1
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Dong HL, Zhang C, Dai L, Zhang Y, Zhang XH, Tan ZJ. The origin of different bending stiffness between double-stranded RNA and DNA revealed by magnetic tweezers and simulations. Nucleic Acids Res 2024; 52:2519-2529. [PMID: 38321947 PMCID: PMC10954459 DOI: 10.1093/nar/gkae063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 01/16/2024] [Accepted: 01/19/2024] [Indexed: 02/08/2024] Open
Abstract
The subtle differences in the chemical structures of double-stranded (ds) RNA and DNA lead to significant variations in their biological roles and medical implications, largely due to their distinct biophysical properties, such as bending stiffness. Although it is well known that A-form dsRNA is stiffer than B-form dsDNA under physiological salt conditions, the underlying cause of this difference remains unclear. In this study, we employ high-precision magnetic-tweezer experiments along with molecular dynamics simulations and reveal that the relative bending stiffness between dsRNA and dsDNA is primarily determined by the structure- and salt-concentration-dependent ion distribution around their helical structures. At near-physiological salt conditions, dsRNA shows a sparser ion distribution surrounding its phosphate groups compared to dsDNA, causing its greater stiffness. However, at very high monovalent salt concentrations, phosphate groups in both dsRNA and dsDNA become fully neutralized by excess ions, resulting in a similar intrinsic bending persistence length of approximately 39 nm. This similarity in intrinsic bending stiffness of dsRNA and dsDNA is coupled to the analogous fluctuations in their total groove widths and further coupled to the similar fluctuation of base-pair inclination, despite their distinct A-form and B-form helical structures.
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Affiliation(s)
- Hai-Long Dong
- School of Physics and Technology, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430072, China
| | - Chen Zhang
- School of Physics and Technology, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430072, China
| | - Liang Dai
- Department of Physics, City University of Hong Kong, Hong Kong 999077, China
| | - Yan Zhang
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan 430072, China
| | - Xing-Hua Zhang
- School of Physics and Technology, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430072, China
| | - Zhi-Jie Tan
- School of Physics and Technology, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430072, China
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2
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Xiang Y, Huang W, Tan L, Chen T, He Y, Irving PS, Weeks KM, Zhang QC, Dong X. Pervasive downstream RNA hairpins dynamically dictate start-codon selection. Nature 2023; 621:423-430. [PMID: 37674078 PMCID: PMC10499604 DOI: 10.1038/s41586-023-06500-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 07/31/2023] [Indexed: 09/08/2023]
Abstract
Translational reprogramming allows organisms to adapt to changing conditions. Upstream start codons (uAUGs), which are prevalently present in mRNAs, have crucial roles in regulating translation by providing alternative translation start sites1-4. However, what determines this selective initiation of translation between conditions remains unclear. Here, by integrating transcriptome-wide translational and structural analyses during pattern-triggered immunity in Arabidopsis, we found that transcripts with immune-induced translation are enriched with upstream open reading frames (uORFs). Without infection, these uORFs are selectively translated owing to hairpins immediately downstream of uAUGs, presumably by slowing and engaging the scanning preinitiation complex. Modelling using deep learning provides unbiased support for these recognizable double-stranded RNA structures downstream of uAUGs (which we term uAUG-ds) being responsible for the selective translation of uAUGs, and allows the prediction and rational design of translating uAUG-ds. We found that uAUG-ds-mediated regulation can be generalized to human cells. Moreover, uAUG-ds-mediated start-codon selection is dynamically regulated. After immune challenge in plants, induced RNA helicases that are homologous to Ded1p in yeast and DDX3X in humans resolve these structures, allowing ribosomes to bypass uAUGs to translate downstream defence proteins. This study shows that mRNA structures dynamically regulate start-codon selection. The prevalence of this RNA structural feature and the conservation of RNA helicases across kingdoms suggest that mRNA structural remodelling is a general feature of translational reprogramming.
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Affiliation(s)
- Yezi Xiang
- Department of Biology, Duke University, Durham, NC, USA
- Howard Hughes Medical Institute, Duke University, Durham, NC, USA
| | - Wenze Huang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
- Beijing Frontier Research Center for Biological Structures, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Lianmei Tan
- Department of Pharmacology and Cancer Biology, Duke Medical Center, Duke University, Durham, NC, USA
| | - Tianyuan Chen
- Department of Biology, Duke University, Durham, NC, USA
- Howard Hughes Medical Institute, Duke University, Durham, NC, USA
| | - Yang He
- Department of Biology, Duke University, Durham, NC, USA
- Howard Hughes Medical Institute, Duke University, Durham, NC, USA
| | - Patrick S Irving
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, USA
| | - Kevin M Weeks
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, USA
| | - Qiangfeng Cliff Zhang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
- Beijing Frontier Research Center for Biological Structures, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Xinnian Dong
- Department of Biology, Duke University, Durham, NC, USA.
