1
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Li J, Kang X, Guidi I, Lu L, Fernández-Millán P, Prats-Ejarque G, Boix E. Structural determinants for tRNA selective cleavage by RNase 2/EDN. Structure 2024; 32:328-341.e4. [PMID: 38228145 DOI: 10.1016/j.str.2023.12.012] [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: 08/22/2023] [Revised: 11/03/2023] [Accepted: 12/20/2023] [Indexed: 01/18/2024]
Abstract
tRNA-derived fragments (tRFs) have emerged as key players of immunoregulation. Some RNase A superfamily members participate in the shaping of the tRFs population. By comparing wild-type and knockout macrophage cell lines, our previous work revealed that RNase 2 can selectively cleave tRNAs. Here, we confirm the in vitro protein cleavage pattern by screening of synthetic tRNAs, single-mutant variants, and anticodon-loop DNA/RNA hairpins. By sequencing of tRF products, we identified the cleavage selectivity of recombinant RNase 2 with base specificity at B1 (U/C) and B2 (A) sites, consistent with a previous cellular study. Lastly, protein-hairpin complexes were predicted by MD simulations. Results reveal the contribution of the α1, loop 3 and loop 4, and β6 RNase 2 regions, where residues Arg36/Asn39/Gln40/Asn65/Arg68/Arg132 provide interactions, spanning from P-1 to P2 sites that are essential for anticodon loop recognition. Knowledge of RNase 2-specific tRFs generation might guide new therapeutic approaches for infectious and immune-related diseases.
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Affiliation(s)
- Jiarui Li
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona (UAB), Cerdanyola del Vallès, 08193 Barcelona, Spain.
| | - Xincheng Kang
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona (UAB), Cerdanyola del Vallès, 08193 Barcelona, Spain
| | - Irene Guidi
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona (UAB), Cerdanyola del Vallès, 08193 Barcelona, Spain
| | - Lu Lu
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona (UAB), Cerdanyola del Vallès, 08193 Barcelona, Spain
| | - Pablo Fernández-Millán
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona (UAB), Cerdanyola del Vallès, 08193 Barcelona, Spain
| | - Guillem Prats-Ejarque
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona (UAB), Cerdanyola del Vallès, 08193 Barcelona, Spain
| | - Ester Boix
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona (UAB), Cerdanyola del Vallès, 08193 Barcelona, Spain.
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2
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Abstract
The ribonuclease A (RNase A) family is one of the best-characterized vertebrate-specific proteins. In humans, eight catalytically active RNases (numbered 1–8) have been identified and have unique tissue distributions. Apart from the digestion of dietary RNA, a broad range of biological actions, including the regulation of intra- or extra-cellular RNA metabolism as well as antiviral, antibacterial, and antifungal activities, neurotoxicity, promotion of cell proliferation, anti-apoptosis, and immunomodulatory abilities, have been recently reported for the members of this family. Based on multiple biological roles, RNases are found to participate in the pathogenic processes of many diseases, such as infection, immune dysfunction, neurodegeneration, cancer, and cardiovascular disorders. This review summarizes the available data on the human RNase A family and illustrates the significant roles of the eight canonical RNases in health and disease, for stimulating further basic research and development of ideas on the potential solutions for disease diagnosis and treatment.
