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Roesch EA, Rahmaoui A, Lazarus RA, Konstan MW. The continuing need for dornase alfa for extracellular airway DNA hydrolysis in the era of CFTR modulators. Expert Rev Respir Med 2024:1-16. [PMID: 39176450 DOI: 10.1080/17476348.2024.2394694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 08/11/2024] [Accepted: 08/16/2024] [Indexed: 08/24/2024]
Abstract
INTRODUCTION The availability of cystic fibrosis transmembrane conductance regulator (CFTR) modulators opens the possibility of discontinuing some chronic pulmonary therapies to decrease cystic fibrosis (CF) treatment burden. However, CFTR modulators may not adequately address neutrophilic inflammation, which contributes to a self-perpetual cycle of viscous CF sputum, airway obstruction, inflammation, and lung function decline. AREAS COVERED This review discusses the emerging role of neutrophil extracellular traps in CF and its role in CF sputum viscosity, airway obstruction, and inflammation, based on a literature search of PubMed (1990-present). We summarize clinical trials and real-world studies that support the efficacy of dornase alfa (Pulmozyme) in improving lung function and reducing pulmonary exacerbation in people with CF (PwCF), and we discuss the potential role of dornase alfa in reducing airway inflammation. We also examine the findings of short-term trials evaluating the discontinuation of mucoactive therapy in PwCF receiving CFTR modulators. EXPERT OPINION Long-term studies are needed to assess the impact of discontinuing mucoactive therapy in PwCF who are clinically stable while receiving CFTR modulatory therapy. Treatment decisions should take into account the severity of underlying lung disease. People with advanced CF will likely require ongoing mucoactive therapy.
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Affiliation(s)
- Erica A Roesch
- Department of Pediatrics, Rainbow Babies and Children's Hospital and Case Western Reserve University, Cleveland, OH, USA
| | | | - Robert A Lazarus
- Departments of Biological Chemistry and Early Discovery Biochemistry, Genentech, Inc., South San Francisco, CA, USA
| | - Michael W Konstan
- Department of Pediatrics, Rainbow Babies and Children's Hospital and Case Western Reserve University, Cleveland, OH, USA
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2
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Phong NV, Kim HS, Park HJ, Yeom E, Yang SY. Assessing the Efficacy of Acanthoic Acid Isolated from Acanthopanax koreanum Nakai in Male Infertility: An In Vivo and In Silico Approach. Curr Issues Mol Biol 2024; 46:7411-7429. [PMID: 39057081 PMCID: PMC11276288 DOI: 10.3390/cimb46070440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Revised: 07/05/2024] [Accepted: 07/11/2024] [Indexed: 07/28/2024] Open
Abstract
Acanthoic acid, a diterpene isolated from the root bark of Acanthopanax koreanum Nakai, possesses diverse pharmacological activities, including anti-inflammatory, anti-diabetic, gastrointestinal protection, and cardiovascular protection. This study is the first to investigate the egg-hatching rates of Drosophila melanogaster affected by acanthoic acid. Notably, male flies supplemented with 10 μM acanthoic acid exhibited a strong increase in hatching rates compared with controls under adverse temperature conditions, suggesting a potential protective effect against environmental stressors. Molecular docking simulations revealed the binding affinities and specific interactions between acanthoic acid and proteins related to male infertility, including SHBG, ADAM17, and DNase I, with binding affinity values of -10.2, -6.8, and -5.8 kcal/mol, respectively. Following the docking studies, molecular dynamic simulations were conducted for a duration of 100 ns to examine the stability of these interactions. Additionally, a total binding energy analysis and decomposition analysis offered insights into the underlying energetic components and identified key contributing residues.
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Affiliation(s)
- Nguyen Viet Phong
- Department of Biology Education, Teachers College and Institute for Phylogenomics and Evolution, Kyungpook National University, Daegu 41566, Republic of Korea;
| | - Hyo-Sung Kim
- School of Life Science and Biotechnology, College of Natural Sciences, Kyungpook National University, Daegu 41566, Republic of Korea;
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea
- KNU-G LAMP Project Group, KNU-Institute of Basic Sciences, School of Life Sciences, College of Natural Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Hyun-Jung Park
- Department of Plant Life and Resource Science, Sangji University, Wonju-si 26339, Republic of Korea;
| | - Eunbyul Yeom
- School of Life Science and Biotechnology, College of Natural Sciences, Kyungpook National University, Daegu 41566, Republic of Korea;
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea
- KNU-G LAMP Project Group, KNU-Institute of Basic Sciences, School of Life Sciences, College of Natural Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Seo Young Yang
- Department of Biology Education, Teachers College and Institute for Phylogenomics and Evolution, Kyungpook National University, Daegu 41566, Republic of Korea;
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Stabach PR, Sims D, Gomez-Bañuelos E, Zehentmeier S, Dammen-Brower K, Bernhisel A, Kujawski S, Lopez SG, Petri M, Goldman DW, Lester ER, Le Q, Ishaq T, Kim H, Srivastava S, Kumar D, Pereira JP, Yarema KJ, Koumpouras F, Andrade F, Braddock DT. A dual-acting DNASE1/DNASE1L3 biologic prevents autoimmunity and death in genetic and induced lupus models. JCI Insight 2024; 9:e177003. [PMID: 38888971 PMCID: PMC11383374 DOI: 10.1172/jci.insight.177003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 06/12/2024] [Indexed: 06/20/2024] Open
Abstract
A defining feature of systemic lupus erythematosus (SLE) is loss of tolerance to self-DNA, and deficiency of DNASE1L3, the main enzyme responsible for chromatin degradation in blood, is also associated with SLE. This association can be found in an ultrarare population of pediatric patients with DNASE1L3 deficiency who develop SLE, adult patients with loss-of-function variants of DNASE1L3 who are at a higher risk for SLE, and patients with sporadic SLE who have neutralizing autoantibodies against DNASE1L3. To mitigate the pathogenic effects of inherited and acquired DNASE1L3 deficiencies, we engineered a long-acting enzyme biologic with dual DNASE1/DNASE1L3 activity that is resistant to DNASE1 and DNASE1L3 inhibitors. Notably, we found that the biologic prevented the development of lupus in Dnase1-/-Dnase1L3-/- double-knockout mice and rescued animals from death in pristane-induced lupus. Finally, we confirmed that the human isoform of the enzyme biologic was not recognized by autoantibodies in SLE and efficiently degraded genomic and mitochondrial cell-free DNA, as well as microparticle DNA, in SLE plasma. Our findings suggest that autoimmune diseases characterized by aberrant DNA accumulation, such as SLE, can be effectively treated with a replacement DNASE tailored to bypass pathogenic mechanisms, both genetic and acquired, that restrict DNASE1L3 activity.
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Affiliation(s)
- Paul R Stabach
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Dominique Sims
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Eduardo Gomez-Bañuelos
- Division of Rheumatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Sandra Zehentmeier
- Department of Immunobiology and Yale Stem Cell Center, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Kris Dammen-Brower
- Translational Tissue Engineering Center and Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Andrew Bernhisel
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Sophia Kujawski
- Department of Rheumatology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Sam G Lopez
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Michelle Petri
- Division of Rheumatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Daniel W Goldman
- Division of Rheumatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Ethan R Lester
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Quan Le
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Tayyaba Ishaq
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Hana Kim
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Shivani Srivastava
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Deepika Kumar
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Joao P Pereira
- Department of Immunobiology and Yale Stem Cell Center, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Kevin J Yarema
- Translational Tissue Engineering Center and Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Fotios Koumpouras
- Department of Rheumatology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Felipe Andrade
- Division of Rheumatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Demetrios T Braddock
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
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Kwak SB, Kim SJ, Kang YJ, Lee WW, Huh J, Park JW. Development of a rectally administrable Dnase1 to treat septic shock by targeting NETs. Life Sci 2024; 342:122526. [PMID: 38417543 DOI: 10.1016/j.lfs.2024.122526] [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: 11/17/2023] [Revised: 02/11/2024] [Accepted: 02/21/2024] [Indexed: 03/01/2024]
Abstract
AIMS Neutrophil extracellular trap (NET), which is formed by DNA threads, induces septic shock by aggravating systemic inflammation. An intravenous administration of deoxyribonuclease is regarded as a compelling modality for treating septic shock. However, alternative routes should be chosen when cutaneous veins are all collapsed due to hypotension. In this study, we genetically engineered this enzyme to develop a rectal suppository formulation to treat septic shock. MAIN METHODS Dnase1 was mutated at two amino acid residues to increase its stability in the blood and fused with a cell-penetrating peptide CR8 to increase its absorption through the rectal mucosa, which is designated AR-CR8. The life-saving effect of AR-CR8 was evaluated in a LPS-induced shock mouse model. KEY FINDINGS AR-CR8 was shown to remove NETs effectively in human neutrophils. When AR-CR8 was administered to the mouse rectum, the deoxyribonuclease activity in the mouse serum was significantly increased. In the LPS-induced shock model, 90 % of the control mice died over 72 h after LPS injection. In contrast, the rectal administration of AR-CR8 showed a mortality rate of 30 % by 72 h after LPS injection. The Log-rank test revealed that the survival rate is significantly higher in the AR-CR8 group. The NET markers in the mouse serum were enhanced by LPS, and significantly downregulated in the AR-CR8 group. These results suggest that AR-CR8 ameliorates LPS-induced shock by degrading NETs. SIGNIFICANCE The engineered DNASE1 could be developed as a rectal suppository formulation to treat septic shock urgently at out-of-hospital places where no syringe is available.