- Howard Hughes Medical Institute, Duke University, Durham, NC, USA.
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3
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Su S, Wang J, Deng T, Yuan X, He J, Liu N, Li X, Huang Y, Wang HW, Ma J. Structural insights into dsRNA processing by Drosophila Dicer-2-Loqs-PD. Nature 2022; 607:399-406. [PMID: 35768513 PMCID: PMC9279154 DOI: 10.1038/s41586-022-04911-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 05/25/2022] [Indexed: 12/21/2022]
Abstract
Small interfering RNAs (siRNAs) are the key components for RNA interference (RNAi), a conserved RNA-silencing mechanism in many eukaryotes1,2. In Drosophila, an RNase III enzyme Dicer-2 (Dcr-2), aided by its cofactor Loquacious-PD (Loqs-PD), has an important role in generating 21 bp siRNA duplexes from long double-stranded RNAs (dsRNAs)3,4. ATP hydrolysis by the helicase domain of Dcr-2 is critical to the successful processing of a long dsRNA into consecutive siRNA duplexes5,6. Here we report the cryo-electron microscopy structures of Dcr-2-Loqs-PD in the apo state and in multiple states in which it is processing a 50 bp dsRNA substrate. The structures elucidated interactions between Dcr-2 and Loqs-PD, and substantial conformational changes of Dcr-2 during a dsRNA-processing cycle. The N-terminal helicase and domain of unknown function 283 (DUF283) domains undergo conformational changes after initial dsRNA binding, forming an ATP-binding pocket and a 5'-phosphate-binding pocket. The overall conformation of Dcr-2-Loqs-PD is relatively rigid during translocating along the dsRNA in the presence of ATP, whereas the interactions between the DUF283 and RIIIDb domains prevent non-specific cleavage during translocation by blocking the access of dsRNA to the RNase active centre. Additional ATP-dependent conformational changes are required to form an active dicing state and precisely cleave the dsRNA into a 21 bp siRNA duplex as confirmed by the structure in the post-dicing state. Collectively, this study revealed the molecular mechanism for the full cycle of ATP-dependent dsRNA processing by Dcr-2-Loqs-PD.
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Affiliation(s)
- Shichen Su
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai, China
| | - Jia Wang
- Ministry of Education Key Laboratory of Protein Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center of Biological Structures, School of Life Sciences, Tsinghua University, Beijing, China
| | - Ting Deng
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai, China
| | - Xun Yuan
- Shanghai Key Laboratory of Biliary Tract Disease Research, Shanghai Research Center of Biliary Tract Disease, Department of General Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jinqiu He
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai, China
| | - Nan Liu
- Ministry of Education Key Laboratory of Protein Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center of Biological Structures, School of Life Sciences, Tsinghua University, Beijing, China
| | - Xiaomin Li
- Ministry of Education Key Laboratory of Protein Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center of Biological Structures, School of Life Sciences, Tsinghua University, Beijing, China
| | - Ying Huang
- Shanghai Key Laboratory of Biliary Tract Disease Research, Shanghai Research Center of Biliary Tract Disease, Department of General Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hong-Wei Wang
- Ministry of Education Key Laboratory of Protein Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center of Biological Structures, School of Life Sciences, Tsinghua University, Beijing, China.
| | - Jinbiao Ma
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai, China.
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4
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Howard JD, Beghyn M, Dewulf N, De Vos Y, Philips A, Portwood D, Kilby PM, Oliver D, Maddelein W, Brown S, Dickman MJ. Chemically-modified dsRNA induces RNAi effects in insects in vitro and in vivo: A potential new tool for improving RNA-based plant protection. J Biol Chem 2022; 298:102311. [PMID: 35921898 PMCID: PMC9478931 DOI: 10.1016/j.jbc.2022.102311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 07/15/2022] [Accepted: 07/16/2022] [Indexed: 11/28/2022] Open
Abstract
Global agriculture loses over $100 billion of produce annually to crop pests such as insects. Many of these crop pests either are not currently controlled by artificial means or have developed resistance against chemical pesticides. Long dsRNAs are capable of inducing RNAi in insects and are emerging as novel, highly selective alternatives for sustainable insect management strategies. However, there are significant challenges associated with RNAi efficacy in insects. In this study, we synthesized a range of chemically modified long dsRNAs in an approach to improve nuclease resistance and RNAi efficacy in insects. Our results showed that dsRNAs containing phosphorothioate modifications demonstrated increased resistance to southern green stink bug saliva nucleases. Phosphorothioate-modified and 2′-fluoro-modified dsRNA also demonstrated increased resistance to degradation by soil nucleases and increased RNAi efficacy in Drosophila melanogaster cell cultures. In live insects, we found chemically modified long dsRNAs successfully resulted in mortality in both stink bug and corn rootworm. These results provide further mechanistic insight into the dependence of RNAi efficacy on nucleotide modifications in the sense or antisense strand of the dsRNA in insects and demonstrate for the first time that RNAi can successfully be triggered by chemically modified long dsRNAs in insect cells or live insects.