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Affiliation(s)
- Desen Sun
- Department of Gastroenterology, The Affiliated Hospital of Medical School, Ningbo University, Ningbo, Zhejiang 315020, China,Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Chenjie Han
- Institute of Environmental Medicine and Affiliated Hangzhou First People’s Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China,Undergraduate Program in Public Health, School of Public Health, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Jinghao Sheng
- Institute of Environmental Medicine and Affiliated Hangzhou First People’s Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China,Corresponding author
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3
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Lu L, Li J, Wei R, Guidi I, Cozzuto L, Ponomarenko J, Prats-Ejarque G, Boix E. Selective cleavage of ncRNA and antiviral activity by RNase2/EDN in THP1-induced macrophages. Cell Mol Life Sci 2022; 79:209. [PMID: 35347428 PMCID: PMC8960563 DOI: 10.1007/s00018-022-04229-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 02/21/2022] [Accepted: 03/03/2022] [Indexed: 12/11/2022]
Abstract
AbstractRNase2 is the member of the RNaseA family most abundant in macrophages. Here, we knocked out RNase2 in THP-1 cells and analysed the response to Respiratory Syncytial Virus (RSV). RSV induced RNase2 expression, which significantly enhanced cell survival. Next, by cP-RNAseq sequencing, which amplifies the cyclic-phosphate endonuclease products, we analysed the ncRNA population. Among the ncRNAs accumulated in WT vs KO cells, we found mostly tRNA-derived fragments (tRFs) and second miRNAs. Differential sequence coverage identified tRFs from only few parental tRNAs, revealing a predominant cleavage at anticodon and d-loops at U/C (B1) and A (B2) sites. Selective tRNA cleavage was confirmed in vitro using the recombinant protein. Likewise, only few miRNAs were significantly more abundant in WT vs RNase2-KO cells. Complementarily, by screening of a tRF & tiRNA array, we identified an enriched population associated to RNase2 expression and RSV exposure. The results confirm the protein antiviral action and provide the first evidence of its cleavage selectivity on ncRNAs.
Graphical abstract
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Affiliation(s)
- Lu Lu
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain.
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China.
| | - Jiarui Li
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Ranlei Wei
- National Frontier Center of Disease Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Irene Guidi
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Luca Cozzuto
- Bioinformatic Unit, Centre de Regulació Genòmica (CRG), Barcelona, Spain
| | - Julia Ponomarenko
- Bioinformatic Unit, Centre de Regulació Genòmica (CRG), Barcelona, Spain
| | - Guillem Prats-Ejarque
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Ester Boix
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain.
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4
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ATAYIK E, AYTEKİN G. Can anti-IgE and anti-IL-5 monoclonal antibodies be protective against household transmission of SARS-CoV-2? JOURNAL OF HEALTH SCIENCES AND MEDICINE 2022. [DOI: 10.32322/jhsm.1026619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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5
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Li J, Boix E. Host Defence RNases as Antiviral Agents against Enveloped Single Stranded RNA Viruses. Virulence 2021; 12:444-469. [PMID: 33660566 PMCID: PMC7939569 DOI: 10.1080/21505594.2021.1871823] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 12/26/2020] [Accepted: 12/30/2020] [Indexed: 02/06/2023] Open
Abstract
Owing to the recent outbreak of Coronavirus Disease of 2019 (COVID-19), it is urgent to develop effective and safe drugs to treat the present pandemic and prevent other viral infections that might come in the future. Proteins from our own innate immune system can serve as ideal sources of novel drug candidates thanks to their safety and immune regulation versatility. Some host defense RNases equipped with antiviral activity have been reported over time. Here, we try to summarize the currently available information on human RNases that can target viral pathogens, with special focus on enveloped single-stranded RNA (ssRNA) viruses. Overall, host RNases can fight viruses by a combined multifaceted strategy, including the enzymatic target of the viral genome, recognition of virus unique patterns, immune modulation, control of stress granule formation, and induction of autophagy/apoptosis pathways. The review also includes a detailed description of representative enveloped ssRNA viruses and their strategies to interact with the host and evade immune recognition. For comparative purposes, we also provide an exhaustive revision of the currently approved or experimental antiviral drugs. Finally, we sum up the current perspectives of drug development to achieve successful eradication of viral infections.