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Affiliation(s)
- Su-Bin Kwak
- Department of Pharmacology, Seoul National University College of Medicine, Daehak-ro 103, Jongno-gu, Seoul 03080, Republic of Korea
| | - Sang-Jin Kim
- Department of Pharmacology, Seoul National University College of Medicine, Daehak-ro 103, Jongno-gu, Seoul 03080, Republic of Korea
| | - Yeon Jun Kang
- Laboratory of Autoimmunity and Inflammation, Department of Biomedical Sciences, Seoul National University College of Medicine, Daehak-ro 103, Jongno-gu, Seoul 03080, Republic of Korea; Department of Microbiology and Immunology, Seoul National University College of Medicine, Daehak-ro 103, Jongno-gu, Seoul 03080, Republic of Korea
| | - Won-Woo Lee
- Laboratory of Autoimmunity and Inflammation, Department of Biomedical Sciences, Seoul National University College of Medicine, Daehak-ro 103, Jongno-gu, Seoul 03080, Republic of Korea; Department of Microbiology and Immunology, Seoul National University College of Medicine, Daehak-ro 103, Jongno-gu, Seoul 03080, Republic of Korea
| | - June Huh
- Department of Chemical and Biological Engineering, Korea University, Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Jong-Wan Park
- Department of Pharmacology, Seoul National University College of Medicine, Daehak-ro 103, Jongno-gu, Seoul 03080, Republic of Korea; Department of Biomedical Science, BK21-plus education program, Seoul National University College of Medicine, Daehak-ro 103, Jongno-gu, Seoul 03080, Republic of Korea; Cancer Research Institute and Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Daehak-ro 103, Jongno-gu, Seoul 03080, Republic of Korea.
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Englert H, Göbel J, Khong D, Omidi M, Wolska N, Konrath S, Frye M, Mailer RK, Beerens M, Gerwers JC, Preston RJS, Odeberg J, Butler LM, Maas C, Stavrou EX, Fuchs TA, Renné T. Targeting NETs using dual-active DNase1 variants. Front Immunol 2023; 14:1181761. [PMID: 37287977 PMCID: PMC10242134 DOI: 10.3389/fimmu.2023.1181761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 05/09/2023] [Indexed: 06/09/2023] Open
Abstract
Background Neutrophil Extracellular Traps (NETs) are key mediators of immunothrombotic mechanisms and defective clearance of NETs from the circulation underlies an array of thrombotic, inflammatory, infectious, and autoimmune diseases. Efficient NET degradation depends on the combined activity of two distinct DNases, DNase1 and DNase1-like 3 (DNase1L3) that preferentially digest double-stranded DNA (dsDNA) and chromatin, respectively. Methods Here, we engineered a dual-active DNase with combined DNase1 and DNase1L3 activities and characterized the enzyme for its NET degrading potential in vitro. Furthermore, we produced a mouse model with transgenic expression of the dual-active DNase and analyzed body fluids of these animals for DNase1 and DNase 1L3 activities. We systematically substituted 20 amino acid stretches in DNase1 that were not conserved among DNase1 and DNase1L3 with homologous DNase1L3 sequences. Results We found that the ability of DNase1L3 to degrade chromatin is embedded into three discrete areas of the enzyme's core body, not the C-terminal domain as suggested by the state-of-the-art. Further, combined transfer of the aforementioned areas of DNase1L3 to DNase1 generated a dual-active DNase1 enzyme with additional chromatin degrading activity. The dual-active DNase1 mutant was superior to native DNase1 and DNase1L3 in degrading dsDNA and chromatin, respectively. Transgenic expression of the dual-active DNase1 mutant in hepatocytes of mice lacking endogenous DNases revealed that the engineered enzyme was stable in the circulation, released into serum and filtered to the bile but not into the urine. Conclusion Therefore, the dual-active DNase1 mutant is a promising tool for neutralization of DNA and NETs with potential therapeutic applications for interference with thromboinflammatory disease states.
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Affiliation(s)
- Hanna Englert
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Josephine Göbel
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Danika Khong
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Maryam Omidi
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Nina Wolska
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sandra Konrath
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Maike Frye
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Reiner K. Mailer
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Manu Beerens
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Julian C. Gerwers
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Roger J. S. Preston
- Irish Centre for Vascular Biology, School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Jacob Odeberg
- Department of Clinical Medicine, The Arctic University of Norway, Tromsø, Norway
- Science for Life Laboratory, Department of Protein Science, CBH, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Lynn M. Butler
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Clinical Medicine, The Arctic University of Norway, Tromsø, Norway
- Science for Life Laboratory, Department of Protein Science, CBH, KTH Royal Institute of Technology, Stockholm, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden
| | - Coen Maas
- Department of Clinical Chemistry and Haematology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Evi X. Stavrou
- Medicine Service, Section of Hematology-Oncology, Louis Stokes Veterans Administration Medical Center, Cleveland, OH, United States
- Department of Medicine, Hematology and Oncology Division, Case Western Reserve University School of Medicine, Cleveland, OH, United States
| | - Tobias A. Fuchs
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Neutrolis, Inc., Cambridge, MA, United States
| | - Thomas Renné
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Irish Centre for Vascular Biology, School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland
- Center for Thrombosis and Hemostasis (CTH), Johannes Gutenberg University Medical Center, Mainz, Germany
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6
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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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Huang L, Zhang Y, Du X, An R, Liang X. Escherichia coli Can Eat DNA as an Excellent Nitrogen Source to Grow Quickly. Front Microbiol 2022; 13:894849. [PMID: 35836416 PMCID: PMC9273947 DOI: 10.3389/fmicb.2022.894849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 05/31/2022] [Indexed: 11/13/2022] Open
Abstract
Is DNA or RNA a good nutrient? Although scientists have raised this question for dozens of years, few textbooks mention the nutritional role of nucleic acids. Paradoxically, mononucleotides are widely added to infant formula milk and animal feed. Interestingly, competent bacteria can bind and ingest extracellular DNA and even integrate it into their genome. These results prompt us to clarify whether bacteria can “eat” DNA as food. We found that Escherichia coli can grow well in the medium with DNA as carbon and nitrogen sources. More interestingly, in the presence of glucose and DNA, bacteria grew more rapidly, showing that bacteria can use DNA as an excellent nitrogen source. Surprisingly, the amount of DNA in the culture media decreased but its length remained unchanged, demonstrating that E. coli ingested long DNA directly. The gene expression study shows that E. coli mainly ingests DNA before digestion and digests it in the periplasm. Bifidobacterium bifidum can also use DNA as the nitrogen source for growth, but not efficiently as E. coli. This study is of great significance to study DNA metabolism and utilization in organisms. It also lays a foundation to understand the nutritional function of DNA in intestinal flora and human health.
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Affiliation(s)
- Lili Huang
- College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Yehui Zhang
- College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Xinmei Du
- College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Ran An
- College of Food Science and Engineering, Ocean University of China, Qingdao, China
- *Correspondence: Ran An
| | - Xingguo Liang
- College of Food Science and Engineering, Ocean University of China, Qingdao, China
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Xingguo Liang
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8
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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] [MESH Headings] [Grants] [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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9
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Delfino D, Mori G, Rivetti C, Grigoletto A, Bizzotto G, Cavozzi C, Malatesta M, Cavazzini D, Pasut G, Percudani R. Actin-Resistant DNase1L2 as a Potential Therapeutics for CF Lung Disease. Biomolecules 2021; 11:biom11030410. [PMID: 33802146 PMCID: PMC8002113 DOI: 10.3390/biom11030410] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/02/2021] [Accepted: 03/05/2021] [Indexed: 02/07/2023] Open
Abstract
In cystic fibrosis (CF), the accumulation of viscous lung secretions rich in DNA and actin is a major cause of chronic inflammation and recurrent infections leading to airway obstruction. Mucolytic therapy based on recombinant human DNase1 reduces CF mucus viscosity and promotes airway clearance. However, the marked susceptibility to actin inhibition of this enzyme prompts the research of alternative treatments that could overcome this limitation. Within the human DNase repertoire, DNase1L2 is ideally suited for this purpose because it exhibits metal-dependent endonuclease activity on plasmid DNA in a broad range of pH with acidic optimum and is minimally inhibited by actin. When tested on CF artificial mucus enriched with actin, submicromolar concentrations of DNase1L2 reduces mucus viscosity by 50% in a few seconds. Inspection of superimposed model structures of DNase1 and DNase1L2 highlights differences at the actin-binding interface that justify the increased resistance of DNase1L2 toward actin inhibition. Furthermore, a PEGylated form of the enzyme with preserved enzymatic activity was obtained, showing interesting results in terms of activity. This work represents an effort toward the exploitation of natural DNase variants as promising alternatives to DNase1 for the treatment of CF lung disease.
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Affiliation(s)
- Danila Delfino
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy; (D.D.); (C.C.); (M.M.); (D.C.); (R.P.)
| | - Giulia Mori
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy; (D.D.); (C.C.); (M.M.); (D.C.); (R.P.)
