Af_Exo in Origami B(DE3) containing a tRNA plasmid with extra copies of argU, ileY and leuW tRNA genes as a host strain. The lack of thioredoxin reductase (trxB) and glutathione reductase (gor) in Origami B(DE3) allowed formation of disulfide bridges in the cytosol. Purification was performed by heat treatment of the soluble fraction at 80 degrees C for 30 min followed by a two-step ion exchange chromatography. The activity of the enzyme could be maintained. Optimal activity was achieved at 80 degrees C and at a pH of 7. Within the characterization of the protein we could not find any data verifying exonucleolytic activity in the presence of Mg2+ as described [Ankenbauer, W., Laue, F., Sobek, H., & Greif, M. (2000), patent number WO2001023583]. Instead strong DNA binding properties of the enzyme and nicking activities of double stranded DNA comparable to unspecific DNases could be observed. In contrast to exonuclease III from Escherichia coli, the xthA gene product of Archaeoglobus fulgidus is able to degrade supercoiled plasmids and shows no preferences for blunt or recessed 3'-termini of linear double stranded DNA. The enzyme is inhibited by EDTA and shows only weak activity when replacing Mg2+ with Ca2+ ions.
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Affiliation(s)
- Mandy Miertzschke
- Junior research group 'Protein Engineering', Institute of Biochemistry, Faculty of Biology, Pharmacy and Psychology, University of Leipzig/Biotechnological-Biomedical Centre Leipzig, Germany
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Meiss G, Scholz SR, Korn C, Gimadutdinow O, Pingoud A. Identification of functionally relevant histidine residues in the apoptotic nuclease CAD. Nucleic Acids Res 2001; 29:3901-9. [PMID: 11574671 PMCID: PMC60245 DOI: 10.1093/nar/29.19.3901] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The caspase-activated DNase CAD (DFF40/CPAN) degrades chromosomal DNA during apoptosis. Chemical modification with DEPC inactivates the enzyme, suggesting that histidine residues play a decisive role in the catalytic mechanism of this nuclease. Sequence alignment of murine CAD with four homologous apoptotic nucleases reveals four completely (His242, His263, His304 and His308) and two partially (His127 and His313) conserved histidine residues in the catalytic domain of the enzyme. We have changed these residues to asparagine and characterised the variant enzymes with respect to their DNA cleavage activity, structural integrity and oligomeric state. All variants show a decrease in activity compared to the wild-type nuclease as measured by a plasmid DNA cleavage assay. H242N, H263N and H313N exhibit DNA cleavage activities below 5% and H308N displays a drastically altered DNA cleavage pattern compared to wild-type CAD. Whereas all variants but one have the same secondary structure composition and oligomeric state, H242N does not, suggesting that His242 has an important structural role. On the basis of these results, possible roles for His127, His263, His304, His308 and His313 in DNA binding and cleavage are discussed for murine CAD.
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Affiliation(s)
- G Meiss
- Institut für Biochemie, Justus-Liebig-Universität Giessen, Heinrich-Buff-Ring 58, 35392 Giessen, Germany
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Lara-Tejero M, Galán JE. CdtA, CdtB, and CdtC form a tripartite complex that is required for cytolethal distending toxin activity. Infect Immun 2001; 69:4358-65. [PMID: 11401974 PMCID: PMC98507 DOI: 10.1128/iai.69.7.4358-4365.2001] [Citation(s) in RCA: 222] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Campylobacter jejuni encodes a cytolethal distending toxin (CDT) that causes cells to arrest in the G(2)/M transition phase of the cell cycle. Highly related toxins are also produced by other important bacterial pathogens. CDT activity requires the function of three genes: cdtA, cdtB, and cdtC. Recent studies have established that CdtB is the active subunit of CDT, exerting its effect as a nuclease that damages the DNA and triggers cell cycle arrest. Microinjection of CdtB into target cells led to G(2)/M arrest and cytoplasmic distention, in a manner indistinguishable from that caused by CDT treatment. Despite this progress, nothing is known about the composition of the CDT holotoxin or the function of CdtA and CdtC. We show here that, when applied individually, purified CdtA, CdtB, or CdtC does not exhibit toxic activity. In contrast, CdtA, CdtB, and CdtC when combined, interact with one another to form an active tripartite holotoxin that exhibits full cellular toxicity. CdtA has a domain that shares similarity with the B chain of ricin-related toxins. We therefore proposed that CDT is a tripartite toxin composed of CdtB as the enzymatically active subunit and of CdtA and CdtC as the heterodimeric B subunit required for the delivery of CdtB.
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Affiliation(s)
- M Lara-Tejero
- Section of Microbial Pathogenesis, Boyer Center for Molecular Medicine, Yale School of Medicine, New Haven, Connecticut 06536, USA
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