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Affiliation(s)
- John D Howard
- Department of Chemical & Biological Engineering, University of Sheffield, Sheffield, United Kingdom
| | | | | | - Yves De Vos
- Syngenta, Ghent Innovation Center, Ghent, Belgium
| | | | - David Portwood
- Syngenta, Jealott's Hill International Research Centre, Bracknell, United Kingdom
| | - Peter M Kilby
- Syngenta, Jealott's Hill International Research Centre, Bracknell, United Kingdom
| | | | | | - Stephen Brown
- Sheffield RNAi Screening Facility, School of Biosciences, University of Sheffield, Sheffield, United Kingdom
| | - Mark J Dickman
- Department of Chemical & Biological Engineering, University of Sheffield, Sheffield, United Kingdom.
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5
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Kuepper A, McLoughlin NM, Neubacher S, Yeste-Vázquez A, Collado Camps E, Nithin C, Mukherjee S, Bethge L, Bujnicki JM, Brock R, Heinrichs S, Grossmann TN. Constrained peptides mimic a viral suppressor of RNA silencing. Nucleic Acids Res 2021; 49:12622-12633. [PMID: 34871435 PMCID: PMC8682738 DOI: 10.1093/nar/gkab1149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 10/01/2021] [Accepted: 11/03/2021] [Indexed: 12/26/2022] Open
Abstract
The design of high-affinity, RNA-binding ligands has proven very challenging. This is due to the unique structural properties of RNA, often characterized by polar surfaces and high flexibility. In addition, the frequent lack of well-defined binding pockets complicates the development of small molecule binders. This has triggered the search for alternative scaffolds of intermediate size. Among these, peptide-derived molecules represent appealing entities as they can mimic structural features also present in RNA-binding proteins. However, the application of peptidic RNA-targeting ligands is hampered by a lack of design principles and their inherently low bio-stability. Here, the structure-based design of constrained α-helical peptides derived from the viral suppressor of RNA silencing, TAV2b, is described. We observe that the introduction of two inter-side chain crosslinks provides peptides with increased α-helicity and protease stability. One of these modified peptides (B3) shows high affinity for double-stranded RNA structures including a palindromic siRNA as well as microRNA-21 and its precursor pre-miR-21. Notably, B3 binding to pre-miR-21 inhibits Dicer processing in a biochemical assay. As a further characteristic this peptide also exhibits cellular entry. Our findings show that constrained peptides can efficiently mimic RNA-binding proteins rendering them potentially useful for the design of bioactive RNA-targeting ligands.
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Affiliation(s)
- Arne Kuepper
- Chemical Genomics Centre of the Max Planck Society, Dortmund 44227, Germany
- Department of Chemistry and Chemical Biology, Technical University Dortmund, Dortmund 44227, Germany
| | - Niall M McLoughlin
- Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, Amsterdam 1081 HZ, The Netherlands
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam 1081 HZ, The Netherlands
| | - Saskia Neubacher
- Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, Amsterdam 1081 HZ, The Netherlands
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam 1081 HZ, The Netherlands
| | - Alejandro Yeste-Vázquez
- Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, Amsterdam 1081 HZ, The Netherlands
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam 1081 HZ, The Netherlands
| | - Estel Collado Camps
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen Medical Center, Nijmegen 6525 GA, The Netherlands
| | - Chandran Nithin
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw 02-109, Poland
| | - Sunandan Mukherjee
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw 02-109, Poland
| | - Lucas Bethge
- Silence Therapeutics GmbH, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Janusz M Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw 02-109, Poland
| | - Roland Brock
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen Medical Center, Nijmegen 6525 GA, The Netherlands
- Department of Medical Biochemistry, College of Medicine and Medical Sciences, Arabian Gulf University, Manama 293, Bahrain
| | - Stefan Heinrichs
- University Hospital Essen, Institute for Transfusion Medicine, Essen 45147, Germany
| | - Tom N Grossmann
- Chemical Genomics Centre of the Max Planck Society, Dortmund 44227, Germany
- Department of Chemistry and Chemical Biology, Technical University Dortmund, Dortmund 44227, Germany
- Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, Amsterdam 1081 HZ, The Netherlands
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam 1081 HZ, The Netherlands
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6
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Hou Q, Zhang H, Bao L, Song Z, Liu C, Jiang Z, Zheng Y. NCs-Delivered Pesticides: A Promising Candidate in Smart Agriculture. Int J Mol Sci 2021; 22:ijms222313043. [PMID: 34884846 PMCID: PMC8657871 DOI: 10.3390/ijms222313043] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/19/2021] [Accepted: 11/24/2021] [Indexed: 02/01/2023] Open
Abstract
Pesticides have been used extensively in the field of plant protection to maximize crop yields. However, the long-term, unmanaged application of pesticides has posed severe challenges such as pesticide resistance, environmental contamination, risk in human health, soil degradation, and other important global issues. Recently, the combination of nanotechnology with plant protection strategies has offered new perspectives to mitigate these global issues, which has promoted a rapid development of NCs-based pesticides. Unlike certain conventional pesticides that have been applied inefficiently and lacked targeted control, pesticides delivered by nanocarriers (NCs) have optimized formulations, controlled release rate, and minimized or site-specific application. They are receiving increasing attention and are considered as an important part in sustainable and smart agriculture. This review discussed the limitation of traditional pesticides or conventional application mode, focused on the sustainable features of NCs-based pesticides such as improved formulation, enhanced stability under harsh condition, and controlled release/degradation. The perspectives of NCs-based pesticides and their risk assessment were also suggested in this view for a better use of NCs-based pesticides to facilitate sustainable, smart agriculture in the future.