- Correspondence: (G.M.); (C.R.); (G.P.)
| | - Claudio Rivetti
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy; (D.D.); (C.C.); (M.M.); (D.C.); (R.P.)
- Correspondence: (G.M.); (C.R.); (G.P.)
| | - Antonella Grigoletto
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, 35131 Padova, Italy; (A.G.); (G.B.)
| | - Gloria Bizzotto
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, 35131 Padova, Italy; (A.G.); (G.B.)
| | - Cristian Cavozzi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy; (D.D.); (C.C.); (M.M.); (D.C.); (R.P.)
| | - Marco Malatesta
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy; (D.D.); (C.C.); (M.M.); (D.C.); (R.P.)
| | - Davide Cavazzini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy; (D.D.); (C.C.); (M.M.); (D.C.); (R.P.)
| | - Gianfranco Pasut
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, 35131 Padova, Italy; (A.G.); (G.B.)
- Correspondence: (G.M.); (C.R.); (G.P.)
| | - Riccardo Percudani
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy; (D.D.); (C.C.); (M.M.); (D.C.); (R.P.)
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10
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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: 51] [Impact Index Per Article: 12.8] [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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11
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Abstract
Human deoxyribonuclease I (DNase I) is an endonuclease that catalyzes the hydrolysis of extracellular DNA and is just one of the numerous types of nucleases found in nature. The enzymatic mechanism for a single turnover is reasonably well understood based on biochemical and structural studies that are consistent with divalent metal ion dependent nonspecific nicking of a phosphodiester bond in one of the strands of double stranded DNA. Recombinant human DNase I (rhDNase I, rhDNase, Pulmozyme®, dornase alfa) has been expressed in mammalian cell culture in Chinese hamster ovary cells and developed clinically where it is aerosolized into the airways for treatment of pulmonary disease in patients with cystic fibrosis (CF). rhDNase I hydrolyzes the DNA in purulent sputum of CF patients and reduces sputum viscoelasticity. Reduction of high molecular weight DNA into smaller fragments by treatment with aerosolized rhDNase I has been proposed as the mechanism to reduce the mucus viscosity and improve mucus clearability from obstructed airways in patients. The improved clearance of the purulent mucus enhances pulmonary function and reduces recurrent exacerbations of respiratory symptoms. rhDNase I was approved for clinical use in 1993 and has been widely used as a safe and effective therapy for CF patients. The use of rhDNase I has also been investigated in other diseases where exogenous DNA has been implicated in the disease pathology.
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12
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Neutrophil extracellular traps in the central nervous system hinder bacterial clearance during pneumococcal meningitis. Nat Commun 2019; 10:1667. [PMID: 30971685 PMCID: PMC6458182 DOI: 10.1038/s41467-019-09040-0] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 02/12/2019] [Indexed: 01/05/2023] Open
Abstract
Neutrophils are crucial mediators of host defense that are recruited to the central nervous system (CNS) in large numbers during acute bacterial meningitis caused by Streptococcus pneumoniae. Neutrophils release neutrophil extracellular traps (NETs) during infections to trap and kill bacteria. Intact NETs are fibrous structures composed of decondensed DNA and neutrophil-derived antimicrobial proteins. Here we show NETs in the cerebrospinal fluid (CSF) of patients with pneumococcal meningitis, and their absence in other forms of meningitis with neutrophil influx into the CSF caused by viruses, Borrelia and subarachnoid hemorrhage. In a rat model of meningitis, a clinical strain of pneumococci induced NET formation in the CSF. Disrupting NETs using DNase I significantly reduces bacterial load, demonstrating that NETs contribute to pneumococcal meningitis pathogenesis in vivo. We conclude that NETs in the CNS reduce bacterial clearance and degrading NETs using DNase I may have significant therapeutic implications. Neutrophils play critical roles in the host response to bacteria, including the production neutrophil extracellular traps (NET). Here the authors show that NET formation in the context of pneumococcal meningitis impairs bacterial clearance and targeting NET formation in this context could be a potential therapeutic option.
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13
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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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14
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Impact of PEGylation on the mucolytic activity of recombinant human deoxyribonuclease I in cystic fibrosis sputum. Clin Sci (Lond) 2018; 132:1439-1452. [PMID: 29871879 DOI: 10.1042/cs20180315] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 04/13/2018] [Accepted: 06/04/2018] [Indexed: 12/28/2022]
Abstract
Highly viscous mucus and its impaired clearance characterize the lungs of patients with cystic fibrosis (CF). Pulmonary secretions of patients with CF display increased concentrations of high molecular weight components such as DNA and actin. Recombinant human deoxyribonuclease I (rhDNase) delivered by inhalation cleaves DNA filaments contained in respiratory secretions and thins them. However, rapid clearance of rhDNase from the lungs implies a daily administration and thereby a high therapy burden and a reduced patient compliance. A PEGylated version of rhDNase could sustain the presence of the protein within the lungs and reduce its administration frequency. Here, we evaluated the enzymatic activity of rhDNase conjugated to a two-arm 40 kDa polyethylene glycol (PEG40) in CF sputa. Rheology data indicated that both rhDNase and PEG40-rhDNase presented similar mucolytic activity in CF sputa, independently of the purulence of the sputum samples as well as of their DNA, actin and ions contents. The macroscopic appearance of the samples correlated with the DNA content of the sputa: the more purulent the sample, the higher the DNA concentration. Finally, quantification of the enzymes in CF sputa following rheology measurement suggests that PEGylation largely increases the stability of rhDNase in CF respiratory secretions, since 24-fold more PEG40-rhDNase than rhDNase was recovered from the samples. The present results are considered positive and provide support to the continuation of the research on a long acting version of rhDNase to treat CF lung disease.
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15
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Lam C, Santell L, Wilson B, Yim M, Louie S, Tang D, Shaw D, Chan P, Lazarus RA, Snedecor B, Misaghi S. Taming hyperactive hDNase I: Stable inducible expression of a hyperactive salt- and actin-resistant variant of human deoxyribonuclease I in CHO cells. Biotechnol Prog 2017; 33:523-533. [PMID: 28127892 DOI: 10.1002/btpr.2439] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 12/22/2016] [Indexed: 12/17/2022]
Abstract
While the most common causes of clonal instability are DNA copy number loss and silencing, toxicity of the expressed protein(s) may also induce clonal instability. Human DNase I (hDNase I) is used therapeutically for the treatment of cystic fibrosis (CF) and may have potential benefit for use in systemic lupus erythematosus (SLE). hDNase I is an endonuclease that catalyzes degradation of extracellular DNA and is inhibited by both salt and G-actin. Engineered versions of hDNase I, bearing multiple point mutations, which renders them Hyperactive, Salt- and Actin-Resistant (HSAR-hDNase I) have been developed previously. However, constitutive expression of HSAR-hDNase I enzymes has been very challenging and, despite considerable efforts and screening thousands of clones, no stable clone capable of constitutive expression had been obtained. Here, we developed a regulated expression system for stable expression of an HSAR-hDNase I in Chinese Hamster Ovary (CHO) cells. The HSAR-hDNase I clones were stable and, upon induction, expressed enzymatically functional protein. Our findings suggest that degradation of host's DNA mediated by HSAR-hDNase I during cell division is the likely cause of clonal instability observed in cells constitutively expressing this protein. Purified HSAR-hDNase I was both hyperactive and resistant to inhibition by salt and G-actin, resulting in an enzyme having ca. 10-fold greater specific activity and the potential to be a superior therapeutic agent to wild type (WT) hDNase I. Furthermore, the ability to regulate hDNase I expression has enabled process development improvements that achieve higher cell growth and product titers while maintaining product quality. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 32:523-533, 2017.
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Affiliation(s)
- Cynthia Lam
- Early Stage Cell Culture, Genentech, Inc, South San Francisco, CA, 94080
| | - Lydia Santell
- Early Discovery Biochemistry, Genentech, Inc, South San Francisco, CA, 94080
| | - Blair Wilson
- Biochemical and Cellular Pharmacology Dept., Genentech, Inc, South San Francisco, CA, 94080
| | - Mandy Yim
- Early Stage Cell Culture, Genentech, Inc, South San Francisco, CA, 94080
| | - Salina Louie
- Early Stage Cell Culture, Genentech, Inc, South San Francisco, CA, 94080
| | - Danming Tang
- Early Stage Cell Culture, Genentech, Inc, South San Francisco, CA, 94080
| | - David Shaw
- Early Stage Cell Culture, Genentech, Inc, South San Francisco, CA, 94080
| | - Pamela Chan
- Biochemical and Cellular Pharmacology Dept., Genentech, Inc, South San Francisco, CA, 94080
| | - Robert A Lazarus
- Early Discovery Biochemistry, Genentech, Inc, South San Francisco, CA, 94080
| | - Brad Snedecor
- Early Stage Cell Culture, Genentech, Inc, South San Francisco, CA, 94080
| | - Shahram Misaghi
- Early Stage Cell Culture, Genentech, Inc, South San Francisco, CA, 94080
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16
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Li C, Chen X, Wang N, Zhang B. An ultrasensitive and label-free electrochemical DNA biosensor for detection of DNase I activity. RSC Adv 2017. [DOI: 10.1039/c7ra01995e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
An ultrasensitive and label-free DNA biosensor was developed to detect deoxyribonuclease I activity based on electrochemical method.