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Affiliation(s)
- Jiarui Li
- Dpt. Of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma De Barcelona, Spain
| | - Ester Boix
- Dpt. Of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma De Barcelona, Spain
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6
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Nucera F, Lo Bello F, Shen SS, Ruggeri P, Coppolino I, Di Stefano A, Stellato C, Casolaro V, Hansbro PM, Adcock IM, Caramori G. Role of Atypical Chemokines and Chemokine Receptors Pathways in the Pathogenesis of COPD. Curr Med Chem 2021; 28:2577-2653. [PMID: 32819230 DOI: 10.2174/0929867327999200819145327] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 06/11/2020] [Accepted: 06/18/2020] [Indexed: 11/22/2022]
Abstract
Chronic obstructive pulmonary disease (COPD) represents a heightened inflammatory response in the lung generally resulting from tobacco smoking-induced recruitment and activation of inflammatory cells and/or activation of lower airway structural cells. Several mediators can modulate activation and recruitment of these cells, particularly those belonging to the chemokines (conventional and atypical) family. There is emerging evidence for complex roles of atypical chemokines and their receptors (such as high mobility group box 1 (HMGB1), antimicrobial peptides, receptor for advanced glycosylation end products (RAGE) or toll-like receptors (TLRs)) in the pathogenesis of COPD, both in the stable disease and during exacerbations. Modulators of these pathways represent potential novel therapies for COPD and many are now in preclinical development. Inhibition of only a single atypical chemokine or receptor may not block inflammatory processes because there is redundancy in this network. However, there are many animal studies that encourage studies for modulating the atypical chemokine network in COPD. Thus, few pharmaceutical companies maintain a significant interest in developing agents that target these molecules as potential antiinflammatory drugs. Antibody-based (biological) and small molecule drug (SMD)-based therapies targeting atypical chemokines and/or their receptors are mostly at the preclinical stage and their progression to clinical trials is eagerly awaited. These agents will most likely enhance our knowledge about the role of atypical chemokines in COPD pathophysiology and thereby improve COPD management.
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Affiliation(s)
- Francesco Nucera
- Department of Biomedical, Dental, Morphological and Functional Imaging Sciences (BIOMORF), University of Messina, Pugliatti Square 1, 98122 Messina, Italy
| | - Federica Lo Bello
- Department of Biomedical, Dental, Morphological and Functional Imaging Sciences (BIOMORF), University of Messina, Pugliatti Square 1, 98122 Messina, Italy
| | - Sj S Shen
- Faculty of Science, Centre for Inflammation, Centenary Institute, University of Technology, Ultimo, Sydney, Australia
| | - Paolo Ruggeri
- Department of Biomedical, Dental, Morphological and Functional Imaging Sciences (BIOMORF), University of Messina, Pugliatti Square 1, 98122 Messina, Italy
| | - Irene Coppolino
- Department of Biomedical, Dental, Morphological and Functional Imaging Sciences (BIOMORF), University of Messina, Pugliatti Square 1, 98122 Messina, Italy
| | - Antonino Di Stefano
- Division of Pneumology, Cyto- Immunopathology Laboratory of the Cardio-Respiratory System, Clinical Scientific Institutes Maugeri IRCCS, Veruno, Italy
| | - Cristiana Stellato
- Department of Medicine, Surgery and Dentistry, Salerno Medical School, University of Salerno, Salerno, Italy
| | - Vincenzo Casolaro
- Department of Medicine, Surgery and Dentistry, Salerno Medical School, University of Salerno, Salerno, Italy
| | - Phil M Hansbro
- Faculty of Science, Centre for Inflammation, Centenary Institute, University of Technology, Ultimo, Sydney, Australia
| | - Ian M Adcock
- Airway Disease Section, National Heart and Lung Institute, Imperial College, London, United Kingdom
| | - Gaetano Caramori
- Department of Biomedical, Dental, Morphological and Functional Imaging Sciences (BIOMORF), University of Messina, Pugliatti Square 1, 98122 Messina, Italy
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7
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Antimicrobial Activity of Human Eosinophil Granule Proteins. Methods Mol Biol 2021; 2241:257-274. [PMID: 33486742 DOI: 10.1007/978-1-0716-1095-4_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Eosinophils secrete a number of proinflammatory mediators that include cytokines, chemokines, and granule proteins which are responsible for the initiation and maintenance of inflammatory responses. The eosinophil granule proteins, ECP, EDN, MBP, and EPO, possess antimicrobial activity against bacteria, helminths, protozoa, and viruses. In this chapter, we describe various assays used to detect and quantitate the antimicrobial activities of eosinophil granule proteins, particularly ECP and EDN. We have taken a model organism for each assay and described the method for antiviral, antihelminthic, antiprotozoan, and antibacterial activity of purified eosinophil granule proteins.