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Affiliation(s)
- Qiuli Hou
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China; (Q.H.); (H.Z.); (C.L.)
| | - Hanqiao Zhang
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China; (Q.H.); (H.Z.); (C.L.)
| | - Lixia Bao
- Analysis & Testing Center, Institute of Engineering Medicine, Beijing Institute of Technology, Beijing 100081, China; (L.B.); (Z.S.)
| | - Zeyu Song
- Analysis & Testing Center, Institute of Engineering Medicine, Beijing Institute of Technology, Beijing 100081, China; (L.B.); (Z.S.)
| | - Changpeng Liu
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China; (Q.H.); (H.Z.); (C.L.)
| | - Zhenqi Jiang
- Analysis & Testing Center, Institute of Engineering Medicine, Beijing Institute of Technology, Beijing 100081, China; (L.B.); (Z.S.)
- Correspondence: (Z.J.); (Y.Z.)
| | - Yang Zheng
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China; (Q.H.); (H.Z.); (C.L.)
- Correspondence: (Z.J.); (Y.Z.)
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7
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Wickenhagen A, Sugrue E, Lytras S, Kuchi S, Noerenberg M, Turnbull ML, Loney C, Herder V, Allan J, Jarmson I, Cameron-Ruiz N, Varjak M, Pinto RM, Lee JY, Iselin L, Palmalux N, Stewart DG, Swingler S, Greenwood EJD, Crozier TWM, Gu Q, Davies EL, Clohisey S, Wang B, Trindade Maranhão Costa F, Freire Santana M, de Lima Ferreira LC, Murphy L, Fawkes A, Meynert A, Grimes G, Da Silva Filho JL, Marti M, Hughes J, Stanton RJ, Wang ECY, Ho A, Davis I, Jarrett RF, Castello A, Robertson DL, Semple MG, Openshaw PJM, Palmarini M, Lehner PJ, Baillie JK, Rihn SJ, Wilson SJ. A prenylated dsRNA sensor protects against severe COVID-19. Science 2021; 374:eabj3624. [PMID: 34581622 PMCID: PMC7612834 DOI: 10.1126/science.abj3624] [Citation(s) in RCA: 105] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 09/23/2021] [Indexed: 12/11/2022]
Abstract
Inherited genetic factors can influence the severity of COVID-19, but the molecular explanation underpinning a genetic association is often unclear. Intracellular antiviral defenses can inhibit the replication of viruses and reduce disease severity. To better understand the antiviral defenses relevant to COVID-19, we used interferon-stimulated gene (ISG) expression screening to reveal that 2′-5′-oligoadenylate synthetase 1 (OAS1), through ribonuclease L, potently inhibits severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We show that a common splice-acceptor single-nucleotide polymorphism (Rs10774671) governs whether patients express prenylated OAS1 isoforms that are membrane-associated and sense-specific regions of SARS-CoV-2 RNAs or if they only express cytosolic, nonprenylated OAS1 that does not efficiently detect SARS-CoV-2. In hospitalized patients, expression of prenylated OAS1 was associated with protection from severe COVID-19, suggesting that this antiviral defense is a major component of a protective antiviral response.