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Affiliation(s)
- Chen Li
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun 130022
- P. R. China
| | - Xuejuan Chen
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun 130022
- P. R. China
| | - Nan Wang
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun 130022
- P. R. China
| | - Bailin Zhang
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun 130022
- P. R. China
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17
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Chen L, Fang S, Xiao X, Zheng B, Zhao M. Single-Stranded DNA Assisted Cell Penetrating Peptide-DNA Conjugation Strategy for Intracellular Imaging of Nucleases. Anal Chem 2016; 88:11306-11309. [PMID: 27934106 DOI: 10.1021/acs.analchem.6b03743] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Cell penetrating peptides (CPPs) are very useful tools for delivery of DNA molecules into living cells without damaging the cell membranes. However, covalent conjugation of DNAs to CPPs is technically difficult, and the reactions between DNA and target nucleases are also liable to be affected by the cationic CPP molecules. In this work, we demonstrate that the electrostatic interactions between CPPs and single-stranded DNA (ssDNA) were stronger than those between CPP and double-stranded DNA (dsDNA). Taking advantage of this property, we developed an ssDNA protected CPP-DNA fluorescent probe which allowed for noninvasive and efficient cellular uptake and rapid imaging of target nucleases in living cells. The probe is highly sensitive and selective. This work represents the first example of using CPP-DNA conjugate to deliver DNA fluorescent probes for in situ imaging of nucleases within cells. The developed approach also holds great potential for the cellular delivery of other nucleic acid molecules for diagnosis or therapeutics purposes.
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Affiliation(s)
- Lu Chen
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University , Beijing 100871, China
| | - Simin Fang
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University , Beijing 100871, China
| | - Xianjin Xiao
- Family Planning Research Institute/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology , Wuhan, Hubei 430030, China
| | - Bo Zheng
- Department of Chemistry, The Chinese University of Hong Kong , Shatin, New Territories, Hong Kong, China
| | - Meiping Zhao
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University , Beijing 100871, China
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18
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Tedcastle A, Illingworth S, Brown A, Seymour LW, Fisher KD. Actin-resistant DNAse I Expression From Oncolytic Adenovirus Enadenotucirev Enhances Its Intratumoral Spread and Reduces Tumor Growth. Mol Ther 2016; 24:796-804. [PMID: 26708004 PMCID: PMC4886935 DOI: 10.1038/mt.2015.233] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 12/17/2015] [Indexed: 12/27/2022] Open
Abstract
Spread of oncolytic viruses through tumor tissue is essential to effective virotherapy. Interstitial matrix is thought to be a significant barrier to virus particle convection between "islands" of tumor cells. One way to address this is to encode matrix-degrading enzymes within oncolytic viruses, for secretion from infected cells. To test the hypothesis that extracellular DNA provides an important barrier, we assessed the ability of DNase to promote virus spread. Nonreplicating Ad5 vectors expressing actin-resistant DNase (aDNAse I), proteinase K (PK), hyaluronidase (rhPH20), and chondroitinase ABC (CABC) were injected into established DLD human colorectal adenocarcinoma xenografts, transcomplemented with a replicating Ad5 virus. Each enzyme improved oncolysis by the replicating adenovirus, with no evidence of tumor cells being shed into the bloodstream. aDNAse I and rhPH20 hyaluronidase were then cloned into conditionally-replicating group B adenovirus, Enadenotucirev (EnAd). EnAd encoding each enzyme showed significantly better antitumor efficacy than the parental virus, with the aDNAse I-expressing virus showing improved spread. Both DNase and hyaluronidase activity was still measurable 32 days postinfection. This is the first time that extracellular DNA has been implicated as a barrier for interstitial virus spread, and suggests that oncolytic viruses expressing aDNAse I may be promising candidates for clinical translation.
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Affiliation(s)
| | | | | | | | - Kerry D Fisher
- Department of Oncology, University of Oxford, Oxford, UK
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19
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Su X, Zhang C, Zhu X, Fang S, Weng R, Xiao X, Zhao M. Simultaneous fluorescence imaging of the activities of DNases and 3' exonucleases in living cells with chimeric oligonucleotide probes. Anal Chem 2013; 85:9939-46. [PMID: 24016314 DOI: 10.1021/ac402615c] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Real-time fluorescence imaging of the activity of nucleases in living cells has been a difficult issue because of unintended degradation of the natural oligonucleotides by nontarget nucleases or interactions with other proteins. In this work, we demonstrate two types of highly selective, sensitive, and robust oligonucleotide probes for simultaneous imaging of the activities of two different nucleases in living cells. The probes consist of the desired substrate structure of the target nuclease and partially phosphorothioate modified backbone labeled with fluorophore and quencher for protection from undesired degradation by other nucleases and signal transduction. Upon reaction with the target nuclease, the initially fluorescence quenched probe was cleaved and the fluorophore was separated from the quencher, giving out strong fluorescence signals. Two nucleases, DNase I and Exonuclease III, were employed as model enzymes to demonstrate the concept. In vitro studies proved that the two probes could discriminate their respective target nucleases in serum with high resistance to other coexisting enzymes. The lower limits of detection for DNase I and Exonuclease III were observed to be 40 U/L and 2.0 U/L, respectively. By labeling the two probes with different fluorophores and quenchers, simultaneous visualization of the activities of DNases and 3' exonucleases was achieved in both HeLa cells and the suspension cells of Arabidopsis thaliana. The developed approaches may greatly facilitate the studies on the intracellular functions of the two nucleases and other related biological processes. The probe design concept may also be further adapted to the detection of many other nucleases.
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Affiliation(s)
- Xin Su
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University , Beijing, 100871, China
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20
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Bioengineered lysozyme reduces bacterial burden and inflammation in a murine model of mucoid Pseudomonas aeruginosa lung infection. Antimicrob Agents Chemother 2013; 57:5559-64. [PMID: 23979752 DOI: 10.1128/aac.00500-13] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The spread of drug-resistant bacterial pathogens is a growing global concern and has prompted an effort to explore potential adjuvant and alternative therapies derived from nature's repertoire of bactericidal proteins and peptides. In humans, the airway surface liquid layer is a rich source of antibiotics, and lysozyme represents one of the most abundant and effective antimicrobial components of airway secretions. Human lysozyme is active against both Gram-positive and Gram-negative bacteria, acting through several mechanisms, including catalytic degradation of cell wall peptidoglycan and subsequent bacterial lysis. In the infected lung, however, lysozyme's dense cationic character can result in sequestration and inhibition by polyanions associated with airway inflammation. As a result, the efficacy of the native enzyme may be compromised in the infected and inflamed lung. To address this limitation, we previously constructed a charge-engineered variant of human lysozyme that was less prone to electrostatic-mediated inhibition in vitro. Here, we employ a murine model to show that this engineered enzyme is superior to wild-type human lysozyme as a treatment for mucoid Pseudomonas aeruginosa lung infections. The engineered enzyme effectively decreases the bacterial burden and reduces markers of inflammation and lung injury. Importantly, we found no evidence of acute toxicity or allergic hypersensitivity upon repeated administration of the engineered biotherapeutic. Thus, the charge-engineered lysozyme represents an interesting therapeutic candidate for P. aeruginosa lung infections.
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21
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Liu Y, Wang S, Zhang C, Su X, Huang S, Zhao M. Enhancing the Selectivity of Enzyme Detection by Using Tailor-Made Nanoparticles. Anal Chem 2013; 85:4853-7. [DOI: 10.1021/ac4007914] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Yibin Liu
- Beijing National
Laboratory for Molecular Sciences,
MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering,
College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Shanshan Wang
- Beijing National
Laboratory for Molecular Sciences,
MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering,
College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Chen Zhang
- Beijing National
Laboratory for Molecular Sciences,
MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering,
College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Xin Su
- Beijing National
Laboratory for Molecular Sciences,
MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering,
College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Shan Huang
- Beijing National
Laboratory for Molecular Sciences,
MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering,
College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Meiping Zhao
- Beijing National
Laboratory for Molecular Sciences,
MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering,
College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
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22
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Shaw A, Bischof D, Jasti A, Ernstberger A, Hawkins T, Cornetta K. Using Pulmozyme DNase treatment in lentiviral vector production. Hum Gene Ther Methods 2013; 23:65-71. [PMID: 22428981 DOI: 10.1089/hgtb.2011.204] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In the production of lentiviral vector for clinical studies the purity of the final product is of vital importance. To remove plasmid and producer cell line DNA, investigators have incubated the vector product with Benzonase, a bacterially derived DNase. As an alternative we investigated the use of Pulmozyme, a U.S. Food and Drug Administration-approved human DNase for the treatment of cystic fibrosis, by comparing the efficiency of DNA removal from lentiviral vector preparations. A green fluorescent protein-expressing lentiviral vector was prepared by transient calcium phosphate transfection of HEK 293T cells and DNA removal was compared when treating vector after harvest or immediately after transfection. The effectiveness of DNase treatment was measured by quantitative PCR using primers for vesicular stomatitis virus glycoprotein G viral envelope plasmid. When treating the final product, 1-hr incubations (37°C) with Pulmozyme at 20 U/ml reduced plasmid DNA to undetectable levels. Longer incubations (up to 4 hr) did not improve DNA removal at lower concentrations and the effectiveness was equivalent to or better than Benzonase at 50 U/ml. Attempting to use Pulmozyme immediately after transfection, but before final medium change, as a means to decrease Pulmozyme concentration in the final product provided a 2-log reduction in DNA but was inferior to treatment at the end of production. Pulmozyme, at concentrations up to 100 U/ml, had no measurable effect on infectious titer of the final vector product. The use of Pulmozyme is likely to increase the cost of DNase treatment when preparing vector product and should be considered when generating clinical-grade vector products.