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8
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Sabogal Piñeros YS, Bal SM, van de Pol MA, Dierdorp BS, Dekker T, Dijkhuis A, Brinkman P, van der Sluijs KF, Zwinderman AH, Majoor CJ, Bonta PI, Ravanetti L, Sterk PJ, Lutter R. Anti-IL-5 in Mild Asthma Alters Rhinovirus-induced Macrophage, B-Cell, and Neutrophil Responses (MATERIAL). A Placebo-controlled, Double-Blind Study. Am J Respir Crit Care Med 2020; 199:508-517. [PMID: 30192638 DOI: 10.1164/rccm.201803-0461oc] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
RATIONALE Eosinophils drive pathophysiology in stable and exacerbating eosinophilic asthma, and therefore treatment is focused on the reduction of eosinophil numbers. Mepolizumab, a humanized monoclonal antibody that neutralizes IL-5 and efficiently attenuates eosinophils, proved clinically effective in severe eosinophilic asthma but not in mild asthma. OBJECTIVES To study the effect of mepolizumab on virus-induced immune responses in mild asthma. METHODS Patients with mild asthma, steroid-naive and randomized for eosinophil numbers, received 750 mg mepolizumab intravenously in a placebo-controlled double-blind trial, 2 weeks after which patients were challenged with rhinovirus (RV) 16. FEV1, FVC, fractional exhaled nitric oxide, symptom scores (asthma control score), viral load (PCR), eosinophil numbers, humoral (luminex, ELISA), and cellular (flow cytometry) immune parameters in blood, BAL fluid, and sputum, before and after mepolizumab and RV16, were assessed. MEASUREMENTS AND MAIN RESULTS Mepolizumab attenuated baseline blood eosinophils and their activation, attenuated trendwise sputum eosinophils, and enhanced circulating natural killer cells. Mepolizumab did not affect FEV1, FVC, and fractional exhaled nitric oxide, neither at baseline nor after RV16. On RV16 challenge mepolizumab did not prevent eosinophil activation but did enhance local B lymphocytes and macrophages and reduce neutrophils and their activation. Mepolizumab also enhanced secretory IgA and reduced tryptase in BAL fluid. Finally, mepolizumab affected particularly RV16-induced macrophage inflammatory protein-3a, vascular endothelial growth factor-A, and IL-1RA production in BAL fluid. CONCLUSIONS Mepolizumab failed to prevent activation of remaining eosinophils and changed RV16-induced immune responses in mild asthma. Although these latter effects likely are caused by attenuated eosinophil numbers, we cannot exclude a role for basophils. Clinical trial registered with www.clinicaltrials.gov (NCT 01520051).
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Affiliation(s)
- Yanaika S Sabogal Piñeros
- 1 Department of Respiratory Medicine.,2 Department of Experimental Immunology (Amsterdam Infection & Immunity Institute), and
| | - Suzanne M Bal
- 1 Department of Respiratory Medicine.,2 Department of Experimental Immunology (Amsterdam Infection & Immunity Institute), and
| | - Marianne A van de Pol
- 2 Department of Experimental Immunology (Amsterdam Infection & Immunity Institute), and
| | - Barbara S Dierdorp
- 2 Department of Experimental Immunology (Amsterdam Infection & Immunity Institute), and
| | - Tamara Dekker
- 2 Department of Experimental Immunology (Amsterdam Infection & Immunity Institute), and
| | - Annemiek Dijkhuis
- 2 Department of Experimental Immunology (Amsterdam Infection & Immunity Institute), and
| | | | - Koen F van der Sluijs
- 2 Department of Experimental Immunology (Amsterdam Infection & Immunity Institute), and
| | - Aeilko H Zwinderman
- 3 Department of Clinical Epidemiology, Bioinformatics, and Biostatistics, University of Amsterdam, Amsterdam UMC, Amsterdam, the Netherlands
| | | | | | - Lara Ravanetti
- 1 Department of Respiratory Medicine.,2 Department of Experimental Immunology (Amsterdam Infection & Immunity Institute), and
| | | | - René Lutter
- 1 Department of Respiratory Medicine.,2 Department of Experimental Immunology (Amsterdam Infection & Immunity Institute), and
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9
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Bafna K, Narayanan C, Chennubhotla SC, Doucet N, Agarwal PK. Nucleotide substrate binding characterization in human pancreatic-type ribonucleases. PLoS One 2019; 14:e0220037. [PMID: 31393891 PMCID: PMC6687278 DOI: 10.1371/journal.pone.0220037] [Citation(s) in RCA: 3] [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: 01/23/2019] [Accepted: 07/07/2019] [Indexed: 12/15/2022] Open
Abstract
Human genome contains a group of more than a dozen similar genes with diverse biological functions including antiviral, antibacterial and angiogenesis activities. The characterized gene products of this group show significant sequence similarity and a common structural fold associated with binding and cleavage of ribonucleic acid (RNA) substrates. Therefore, these proteins have been categorized as members of human pancreatic-type ribonucleases (hRNases). hRNases differ in cell/tissue localization and display distinct substrate binding preferences and a wide range of ribonucleolytic catalytic efficiencies. Limited information is available about structural and dynamical properties that influence this diversity among these homologous RNases. Here, we use computer simulations to characterize substrate interactions, electrostatics and dynamical properties of hRNases 1-7 associated with binding to two nucleotide substrates (ACAC and AUAU). Results indicate that even with complete conservation of active-site catalytic triad associated with ribonucleolytic activity, these enzymes show significant differences in substrate interactions. Detailed characterization suggests that in addition to binding site electrostatic and van der Waals interactions, dynamics of distal regions may also play a role in binding. Another key insight is that a small difference in temperature of 300 K (used in experimental studies) and 310 K (physiological temperature) shows significant changes in enzyme-substrate interactions.