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Affiliation(s)
- Arthur Wickenhagen
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Elena Sugrue
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Spyros Lytras
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Srikeerthana Kuchi
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Marko Noerenberg
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Matthew L. Turnbull
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Colin Loney
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Vanessa Herder
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Jay Allan
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Innes Jarmson
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Natalia Cameron-Ruiz
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Margus Varjak
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Rute M. Pinto
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Jeffrey Y. Lee
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Louisa Iselin
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
- Department of Biochemistry, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Natasha Palmalux
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Douglas G. Stewart
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Simon Swingler
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Edward J. D. Greenwood
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
| | - Thomas W. M. Crozier
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
| | - Quan Gu
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Emma L. Davies
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Sara Clohisey
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Bo Wang
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Fabio Trindade Maranhão Costa
- Laboratory of Tropical Diseases, Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Sao Paolo, Brazil
| | - Monique Freire Santana
- Department of Education and Research, Oncology Control Centre of Amazonas State (FCECON), Manaus, Amazonas, Brazil
| | - Luiz Carlos de Lima Ferreira
- Postgraduate Program in Tropical Medicine, Tropical Medicine Foundation Dr. Heitor Vieira Dourado, Manaus, Amazonas, Brazil
| | - Lee Murphy
- Edinburgh Clinical Research Facility, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Angie Fawkes
- Edinburgh Clinical Research Facility, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Alison Meynert
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Graeme Grimes
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - ISARIC4C Investigators
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
- Department of Biochemistry, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- Laboratory of Tropical Diseases, Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Sao Paolo, Brazil
- Department of Education and Research, Oncology Control Centre of Amazonas State (FCECON), Manaus, Amazonas, Brazil
- Postgraduate Program in Tropical Medicine, Tropical Medicine Foundation Dr. Heitor Vieira Dourado, Manaus, Amazonas, Brazil
- Edinburgh Clinical Research Facility, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
- Division of Infection & Immunity, Cardiff University, Cardiff, UK
- NIHR Health Protection Research Unit for Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Respiratory Medicine, Alder Hey Children’s Hospital, Liverpool, UK
- National Heart and Lung Institute, Imperial College London, London, UK
- Imperial College Healthcare, National Health Service Trust London, London, UK
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Joao Luiz Da Silva Filho
- Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
| | - Matthias Marti
- Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
| | - Joseph Hughes
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | | | - Eddie C. Y. Wang
- Division of Infection & Immunity, Cardiff University, Cardiff, UK
| | - Antonia Ho
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Ilan Davis
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Ruth F. Jarrett
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Alfredo Castello
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - David L. Robertson
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Malcolm G. Semple
- NIHR Health Protection Research Unit for Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Respiratory Medicine, Alder Hey Children’s Hospital, Liverpool, UK
| | - Peter J. M. Openshaw
- National Heart and Lung Institute, Imperial College London, London, UK
- Imperial College Healthcare, National Health Service Trust London, London, UK
| | - Massimo Palmarini
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Paul J. Lehner
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
| | - J. Kenneth Baillie
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Suzannah J. Rihn
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Sam J. Wilson
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
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8
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Wayment-Steele HK, Kim DS, Choe CA, Nicol JJ, Wellington-Oguri R, Watkins AM, Parra Sperberg RA, Huang PS, Participants E, Das R. Theoretical basis for stabilizing messenger RNA through secondary structure design. Nucleic Acids Res 2021; 49:10604-10617. [PMID: 34520542 PMCID: PMC8499941 DOI: 10.1093/nar/gkab764] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 08/17/2021] [Accepted: 08/27/2021] [Indexed: 01/08/2023] Open
Abstract
RNA hydrolysis presents problems in manufacturing, long-term storage, world-wide delivery and in vivo stability of messenger RNA (mRNA)-based vaccines and therapeutics. A largely unexplored strategy to reduce mRNA hydrolysis is to redesign RNAs to form double-stranded regions, which are protected from in-line cleavage and enzymatic degradation, while coding for the same proteins. The amount of stabilization that this strategy can deliver and the most effective algorithmic approach to achieve stabilization remain poorly understood. Here, we present simple calculations for estimating RNA stability against hydrolysis, and a model that links the average unpaired probability of an mRNA, or AUP, to its overall hydrolysis rate. To characterize the stabilization achievable through structure design, we compare AUP optimization by conventional mRNA design methods to results from more computationally sophisticated algorithms and crowdsourcing through the OpenVaccine challenge on the Eterna platform. We find that rational design on Eterna and the more sophisticated algorithms lead to constructs with low AUP, which we term 'superfolder' mRNAs. These designs exhibit a wide diversity of sequence and structure features that may be desirable for translation, biophysical size, and immunogenicity. Furthermore, their folding is robust to temperature, computer modeling method, choice of flanking untranslated regions, and changes in target protein sequence, as illustrated by rapid redesign of superfolder mRNAs for B.1.351, P.1 and B.1.1.7 variants of the prefusion-stabilized SARS-CoV-2 spike protein. Increases in in vitro mRNA half-life by at least two-fold appear immediately achievable.