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Affiliation(s)
- Aaron Shaw
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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23
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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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24
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Abstract
Actin exists as a monomer (G-actin) which can be polymerized to filaments) F-actin) that under the influence of actin-binding proteins and polycations bundle and contribute to the formation of the cytoskeleton. Bundled actin from lysed cells increases the viscosity of sputum in lungs of cystic fibrosis patients. The human host defense peptide LL-37 was previously shown to induce actin bundling and was thus hypothesized to contribute to the pathogenicity of this disease. In this work, interactions between actin and the cationic LL-37 were studied by optical, proteolytic and surface plasmon resonance methods and compared to those obtained with scrambled LL-37 and with the cationic protein lysozyme. We show that LL-37 binds strongly to CaATP-G-actin while scrambled LL-37 does not. While LL-37, at superstoichiometric LL-37/actin concentrations polymerizes MgATP-G-actin, at lower non-polymerizing concentrations LL-37 inhibits actin polymerization by MgCl2 or NaCl. LL-37 bundles Mg-F-actin filaments both at low and physiological ionic strength when in equimolar or higher concentrations than those of actin. The LL-37 induced bundles are significantly less sensitive to increase in ionic strength than those induced by scrambled LL-37 and lysozyme. LL-37 in concentrations lower than those needed for actin polymerization or bundling, accelerates cleavage of both monomer and polymer actin by subtilisin. Our results indicate that the LL-37-actin interaction is partially electrostatic and partially hydrophobic and that a specific actin binding sequence in the peptide is responsible for the hydrophobic interaction. LL-37-induced bundles, which may contribute to the accumulation of sputum in cystic fibrosis, are dissociated very efficiently by DNase-1 and also by cofilin.
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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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Surface-localized spermidine protects the Pseudomonas aeruginosa outer membrane from antibiotic treatment and oxidative stress. J Bacteriol 2011; 194:813-26. [PMID: 22155771 DOI: 10.1128/jb.05230-11] [Citation(s) in RCA: 122] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Extracellular DNA acts as a cation chelator and induces the expression of antibiotic resistance genes regulated by Mg(2+) levels. Here we report the characterization of novel DNA-induced genes in Pseudomonas aeruginosa that are annotated as homologs of the spermidine synthesis genes speD (PA4773) and speE (PA4774). The addition of sublethal concentrations of DNA and membrane-damaging antibiotics induced expression of the genes PA4773 to PA4775, as shown using transcriptional lux fusions and quantitative RT-PCR. Exogenous polyamine addition prevented DNA- and peptide-mediated gene induction. Mutation of PA4774 resulted in an increased outer membrane (OM) susceptibility phenotype upon polymyxin B, CP10A, and gentamicin treatment. When the membrane-localized fluorescent probe C(11)-BODIPY(581/591) was used as an indicator of peroxidation of membrane lipids, the PA4774::lux mutant demonstrated an increased susceptibility to oxidative membrane damage from H(2)O(2) treatment. Addition of exogenous polyamines protected the membranes of the PA4774::lux mutant from polymyxin B and H(2)O(2) treatment. Polyamines from the outer surface were isolated and shown to contain putrescine and spermidine by using high-performance liquid chromatography and mass spectrometry. The PA4774::lux mutant did not produce spermidine on the cell surface, but genetic complementation restored surface spermidine production as well as the antibiotic and oxidative stress resistance phenotypes of the membrane. We have identified new functions for spermidine on the cell surface and propose that polyamines are produced under Mg(2+)-limiting conditions as an organic polycation to bind lipopolysaccharide (LPS) and to stabilize and protect the outer membrane against antibiotic and oxidative damage.
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27
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Mulcahy H, Lewenza S. Magnesium limitation is an environmental trigger of the Pseudomonas aeruginosa biofilm lifestyle. PLoS One 2011; 6:e23307. [PMID: 21858064 PMCID: PMC3156716 DOI: 10.1371/journal.pone.0023307] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2011] [Accepted: 07/15/2011] [Indexed: 11/30/2022] Open
Abstract
Biofilm formation is a conserved strategy for long-term bacterial survival in nature and during infections. Biofilms are multicellular aggregates of cells enmeshed in an extracellular matrix. The RetS, GacS and LadS sensors control the switch from a planktonic to a biofilm mode of growth in Pseudomonas aeruginosa. Here we detail our approach to identify environmental triggers of biofilm formation by investigating environmental conditions that repress expression of the biofilm repressor RetS. Mg2+ limitation repressed the expression of retS leading to increased aggregation, exopolysaccharide (EPS) production and biofilm formation. Repression of retS expression under Mg2+ limitation corresponded with induced expression of the GacA-controlled small regulatory RNAs rsmZ and rsmY and the EPS biosynthesis operons pel and psl. We recently demonstrated that extracellular DNA sequesters Mg2+ cations and activates the cation-sensing PhoPQ two-component system, which leads to increased antimicrobial peptide resistance in biofilms. Here we show that exogenous DNA and EDTA, through their ability to chelate Mg2+, promoted biofilm formation. The repression of retS in low Mg2+ was directly controlled by PhoPQ. PhoP also directly controlled expression of rsmZ but not rsmY suggesting that PhoPQ controls the equilibrium of the small regulatory RNAs and thus fine-tunes the expression of genes in the RetS pathway. In summary, Mg2+ limitation is a biologically relevant environmental condition and the first bonafide environmental signal identified that results in transcriptional repression of retS and promotes P. aeruginosa biofilm formation.
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Affiliation(s)
- Heidi Mulcahy
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Canada
| | - Shawn Lewenza
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Canada
- * E-mail:
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Rogers GB, Hoffman LR, Döring G. Novel concepts in evaluating antimicrobial therapy for bacterial lung infections in patients with cystic fibrosis. J Cyst Fibros 2011; 10:387-400. [PMID: 21775220 DOI: 10.1016/j.jcf.2011.06.014] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2011] [Revised: 06/04/2011] [Accepted: 06/17/2011] [Indexed: 10/17/2022]
Abstract
Cystic fibrosis (CF) patients suffer typically from bacterial infections of their airways. Whilst current antibiotic-based treatment of these infections has brought much benefit to patients, it has been difficult to make either direct or indirect assessments of the in vivo efficacy of any specific treatment used. Traditional culture-based assessment has for example been rarely used to determine the direct impact of therapy on the bacteria in the airways. Instead, the "success" of a treatment is most often gauged through measures of respiratory and general health. New culture-independent approaches though are emerging that offer much promise here however in allowing a more comprehensive evaluation of antimicrobial efficacy. These new methods offer an opportunity to examine bacterial outcomes rather than host outcomes alone. Application of these novel techniques in a systematic way will lead to the rationalisation and, likely greater still individualisation, of therapy for CF patients. This review discusses host and microbiological factors that may influence antibiotic efficacy. Moreover, the degree to which the inherent complexity of CF respiratory infections complicates the process of determining treatment impact and the need to identify more robust microbiological outcome measures will also be reviewed.
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Affiliation(s)
- Geraint B Rogers
- Molecular Microbiology Research Laboratory, King's College London, United Kingdom.
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Next-generation sequencing in the analysis of human microbiota: essential considerations for clinical application. Mol Diagn Ther 2011; 14:343-50. [PMID: 21275452 DOI: 10.1007/bf03256391] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The development of next-generation sequencing (NGS) presents an unprecedented opportunity to investigate the complex microbial communities that are associated with the human body. It offers for the first time a basis for detailed temporal and spatial analysis, with the potential to revolutionize our understanding of many clinically important systems. However, while advances continue to be made in areas such as PCR amplification for NGS, sequencing protocols, and data analysis, in many cases the quality of the data generated is undermined by a failure to address fundamental aspects of experimental design. While little is added in terms of time or cost by the analysis of repeat samples, the exclusion of DNA from dead bacterial cells and the extracellular matrix, the use of efficient nucleic acid extraction methodologies, and the implementation of safeguards to minimize the introduction of contaminating nucleic acids, such considerations are essential in achieving an accurate representation of the system being studied. In this review, the chronic bacterial infections that characterize lower respiratory tract infections in cystic fibrosis patients are used as an example system to examine the implications of a failure to address these issues when designing NGS-based analysis of human-associated microbiota. Further, ways in which the impact of these factors can be minimized are discussed.