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Affiliation(s)
- Khushboo Bafna
- Genome Science and Technology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Chitra Narayanan
- INRS-Institut Armand-Frappier, Université du Québec, Laval, Québec, Canada
| | - S. Chakra Chennubhotla
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Nicolas Doucet
- INRS-Institut Armand-Frappier, Université du Québec, Laval, Québec, Canada
- PROTEO, the Quebec Network for Research on Protein Function, Structure, and Engineering, Université Laval, Québec, Quebec, Canada
| | - Pratul K. Agarwal
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, United States of America
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10
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Lu L, Li J, Moussaoui M, Boix E. Immune Modulation by Human Secreted RNases at the Extracellular Space. Front Immunol 2018; 9:1012. [PMID: 29867984 PMCID: PMC5964141 DOI: 10.3389/fimmu.2018.01012] [Citation(s) in RCA: 102] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 04/23/2018] [Indexed: 12/23/2022] Open
Abstract
The ribonuclease A superfamily is a vertebrate-specific family of proteins that encompasses eight functional members in humans. The proteins are secreted by diverse innate immune cells, from blood cells to epithelial cells and their levels in our body fluids correlate with infection and inflammation processes. Recent studies ascribe a prominent role to secretory RNases in the extracellular space. Extracellular RNases endowed with immuno-modulatory and antimicrobial properties can participate in a wide variety of host defense tasks, from performing cellular housekeeping to maintaining body fluid sterility. Their expression and secretion are induced in response to a variety of injury stimuli. The secreted proteins can target damaged cells and facilitate their removal from the focus of infection or inflammation. Following tissue damage, RNases can participate in clearing RNA from cellular debris or work as signaling molecules to regulate the host response and contribute to tissue remodeling and repair. We provide here an overall perspective on the current knowledge of human RNases’ biological properties and their role in health and disease. The review also includes a brief description of other vertebrate family members and unrelated extracellular RNases that share common mechanisms of action. A better knowledge of RNase mechanism of actions and an understanding of their physiological roles should facilitate the development of novel therapeutics.
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Affiliation(s)
- Lu Lu
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Jiarui Li
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Mohammed Moussaoui
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Ester Boix
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
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11
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Gagné D, Narayanan C, Bafna K, Charest LA, Agarwal PK, Doucet N. Sequence-specific backbone resonance assignments and microsecond timescale molecular dynamics simulation of human eosinophil-derived neurotoxin. BIOMOLECULAR NMR ASSIGNMENTS 2017; 11:143-149. [PMID: 28271277 PMCID: PMC5589483 DOI: 10.1007/s12104-017-9736-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 02/20/2017] [Indexed: 06/06/2023]
Abstract
Eight active canonical members of the pancreatic-like ribonuclease A (RNase A) superfamily have been identified in human. All structural homologs share similar RNA-degrading functions, while also cumulating other various biological activities in different tissues. The functional homologs eosinophil-derived neurotoxin (EDN, or RNase 2) and eosinophil cationic protein (ECP, or RNase 3) are known to be expressed and secreted by eosinophils in response to infection, and have thus been postulated to play an important role in host defense and inflammatory response. We recently initiated the biophysical and dynamical investigation of several vertebrate RNase homologs and observed that clustering residue dynamics appear to be linked with the phylogeny and biological specificity of several members. Here we report the 1H, 13C and 15N backbone resonance assignments of human EDN (RNase 2) and its molecular dynamics simulation on the microsecond timescale, providing means to pursue this comparative atomic-scale functional and dynamical analysis by NMR and computation over multiple time frames.