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MESH Headings
- Algorithms
- Base Pairing
- Base Sequence
- COVID-19/prevention & control
- Humans
- Hydrolysis
- RNA Stability
- RNA, Double-Stranded/chemistry
- RNA, Double-Stranded/genetics
- RNA, Double-Stranded/immunology
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Messenger/immunology
- RNA, Viral/chemistry
- RNA, Viral/genetics
- RNA, Viral/immunology
- SARS-CoV-2/genetics
- SARS-CoV-2/immunology
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
- Thermodynamics
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Affiliation(s)
- Hannah K Wayment-Steele
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
- Eterna Massive Open Laboratory
| | - Do Soon Kim
- Eterna Massive Open Laboratory
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - Christian A Choe
- Eterna Massive Open Laboratory
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | | | | | - Andrew M Watkins
- Eterna Massive Open Laboratory
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | | | - Po-Ssu Huang
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | | | - Rhiju Das
- Eterna Massive Open Laboratory
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
- Department of Physics, Stanford University, Stanford, CA 94305, USA
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9
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Yong J, Zhang R, Bi S, Li P, Sun L, Mitter N, Carroll BJ, Xu ZP. Sheet-like clay nanoparticles deliver RNA into developing pollen to efficiently silence a target gene. Plant Physiol 2021; 187:886-899. [PMID: 34608968 PMCID: PMC8491087 DOI: 10.1093/plphys/kiab303] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 06/08/2021] [Indexed: 05/25/2023]
Abstract
Topical application of double-stranded RNA (dsRNA) can induce RNA interference (RNAi) and modify traits in plants without genetic modification. However, delivering dsRNA into plant cells remains challenging. Using developing tomato (Solanum lycopersicum) pollen as a model plant cell system, we demonstrate that layered double hydroxide (LDH) nanoparticles up to 50 nm in diameter are readily internalized, particularly by early bicellular pollen, in both energy-dependent and energy-independent manners and without physical or chemical aids. More importantly, these LDH nanoparticles efficiently deliver dsRNA into tomato pollen within 2-4 h of incubation, resulting in an 89% decrease in transgene reporter mRNA levels in early bicellular pollen 3-d post-treatment, compared with a 37% decrease induced by the same dose of naked dsRNA. The target gene silencing is dependent on the LDH particle size, the dsRNA dose, the LDH-dsRNA complexing ratio, and the treatment time. Our findings indicate that LDH nanoparticles are an effective nonviral vector for the effective delivery of dsRNA and other biomolecules into plant cells.
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Affiliation(s)
- Jiaxi Yong
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Run Zhang
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Shengnan Bi
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Peng Li
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Luyao Sun
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Neena Mitter
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Bernard J. Carroll
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Zhi Ping Xu
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
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10
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Perry JK, Appleby TC, Bilello JP, Feng JY, Schmitz U, Campbell EA. An atomistic model of the coronavirus replication-transcription complex as a hexamer assembled around nsp15. J Biol Chem 2021; 297:101218. [PMID: 34562452 PMCID: PMC8494237 DOI: 10.1016/j.jbc.2021.101218] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 09/15/2021] [Accepted: 09/16/2021] [Indexed: 12/23/2022] Open
Abstract
The SARS-CoV-2 replication-transcription complex is an assembly of nonstructural viral proteins that collectively act to reproduce the viral genome and generate mRNA transcripts. While the structures of the individual proteins involved are known, how they assemble into a functioning superstructure is not. Applying molecular modeling tools, including protein-protein docking, to the available structures of nsp7-nsp16 and the nucleocapsid, we have constructed an atomistic model of how these proteins associate. Our principal finding is that the complex is hexameric, centered on nsp15. The nsp15 hexamer is capped on two faces by trimers of nsp14/nsp16/(nsp10)2, which then recruit six nsp12/nsp7/(nsp8)2 polymerase subunits to the complex. To this, six subunits of nsp13 are arranged around the superstructure, but not evenly distributed. Polymerase subunits that coordinate dimers of nsp13 are capable of binding the nucleocapsid, which positions the 5'-UTR TRS-L RNA over the polymerase active site, a state distinguishing transcription from replication. Analysis of the viral RNA path through the complex indicates the dsRNA that exits the polymerase passes over the nsp14 exonuclease and nsp15 endonuclease sites before being unwound by a convergence of zinc fingers from nsp10 and nsp14. The template strand is then directed away from the complex, while the nascent strand is directed to the sites responsible for mRNA capping. The model presents a cohesive picture of the multiple functions of the coronavirus replication-transcription complex and addresses fundamental questions related to proofreading, template switching, mRNA capping, and the role of the endonuclease.