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Gill A, Scanlon TC, Osipovitch DC, Madden DR, Griswold KE. Crystal structure of a charge engineered human lysozyme having enhanced bactericidal activity. PLoS One 2011; 6:e16788. [PMID: 21408218 PMCID: PMC3049763 DOI: 10.1371/journal.pone.0016788] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2010] [Accepted: 01/14/2011] [Indexed: 11/18/2022] Open
Abstract
Human lysozyme is a key component of the innate immune system, and recombinant forms of the enzyme represent promising leads in the search for therapeutic agents able to treat drug-resistant infections. The wild type protein, however, fails to participate effectively in clearance of certain infections due to inherent functional limitations. For example, wild type lysozymes are subject to electrostatic sequestration and inactivation by anionic biopolymers in the infected airway. A charge engineered variant of human lysozyme has recently been shown to possess improved antibacterial activity in the presence of disease associated inhibitory molecules. Here, the 2.04 Å crystal structure of this variant is presented along with an analysis that provides molecular level insights into the origins of the protein's enhanced performance. The charge engineered variant's two mutated amino acids exhibit stabilizing interactions with adjacent native residues, and from a global perspective, the mutations cause no gross structural perturbations or loss of stability. Importantly, the two substitutions dramatically expand the negative electrostatic potential that, in the wild type enzyme, is restricted to a small region near the catalytic residues. The net result is a reduction in the overall strength of the engineered enzyme's electrostatic potential field, and it appears that the specific nature of this remodeled field underlies the variant's reduced susceptibility to inhibition by anionic biopolymers.
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Affiliation(s)
- Avinash Gill
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire, United States of America
| | - Thomas C. Scanlon
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire, United States of America
| | - Daniel C. Osipovitch
- Program in Experimental and Molecular Medicine, Dartmouth College, Hanover, New Hampshire, United States of America
| | - Dean R. Madden
- Department of Biochemistry, Dartmouth Medical School, Dartmouth College, Hanover, New Hampshire, United States of America
- Program in Molecular and Cellular Biology, Dartmouth College, Hanover, New Hampshire, United States of America
| | - Karl E. Griswold
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire, United States of America
- Program in Molecular and Cellular Biology, Dartmouth College, Hanover, New Hampshire, United States of America
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, United States of America
- * E-mail:
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31
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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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Scanlon TC, Teneback CC, Gill A, Bement JL, Weiner JA, Lamppa JW, Leclair LW, Griswold KE. Enhanced antimicrobial activity of engineered human lysozyme. ACS Chem Biol 2010; 5:809-18. [PMID: 20604527 DOI: 10.1021/cb1001119] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Lysozymes contain a disproportionately large fraction of cationic residues, and are thereby attracted toward the negatively charged surface of bacterial targets. Importantly, this conserved biophysical property may inhibit lysozyme antibacterial function during acute and chronic infections. A mouse model of acute pulmonary Pseudomonas aeruginosa infection demonstrated that anionic biopolymers accumulate to high concentrations in the infected lung, and the presence of these species correlates with decreased endogenous lysozyme activity. To develop antibacterial enzymes designed specifically to be used as antimicrobial agents in the infected airway, the electrostatic potential of human lysozyme (hLYS) was remodeled by protein engineering. A novel, high-throughput screen was implemented to functionally interrogate combinatorial libraries of charge-engineered hLYS proteins, and variants with improved bactericidal activity were isolated and characterized in detail. These studies illustrate a general mechanism by which polyanions inhibit lysozyme function, and they are the first direct demonstration that decreasing hLYS's net cationic character improves its antibacterial activity in the presence of disease-associated biopolymers. In addition to avoiding electrostatic sequestration, at least one charge-engineered variant also kills bacteria more rapidly in the absence of inhibitory biopolymers; this observation supports a novel hypothesis that tuning the cellular affinity of peptidoglycan hydrolases may be a general strategy for improving kinetics of bacterial killing.
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Affiliation(s)
| | - Charlotte C. Teneback
- The Vermont Lung Center, Department of Medicine, University of Vermont College of Medicine, Burlington, Vermont 05405
| | | | - Jenna L. Bement
- The Vermont Lung Center, Department of Medicine, University of Vermont College of Medicine, Burlington, Vermont 05405
| | | | | | - Laurie W. Leclair
- The Vermont Lung Center, Department of Medicine, University of Vermont College of Medicine, Burlington, Vermont 05405
| | - Karl E. Griswold
- Thayer School of Engineering
- Program in Molecular and Cellular Biology
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755
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Mulcahy H, Charron-Mazenod L, Lewenza S. Pseudomonas aeruginosa produces an extracellular deoxyribonuclease that is required for utilization of DNA as a nutrient source. Environ Microbiol 2010; 12:1621-9. [PMID: 20370819 DOI: 10.1111/j.1462-2920.2010.02208.x] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen that occupies a wide variety of environmental niches. Extracellular DNA is ubiquitous in various environments and is a rich source of carbon, nitrogen and phosphate. Here we show that P. aeruginosa is capable of using DNA as a nutrient source. Under phosphate-limiting conditions, or when DNA is supplied as a source of phosphate, expression of PA3909 is induced. PA3909 encodes an extracellular deoxyribonuclease (DNase), which is required for degradation of DNA and utilization of DNA as a source of carbon, nitrogen and phosphate. Stabilization of PA3909 by the addition of excess Mg(2+) and Ca(2+) was required for DNase activity in culture supernatants. Extracellular DNase activity was seen in multiple P. aeruginosa strains and isolates from cystic fibrosis patients. The primary Xcp type II secretion system but not the Hxc type II secretion system is required for DNase activity and the ability to use DNA as a source of nutrients. This study identifies an extracellular DNase produced by P. aeruginosa that enables degradation of extracellular DNA into an accessible source of carbon, nitrogen and phosphate. DNase production by P. aeruginosa also has important implications for virulence and biofilm formation.
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Affiliation(s)
- Heidi Mulcahy
- Department of Microbiology and Infectious Diseases, University of Calgary, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada
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Lee W, Zhang Y, Mukhyala K, Lazarus RA, Zhang Z. Bi-directional SIFT predicts a subset of activating mutations. PLoS One 2009; 4:e8311. [PMID: 20011534 PMCID: PMC2788704 DOI: 10.1371/journal.pone.0008311] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2009] [Accepted: 11/18/2009] [Indexed: 11/19/2022] Open
Abstract
Advancements in sequencing technologies have empowered recent efforts to identify polymorphisms and mutations on a global scale. The large number of variations and mutations found in these projects requires high-throughput tools to identify those that are most likely to have an impact on function. Numerous computational tools exist for predicting which mutations are likely to be functional, but none that specifically attempt to identify mutations that result in hyperactivation or gain-of-function. Here we present a modified version of the SIFT (Sorting Intolerant from Tolerant) algorithm that utilizes protein sequence alignments with homologous sequences to identify functional mutations based on evolutionary fitness. We show that this bi-directional SIFT (B-SIFT) is capable of identifying experimentally verified activating mutants from multiple datasets. B-SIFT analysis of large-scale cancer genotyping data identified potential activating mutations, some of which we have provided detailed structural evidence to support. B-SIFT could prove to be a valuable tool for efforts in protein engineering as well as in identification of functional mutations in cancer.
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Affiliation(s)
- William Lee
- Department of Bioinformatics, Genentech, Inc., South San Francisco, California, United States of America
| | - Yan Zhang
- Department of Bioinformatics, Genentech, Inc., South San Francisco, California, United States of America
| | - Kiran Mukhyala
- Department of Bioinformatics, Genentech, Inc., South San Francisco, California, United States of America
| | - Robert A. Lazarus
- Department of Protein Engineering, Genentech, Inc., South San Francisco, California, United States of America
| | - Zemin Zhang
- Department of Bioinformatics, Genentech, Inc., South San Francisco, California, United States of America
- * E-mail:
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35
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Nakajima T, Takagi R, Tajima Y, Makita C, Kominato Y, Kuribara J, Ohshima S, Tada H, Tsurugaya H, Kobayashi Y, Takeshita H, Kawai Y, Yasuda T. Development of a sensitive enzyme-linked immunosorbent assay for measurement of DNase I in human serum. Clin Chim Acta 2009; 403:219-22. [DOI: 10.1016/j.cca.2009.03.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2008] [Revised: 01/28/2009] [Accepted: 03/09/2009] [Indexed: 11/26/2022]
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Lai SK, Wang YY, Wirtz D, Hanes J. Micro- and macrorheology of mucus. Adv Drug Deliv Rev 2009; 61:86-100. [PMID: 19166889 PMCID: PMC2736374 DOI: 10.1016/j.addr.2008.09.012] [Citation(s) in RCA: 711] [Impact Index Per Article: 47.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2007] [Accepted: 09/22/2008] [Indexed: 11/30/2022]
Abstract
Mucus is a complex biological material that lubricates and protects the human lungs, gastrointestinal (GI) tract, vagina, eyes, and other moist mucosal surfaces. Mucus serves as a physical barrier against foreign particles, including toxins, pathogens, and environmental ultrafine particles, while allowing rapid passage of selected gases, ions, nutrients, and many proteins. Its selective barrier properties are precisely regulated at the biochemical level across vastly different length scales. At the macroscale, mucus behaves as a non-Newtonian gel, distinguished from classical solids and liquids by its response to shear rate and shear stress, while, at the nanoscale, it behaves as a low viscosity fluid. Advances in the rheological characterization of mucus from the macroscopic to nanoscopic levels have contributed critical understanding to mucus physiology, disease pathology, and the development of drug delivery systems designed for use at mucosal surfaces. This article reviews the biochemistry that governs mucus rheology, the macro- and microrheology of human and laboratory animal mucus, rheological techniques applied to mucus, and the importance of an improved understanding of the physical properties of mucus to advancing the field of drug and gene delivery.