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Affiliation(s)
- Donald Gagné
- INRS-Institut Armand-Frappier, Université du Québec, 531 Boulevard des Prairies, Laval, QC, H7V 1B7, Canada
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY, 10031, USA
| | - Chitra Narayanan
- INRS-Institut Armand-Frappier, Université du Québec, 531 Boulevard des Prairies, Laval, QC, H7V 1B7, Canada
| | - Khushboo Bafna
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Laurie-Anne Charest
- INRS-Institut Armand-Frappier, Université du Québec, 531 Boulevard des Prairies, Laval, QC, H7V 1B7, Canada
| | - Pratul K Agarwal
- Computational Biology Institute and Computer Science and Mathematics Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN, 37830, USA
- Department of Biochemistry, Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Nicolas Doucet
- INRS-Institut Armand-Frappier, Université du Québec, 531 Boulevard des Prairies, Laval, QC, H7V 1B7, Canada.
- PROTEO, The Québec Network for Research on Protein Function, Engineering, and Applications, Université Laval, 1045 Avenue de la Médecine, Quebec, QC, G1V 0A6, Canada.
- GRASP, The Groupe de recherche Axé sur la Structure des Protéines, McGill University, 3649 Promenade Sir William Osler, Montreal, QC, H3G 0B1, Canada.
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12
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Abstract
Many ribonucleases (RNases) are able to inhibit the reproduction of viruses in infected cell cultures and laboratory animals, but the molecular mechanisms of their antiviral activity remain unclear. The review discusses the well-known RNases that possess established antiviral effects, including both intracellular RNases (RNase L, MCPIP1 protein, and eosinophil-associated RNases) and exogenous RNases (RNase A, BS-RNase, onconase, binase, and synthetic RNases). Attention is paid to two important, but not always obligatory, aspects of molecules of RNases that have antiviral properties, i.e., catalytic activity and ability to dimerize. The hypothetic scheme of virus elimination by exogenous RNases that reflects possible types of interaction of viruses and RNases with a cell is proposed. The evidence for RNases as classical components of immune defense and thus perspective agents for the development of new antiviral therapeutics is proposed.
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Affiliation(s)
- O. N. Ilinskaya
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, ul. Kremlevskaya 18, Kazan, 420008 Russia
| | - R. Shah Mahmud
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, ul. Kremlevskaya 18, Kazan, 420008 Russia
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13
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Chopra A, Batra JK. Antimicrobial activity of human eosinophil granule proteins. Methods Mol Biol 2014; 1178:267-281. [PMID: 24986624 DOI: 10.1007/978-1-4939-1016-8_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Eosinophils secrete a number of proinflammatory mediators, like cytokines, chemokines, and granule proteins which are responsible for the initiation and sustenance of inflammatory response caused by them. The eosinophil granule proteins, ECP, EDN, MBP, and EPO possess antimicrobial activity against bacteria, helminths, protozoa, and viruses. In this chapter, we describe various assays used to detect and quantitate the antimicrobial activities of eosinophil granule proteins, particularly ECP and EDN. We have taken a model organism for each assay and described the method for antiviral, antihelminthic, antiprotozoan, and antibacterial activity of purified eosinophil granule proteins.