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Affiliation(s)
| | | | | | - Joy Y Feng
- Gilead Sciences, Inc, Foster City, California, USA
| | - Uli Schmitz
- Gilead Sciences, Inc, Foster City, California, USA
| | - Elizabeth A Campbell
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, New York, USA
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11
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Pavlova AS, Yakovleva KI, Epanchitseva AV, Kupryushkin MS, Pyshnaya IA, Pyshnyi DV, Ryabchikova EI, Dovydenko IS. An Influence of Modification with Phosphoryl Guanidine Combined with a 2'-O-Methyl or 2'-Fluoro Group on the Small-Interfering-RNA Effect. Int J Mol Sci 2021; 22:ijms22189784. [PMID: 34575949 PMCID: PMC8467447 DOI: 10.3390/ijms22189784] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/30/2021] [Accepted: 09/08/2021] [Indexed: 11/16/2022] Open
Abstract
Small interfering RNA (siRNA) is the most important tool for the manipulation of mRNA expression and needs protection from intracellular nucleases when delivered into the cell. In this work, we examined the effects of siRNA modification with the phosphoryl guanidine (PG) group, which, as shown earlier, makes oligodeoxynucleotides resistant to snake venom phosphodiesterase. We obtained a set of siRNAs containing combined modifications PG/2'-O-methyl (2'-OMe) or PG/2'-fluoro (2'-F); biophysical and biochemical properties were characterized for each duplex. We used the UV-melting approach to estimate the thermostability of the duplexes and RNAse A degradation assays to determine their stability. The ability to induce silencing was tested in cultured cells stably expressing green fluorescent protein. The introduction of the PG group as a rule decreased the thermodynamic stability of siRNA. At the same time, the siRNAs carrying PG groups showed increased resistance to RNase A. A gene silencing experiment indicated that the PG-modified siRNA retained its activity if the modifications were introduced into the passenger strand.
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Affiliation(s)
| | | | | | | | | | | | | | - Ilya S. Dovydenko
- Correspondence: (E.I.R.); (I.S.D.); Tel.: +7-383-363-5163 (E.I.R. & I.S.D.)
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12
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Huang L, Liao X, Li M, Wang J, Peng X, Wilson TJ, Lilley DMJ. Structure and folding of four putative kink turns identified in structured RNA species in a test of structural prediction rules. Nucleic Acids Res 2021; 49:5916-5924. [PMID: 33978763 PMCID: PMC8191799 DOI: 10.1093/nar/gkab333] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/13/2021] [Accepted: 05/09/2021] [Indexed: 01/25/2023] Open
Abstract
k-Turns are widespread key architectural elements that occur in many classes of RNA molecules. We have shown previously that their folding properties (whether or not they fold into their tightly kinked structure on addition of metal ions) and conformation depend on their local sequence, and we have elucidated a series of rules for prediction of these properties from sequence. In this work, we have expanded the rules for prediction of folding properties, and then applied the full set to predict the folding and conformation of four probable k-turns we have identified amongst 224 structured RNA species found in bacterial intergenenic regions by the Breaker lab (1). We have analyzed the ion-dependence of folding of the four k-turns using fluorescence resonance energy transfer, and determined the conformation of two of them using X-ray crystallography. We find that the experimental data fully conform to both the predicted folding and conformational properties. We conclude that our folding rules are robust, and can be applied to new k-turns of unknown characteristics with confidence.
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Affiliation(s)
- Lin Huang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, PR China
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Xinli Liao
- Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, PR China
| | - Mengxiao Li
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, PR China
| | - Jia Wang
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Xuemei Peng
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, PR China
| | - Timothy J Wilson
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - David M J Lilley
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK
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13
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Abstract
Double-stranded RNA (dsRNA) is produced both by virus and host. Its recognition by the melanoma differentiation-associated gene 5 (MDA5) initiates type I interferon responses. How can a host distinguish self-transcripts from nonself to ensure that responses are targeted correctly? Here, I discuss a role for MDA5 helicase in inducing Z-RNA formation by Alu inverted repeat (AIR) elements. These retroelements have highly conserved sequences that favor Z-formation, creating a site for the dsRNA-specific deaminase enzyme ADAR1 to dock. The subsequent editing destabilizes the dsRNA, ending further interaction with MDA5 and terminating innate immune responses directed against self. By enabling self-recognition, Alu retrotransposons, once invaders, now are genetic elements that keep immune responses in check. I also discuss the possible but less characterized roles of the other helicases in modulating innate immune responses, focusing on DExH-box helicase 9 (DHX9) and Mov10 RISC complex RNA helicase (MOV10). DHX9 and MOV10 function differently from MDA5, but still use nucleic acid structure, rather than nucleotide sequence, to define self. Those genetic elements encoding the alternative conformations involved, referred to as flipons, enable helicases to dynamically shape a cell's repertoire of responses. In the case of MDA5, Alu flipons switch off the dsRNA-dependent responses against self. I suggest a number of genetic systems in which to study interactions between flipons and helicases further.