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Affiliation(s)
- Samuel K. Lai
- Department of Chemical & Biomolecular Engineering (JH Primary Appointment), Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218
| | - Ying-Ying Wang
- Department of Biomedical Engineering, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Denis Wirtz
- Department of Chemical & Biomolecular Engineering (JH Primary Appointment), Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218
- Institute for NanoBioTechnology, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218
| | - Justin Hanes
- Department of Chemical & Biomolecular Engineering (JH Primary Appointment), Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218
- Institute for NanoBioTechnology, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218
- Department of Biomedical Engineering, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205
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Abstract
Mucus is tenacious. It sticks to most particles, preventing their penetration to the epithelial surface. Multiple low-affinity hydrophobic interactions play a major role in these adhesive interactions. Mucus gel is also shear-thinning, making it an excellent lubricant that ensures an unstirred layer of mucus remains adherent to the epithelial surface. Thus nanoparticles (NP) must diffuse readily through the unstirred adherent layer if they are to contact epithelial cells efficiently. This article reviews some of the physiological and biochemical properties that form the mucus barrier. Capsid viruses can diffuse through mucus as rapidly as through water and thereby penetrate to the epithelium even though they have to diffuse 'upstream' through mucus that is being continuously secreted. These viruses are smaller than the mucus mesh spacing, and have surfaces that do not stick to mucus. They form a useful model for developing NP for mucosal drug delivery.
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DiRienzo JM, Cao L, Volgina A, Bandelac G, Korostoff J. Functional and structural characterization of chimeras of a bacterial genotoxin and human type I DNAse. FEMS Microbiol Lett 2008; 291:222-31. [PMID: 19087203 DOI: 10.1111/j.1574-6968.2008.01457.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Chimeras composed of the cdtB gene of a novel bacterial genotoxin and the human type I DNAse I gene were constructed and their products characterized relative to the biochemical and enzymatic properties of the native proteins. The product of a cdtB/DNAse I chimera formed a heterotrimer with the CdtA and CdtC subunits of the genotoxin, and targeted mutations increased the specific activity of the hybrid protein. Expression of active chimeric gene products established that the CdtB protein is an atypical divalent cation-dependent endonuclease and demonstrated the potential for genetically engineering a new class of therapeutic agent for inhibiting the proliferation of cancer cells.
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Affiliation(s)
- Joseph M DiRienzo
- Department of Microbiology, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA 19104-6030, USA.
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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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Bucki R, Sostarecz AG, Byfield FJ, Savage PB, Janmey PA. Resistance of the antibacterial agent ceragenin CSA-13 to inactivation by DNA or F-actin and its activity in cystic fibrosis sputum. J Antimicrob Chemother 2007; 60:535-45. [PMID: 17584802 DOI: 10.1093/jac/dkm218] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
OBJECTIVES The goal of this study was to evaluate the effects of DNA and F-actin [polyanions present in high concentration in cystic fibrosis (CF) airway fluid] on the antibacterial activities of the cationic steroid antibiotic CSA-13 and the cationic peptides LL37, WLBU2 and HB71. METHODS Light scattering intensity was used to evaluate the aggregation of DNA and F-actin by the cationic antibacterial agents. Bacterial killing assays, atomic force microscopy, determination of MIC values and bacterial load of CF sputa were used to determine the bactericidal activity. Inhibition of nuclear factor-kappaB (NF-kappaB) translocation in human aorta endothelial cells (HAECs) was quantified as an assay of anti-inflammatory action. RESULTS CSA-13 is significantly more effective than cationic antibacterial peptides against kanamycin-resistant Pseudomonas aeruginosa and less susceptible to inactivation by DNA or F-actin. The concentration of CSA-13 sufficient to decrease the CF sputa bacteria load by approximately 90% is at least 10 times lower than that at which CSA-13 formed aggregates with DNA or F-actin. Both CSA-13 and LL37 prevent lipopolysaccharide-induced translocation of NF-kappaB in HAEC, thereby suggesting that these antibacterial molecules might prevent systemic inflammation caused by bacterial wall components. CONCLUSIONS Charge-based interactions that strongly inhibit the antibacterial activity of host cationic antibacterial peptides present in CF sputa have significantly less effect on molecules from the ceragenin family such as CSA-13 due in part to their smaller net charge and distribution of this charge over a hydrophobic scaffold. CSA molecules therefore have potential for the treatment of chronic infections and inflammation that occur in CF airways and other settings in which extracellular polyanions accumulate.
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Affiliation(s)
- Robert Bucki
- Department of Physiology and the Institute for Medicine and Engineering, 1010 Vagelos Research Laboratories, University of Pennsylvania, 3340 Smith Walk, Philadelphia, PA 19104, USA.
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Eulitz D, Mannherz HG. Inhibition of deoxyribonuclease I by actin is to protect cells from premature cell death. Apoptosis 2007; 12:1511-21. [PMID: 17468836 DOI: 10.1007/s10495-007-0078-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Deoxyribonuclease I (Dnase1) is the major extracellular endonuclease. It is secreted by digestive glands into the alimentary tract and into the plasma, lacrimal fluid and urine by hepatocytes, lacrimal glands and renal proximal tubular cells, respectively. In many species the activity of Dnase1 is inhibited by monomeric actin. However, the biological significance of this high affinity interaction is unknown. We generated a Dnase1 mutant with extremely reduced actin binding capacity. EGFP-constructs of wild-type and mutant Dnase1 were transfected into MCF-7 breast cancer cells and apoptosis or necrosis was induced by staurosporine or oxidative stress. During apoptosis faster chromatin fragmentation occurred in cells transfected with mutant Dnase1. When wt (wild-type)- or mutated Dnase1 were added to cells after induction of necrosis, faster chromatin degradation occurred in the presence of mutant Dnase1. Inclusion of actin under these conditions inhibited chromatin degradation by wt- but not by mutated Dnase1. Thus, inhibition of Dnase1 by actin may serve as a self-protection mechanism against premature DNA degradation during cell damage.
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Affiliation(s)
- Dirk Eulitz
- Department of Anatomy and Embryology, Ruhr-University Bochum, Germany.
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Sanders NN, Franckx H, De Boeck K, Haustraete J, De Smedt SC, Demeester J. Role of magnesium in the failure of rhDNase therapy in patients with cystic fibrosis. Thorax 2006; 61:962-8. [PMID: 17071834 PMCID: PMC2121161 DOI: 10.1136/thx.2006.060814] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BACKGROUND In the management of cystic fibrosis (CF), rhDNase-I inhalation is widely used to facilitate the removal of the highly viscous and elastic mucus (often called sputum) from the lungs. However, an important group of CF patients does not benefit from rhDNase-I treatment. A study was undertaken to elucidate the reason for the failure of rhDNase-I in these patients and to evaluate strategies to overcome this. METHODS The biochemical properties, physical properties, and degradation by rhDNase-I of sputum obtained from clinical responders and non-responders to rhDNase-I were compared, and the ability of magnesium to reactivate rhDNase-I in DNA solutions and in sputum was investigated. The effect of oral magnesium supplements on magnesium levels in the sputum of patients with CF was also examined. RESULTS Sputum from clinical responders was extensively degraded in vitro on incubation with rhDNase-I, while sputum from clinical non-responders was not degraded: the median decrease in sputum elasticity in the two groups was 32% and 5%, respectively. Sputum from clinical responders contained significantly higher concentrations of magnesium than sputum from non-responders (2.0 mM v 1.3 mM; p = 0.020). Sputum that could not be degraded by rhDNase-I became degradable after preincubation with magnesium. The effect of magnesium on rhDNase-I activity was mediated through actin. Oral intake of magnesium enhanced the magnesium concentration in the sputum of CF patients. CONCLUSION Increasing the magnesium concentration in sputum by, for example, oral magnesium supplements may be a promising new strategy to overcome the failure of rhDNase-I in patients with CF.
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Affiliation(s)
- N N Sanders
- Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmacy, Ghent University, Harelbekestraat 72, 9000 Ghent, Belgium.