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Affiliation(s)
- Anu Chopra
- Immunochemistry Laboratory, National Institute of Immunology, New Delhi, India
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14
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Pulido D, Moussaoui M, Nogués MV, Torrent M, Boix E. Towards the rational design of antimicrobial proteins. FEBS J 2013; 280:5841-52. [DOI: 10.1111/febs.12506] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Revised: 08/19/2013] [Accepted: 08/23/2013] [Indexed: 12/15/2022]
Affiliation(s)
- David Pulido
- Department of Biochemistry and Molecular Biology; Universitat Autònoma de Barcelona; Cerdanyola del Vallès Spain
| | - Mohammed Moussaoui
- Department of Biochemistry and Molecular Biology; Universitat Autònoma de Barcelona; Cerdanyola del Vallès Spain
| | - M. Victòria Nogués
- Department of Biochemistry and Molecular Biology; Universitat Autònoma de Barcelona; Cerdanyola del Vallès Spain
| | - Marc Torrent
- Department of Biochemistry and Molecular Biology; Universitat Autònoma de Barcelona; Cerdanyola del Vallès Spain
- Medical Research Council Laboratory of Molecular Biology; Francis Crick Avenue; Cambridge CB2 0QH UK
| | - Ester Boix
- Department of Biochemistry and Molecular Biology; Universitat Autònoma de Barcelona; Cerdanyola del Vallès Spain
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15
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Hung TJ, Chang WT, Tomiya N, Lee YC, Chang HT, Chen CJ, Kuo PH, Fan TC, Chang MDT. Basic amino acid residues of human eosinophil derived neurotoxin essential for glycosaminoglycan binding. Int J Mol Sci 2013; 14:19067-85. [PMID: 24065103 PMCID: PMC3794821 DOI: 10.3390/ijms140919067] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Revised: 09/06/2013] [Accepted: 09/11/2013] [Indexed: 12/26/2022] Open
Abstract
Human eosinophil derived neurotoxin (EDN), a granule protein secreted by activated eosinophils, is a biomarker for asthma in children. EDN belongs to the human RNase A superfamily possessing both ribonucleolytic and antiviral activities. EDN interacts with heparin oligosaccharides and heparin sulfate proteoglycans on bronchial epithelial Beas-2B cells. In this study, we demonstrate that the binding of EDN to cells requires cell surface glycosaminoglycans (GAGs), and the binding strength between EDN and GAGs depends on the sulfation levels of GAGs. Furthermore, in silico computer modeling and in vitro binding assays suggest critical roles for the following basic amino acids located within heparin binding regions (HBRs) of EDN 34QRRCKN39 (HBR1), 65NKTRKN70 (HBR2), and 113NRDQRRD119 (HBR3) and in particular Arg35, Arg36, and Arg38 within HBR1, and Arg114 and Arg117 within HBR3. Our data suggest that sulfated GAGs play a major role in EDN binding, which in turn may be related to the cellular effects of EDN.
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Affiliation(s)
- Ta-Jen Hung
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu 300, Taiwan; E-Mails: (T.-J.H.); (W.-T.C.); (Y.-C.L.); (C.-J.C.); (P.-H.K.)
| | - Wei-Tang Chang
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu 300, Taiwan; E-Mails: (T.-J.H.); (W.-T.C.); (Y.-C.L.); (C.-J.C.); (P.-H.K.)
| | - Noboru Tomiya
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA; E-Mail:
| | - Yuan-Chuan Lee
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu 300, Taiwan; E-Mails: (T.-J.H.); (W.-T.C.); (Y.-C.L.); (C.-J.C.); (P.-H.K.)
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA; E-Mail:
| | - Hao-Teng Chang
- Graduate Institute of Basic Medical Science, China Medical University, Taichung 404, Taiwan; E-Mail:
| | - Chien-Jung Chen
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu 300, Taiwan; E-Mails: (T.-J.H.); (W.-T.C.); (Y.-C.L.); (C.-J.C.); (P.-H.K.)
| | - Ping-Hsueh Kuo
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu 300, Taiwan; E-Mails: (T.-J.H.); (W.-T.C.); (Y.-C.L.); (C.-J.C.); (P.-H.K.)
| | - Tan-chi Fan
- Stem Cell and Translational Cancer Research Center, Chang Gung Memorial Hospital at Linkou, Taoyuan 333, Taiwan; E-Mail:
| | - Margaret Dah-Tsyr Chang
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu 300, Taiwan; E-Mails: (T.-J.H.); (W.-T.C.); (Y.-C.L.); (C.-J.C.); (P.-H.K.)
- Department of Medical Science, National Tsing Hua University, Hsinchu 300, Taiwan
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +886-3-574-2463; Fax: +886-3-571-5934
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