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43
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Manderson AP, Carlucci F, Lachmann PJ, Lazarus RA, Festenstein RJ, Cook HT, Walport MJ, Botto M. The in vivo expression of actin/salt-resistant hyperactive DNase I inhibits the development of anti-ssDNA and anti-histone autoantibodies in a murine model of systemic lupus erythematosus. Arthritis Res Ther 2006; 8:R68. [PMID: 16606442 PMCID: PMC1526614 DOI: 10.1186/ar1936] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2006] [Revised: 03/10/2006] [Accepted: 03/14/2006] [Indexed: 11/19/2022] Open
Abstract
Systemic lupus erythematosus (SLE) is characterised by the production of autoantibodies against ubiquitous antigens, especially nuclear components. Evidence makes it clear that the development of these autoantibodies is an antigen-driven process and that immune complexes involving DNA-containing antigens play a key role in the disease process. In rodents, DNase I is the major endonuclease present in saliva, urine and plasma, where it catalyses the hydrolysis of DNA, and impaired DNase function has been implicated in the pathogenesis of SLE. In this study we have evaluated the effects of transgenic over-expression of murine DNase I endonucleases in vivo in a mouse model of lupus. We generated transgenic mice having T-cells that express either wild-type DNase I (wt.DNase I) or a mutant DNase I (ash.DNase I), engineered for three new properties – resistance to inhibition by G-actin, resistance to inhibition by physiological saline and hyperactivity compared to wild type. By crossing these transgenic mice with a murine strain that develops SLE we found that, compared to control non-transgenic littermates or wt.DNase I transgenic mice, the ash.DNase I mutant provided significant protection from the development of anti-single-stranded DNA and anti-histone antibodies, but not of renal disease. In summary, this is the first study in vivo to directly test the effects of long-term increased expression of DNase I on the development of SLE. Our results are in line with previous reports on the possible clinical benefits of recombinant DNase I treatment in SLE, and extend them further to the use of engineered DNase I variants with increased activity and resistance to physiological inhibitors.
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Affiliation(s)
- Anthony P Manderson
- Rheumatology Section, Division of Medicine, Faculty of Medicine, Imperial College, London, UK
- Institute of Molecular Biosciences, The University of Queensland, Brisbane, 4072, Australia
| | - Francesco Carlucci
- Rheumatology Section, Division of Medicine, Faculty of Medicine, Imperial College, London, UK
| | - Peter J Lachmann
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | | | | | - H Terence Cook
- Department of Histopathology, Faculty of Medicine, Imperial College, London, UK
| | - Mark J Walport
- Rheumatology Section, Division of Medicine, Faculty of Medicine, Imperial College, London, UK
- The Wellcome Trust, London, UK
| | - Marina Botto
- Rheumatology Section, Division of Medicine, Faculty of Medicine, Imperial College, London, UK
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Fujihara J, Hieda Y, Xue Y, Nakagami N, Imamura S, Takayama K, Kataoka K, Takeshita H. Actin-inhibition and folding of vertebrate deoxyribonuclease I are affected by mutations at residues 67 and 114. Comp Biochem Physiol B Biochem Mol Biol 2006; 143:70-5. [PMID: 16311052 DOI: 10.1016/j.cbpb.2005.10.004] [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: 05/27/2005] [Revised: 10/10/2005] [Accepted: 10/11/2005] [Indexed: 10/25/2022]
Abstract
Amino acid (aa) residues (Val-67 and Ala-114) have been suggested as being mainly responsible for actin-binding in human and bovine deoxyribonucleases I (DNase I). This study presents evidence of these two aa mutational mechanisms, not only for actin-binding but also for folding of DNase I in mammals, reptiles and amphibians. Human and viper snake (Agkistrodon blomhoffii) enzymes are inhibited by actin, whereas porcine, rat snake (Elaphe quadrivirgata), and African clawed frog (Xenopus laevis) enzymes are not. To investigate the role of aa at 67, mutants of rat snake (Ile67Val) and viper snake (Val67Ile) enzymes were constructed. After substitution, the rat snake was inhibited by actin, while the viper snake was not. For the role of aa at 114, mutants of viper snake (Phe114Ala), rat snake (Phe114Ala), African clawed frog (Phe114Ala), and porcine (Ser114Ala/Ser114Phe) enzymes were constructed. Strikingly, the substitute mutants for viper snake, rat snake and African clawed frog expressed no protein. The porcine (Ser114Ala) enzyme was inhibited by actin, but not the porcine (Ser114Phe) enzyme. These results suggest that Val-67 may be essential for actin-binding, that Phe-114 may be related to the folding of DNase I in reptiles and amphibians, and that Ala-114 may be indispensable for actin-binding in mammals.
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Affiliation(s)
- Junko Fujihara
- Department of Legal Medicine, Shimane University School of Medicine 89-1 Enya, Izumo, Shimane 693-8501, Japan
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45
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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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46
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Jansson V, Jansson K. A bioluminescent DNA nickase assay of deoxyribonuclease I. Anal Biochem 2004; 333:402-4. [PMID: 15450819 DOI: 10.1016/j.ab.2004.05.060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2004] [Indexed: 11/16/2022]
Affiliation(s)
- Vuokko Jansson
- CSI Biotech Ltd., Tapionkatu 4 B, FIN-40100 Jyväskylä, Finland.
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47
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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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Abstract
The dominant autoantigen in SLE is the nucleosome and immune complexes involving nucleosomes are the major cause of tissue damage. Nucleosomes can be broken down in vivo with Desoxyribonuclease 1. DNase 1 from humans and mice is inhibited by actin and it is proposed that the release of platelet actin at inflammatory sites is one mechanism which causes nucleosomes to become antigenic. Rats whose DNase 1 is not inhibited by actin do not get lupus. Treatment of NZB/W mice with recombinant DNase slows the onset of their disease if given early and improves the renal disease if given later. This disease can also be entirely prevented by treatment with dexamethasone. Mice whose DNase 1 gene is knocked out are known to develop lupus and to be otherwise normal. DNase 1 especially in its mutant actin and salt resistant forms remains an attractive candidate for the treatment of SLE.
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Affiliation(s)
- P J Lachmann
- Microbial Immunology Group, Centre for Veterinary Science, Cambridge, UK.
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Takeshita H, Yasuda T, Nakajima T, Mogi K, Kaneko Y, Iida R, Kishi K. A single amino acid substitution of Leu130Ile in snake DNases I contributes to the acquisition of thermal stability. EUROPEAN JOURNAL OF BIOCHEMISTRY 2003; 270:307-14. [PMID: 12605681 DOI: 10.1046/j.1432-1033.2003.03387.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We purified pancreatic deoxyribonucleases I (DNases I) from three snakes, Elaphe quadrivirgata, Elaphe climacophora and Agkistrodon blomhoffii, and cloned their cDNAs. Each mature snake DNase I protein comprised 262 amino acids. Wild-type snake DNases I with Leu130 were more thermally unstable than wild-type mammalian and avian DNases I with Ile130. After substitution of Leu130Ile, the thermal stabilities of the snake enzymes were higher than those of their wild-type counterparts and similar to mammalian wild-type enzyme levels. Conversely, substituting Ile130Leu of mammalian DNases I made them more thermally unstable than their wild-type counterparts. Therefore, a single amino acid substitution, Leu130Ile, might be involved in an evolutionally critical change in the thermal stabilities of vertebrate DNases I. Amphibian DNases I have a Ser205 insertion in a Ca2+-binding site of mammalian and avian enzymes that reduces their thermal stabilities [Takeshita, H., Yasuda, T., Iida, R., Nakajima, T., Mori, S., Mogi, K., Kaneko, Y. & Kishi, K. (2001) Biochem. J.357, 473-480]. Thus, it is plausible that the thermally stable wild-type DNases I of the higher vertebrates, such as mammals and birds, have been generated by a single Leu130Ile substitution of reptilian enzymes through molecular evolution following Ser205 deletion from amphibian enzymes. This mechanism may reflect one of the evolutionary changes from cold-blooded to warm-blooded vertebrates.
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Affiliation(s)
- Haruo Takeshita
- Department of Legal Medicine, Gunma University School of Medicine, Maebashi, Japan
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50
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Takeshita H, Yasuda T, Iida R, Nakajima T, Mori S, Mogi K, Kaneko Y, Kishi K. Amphibian DNases I are characterized by a C-terminal end with a unique, cysteine-rich stretch and by the insertion of a serine residue into the Ca2+-binding site. Biochem J 2001; 357:473-80. [PMID: 11439097 PMCID: PMC1221974 DOI: 10.1042/0264-6021:3570473] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
We purified four amphibian deoxyribonucleases I from the pancreases of one toad, two frog and one newt species, by using three different column chromatography methods in sequence. Each of the purified enzymes had a molecular mass of approx. 40 kDa and an optimal pH for activity of approx. 8.0. These values were significantly greater than those for other vertebrate DNases I. The full-length cDNA encoding each amphibian DNase I was constructed from the total RNA of the pancreas by using rapid amplification of cDNA ends. Nucleotide sequence analyses revealed two structural characteristics unique to amphibian DNases I: a stretch of approx. 70 amino acids with a high cysteine content (approx. 15%) in the C-terminal region, and the insertion of a serine residue at position 205 (in a domain containing an essential Ca2+-binding site). Expression analysis of a series of mutant constructs indicated that both of these structures are essential in generating the active form of the enzyme. 'DNase I signature sequences', which are well conserved in other vertebrate DNases I, could not be found in any of the amphibian DNases I tested, whereas a 'somatomedin B motif' was identified in the Cys-rich stretches of all four. Although DNase I has so far been considered to be a secretory glycoprotein, amphibian DNase I seems to be non-glycosylated. These structural findings indicate strongly that amphibian DNases I are situated in a unique position on the phylogenetic tree of the DNase I family.
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Affiliation(s)
- H Takeshita
- Department of Legal Medicine, Gunma University School of Medicine, Maebashi, Gunma 371-8511, Japan
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