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Affiliation(s)
- Alan Herbert
- Discovery, InsideOutBio, Charlestown, Massachusetts, United States of America
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14
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Karachevtsev MV, Valeev VA, Karachevtsev VA. Interaction of double-stranded polynucleotide poly(A:U) with graphene/graphene oxide. Eur Phys J E Soft Matter 2021; 44:24. [PMID: 33686498 DOI: 10.1140/epje/s10189-021-00030-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 01/29/2021] [Indexed: 06/12/2023]
Abstract
Hybrids formed by DNA/RNA and graphene family nanomaterials are considered as potentially useful multifunctional agents in biosensing and nanomedicine. In this work, we study the noncovalent interaction between double-stranded (ds) RNA, polyadenylic:polyuridylic acids (poly(A:U)) and graphene oxide/graphene (GO/Gr) using UV absorption spectroscopy and molecular dynamics (MD) simulations. RNA melting showed that relatively long ds-RNA is adsorbed onto GO (at an ionic strength of [Formula: see text]) at that a large fraction of RNA maintains the duplex structure. It was revealed that this fraction decreases over long time (during a few days), indicating a slow adsorption process of the long polymer. MD simulations showed that the adsorption of duplex (rA)[Formula: see text]: (rU)[Formula: see text] or (rA)[Formula: see text]: (rU)[Formula: see text] on graphene starts with the interaction between [Formula: see text]-systems of graphene and base pairs located at a duplex tail. In contrast to relatively long duplex (rA)[Formula: see text]: (rU)[Formula: see text] which keeps parallel arrangement along the graphene surface, the shorter one ((rA)[Formula: see text]: (rU)[Formula: see text]) always adopts a perpendicular orientation relative to graphene even in case of the initial parallel orientation. It was found out that (rA)[Formula: see text]: (rU)[Formula: see text] forms the stable hybrid with graphene keeping essential fraction of the duplex, while (rA)[Formula: see text]: (rU)[Formula: see text] demonstrates the duplex unzipping into two single strands with time. The interaction energies between adenine/uracil stacked with graphene as well between nucleotides in water environment were determined.
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Affiliation(s)
- Maksym V Karachevtsev
- B. Verkin Institute for Low Temperature Physics and Engineering, National Academy of Sciences of Ukraine, 47, Nauky Ave., Kharkiv, 61103, Ukraine.
| | - Vladimir A Valeev
- B. Verkin Institute for Low Temperature Physics and Engineering, National Academy of Sciences of Ukraine, 47, Nauky Ave., Kharkiv, 61103, Ukraine
| | - Victor A Karachevtsev
- B. Verkin Institute for Low Temperature Physics and Engineering, National Academy of Sciences of Ukraine, 47, Nauky Ave., Kharkiv, 61103, Ukraine
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15
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Collauto A, von Bülow S, Gophane DB, Saha S, Stelzl LS, Hummer G, Sigurdsson ST, Prisner TF. Compaction of RNA Duplexes in the Cell*. Angew Chem Int Ed Engl 2020; 59:23025-23029. [PMID: 32804430 PMCID: PMC7756485 DOI: 10.1002/anie.202009800] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Indexed: 11/15/2022]
Abstract
The structure and flexibility of RNA depends sensitively on the microenvironment. Using pulsed electron-electron double-resonance (PELDOR)/double electron-electron resonance (DEER) spectroscopy combined with advanced labeling techniques, we show that the structure of double-stranded RNA (dsRNA) changes upon internalization into Xenopus laevis oocytes. Compared to dilute solution, the dsRNA A-helix is more compact in cells. We recapitulate this compaction in a densely crowded protein solution. Atomic-resolution molecular dynamics simulations of dsRNA semi-quantitatively capture the compaction, and identify non-specific electrostatic interactions between proteins and dsRNA as a possible driver of this effect.
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Affiliation(s)
- Alberto Collauto
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic ResonanceGoethe University FrankfurtMax-von-Laue-Str. 760438Frankfurt am MainGermany
| | - Sören von Bülow
- Department of Theoretical BiophysicsMax Planck Institute of BiophysicsMax-von-Laue-Str. 360438Frankfurt am MainGermany
| | - Dnyaneshwar B. Gophane
- Department of ChemistryScience InstituteUniversity of IcelandDunhagi 3107ReykjavíkIceland
| | - Subham Saha
- Department of ChemistryScience InstituteUniversity of IcelandDunhagi 3107ReykjavíkIceland
| | - Lukas S. Stelzl
- Department of Theoretical BiophysicsMax Planck Institute of BiophysicsMax-von-Laue-Str. 360438Frankfurt am MainGermany
| | - Gerhard Hummer
- Department of Theoretical BiophysicsMax Planck Institute of BiophysicsMax-von-Laue-Str. 360438Frankfurt am MainGermany
- Institute for BiophysicsGoethe University FrankfurtMax-von-Laue-Str. 960438Frankfurt am MainGermany
| | - Snorri T. Sigurdsson
- Department of ChemistryScience InstituteUniversity of IcelandDunhagi 3107ReykjavíkIceland
| | - Thomas F. Prisner
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic ResonanceGoethe University FrankfurtMax-von-Laue-Str. 760438Frankfurt am MainGermany
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16
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Šmidlehner T, Košćak M, Božinović K, Majhen D, Schmuck C, Piantanida I. Fluorimetric and CD Recognition between Various ds-DNA/RNA Depends on a Cyanine Connectivity in Cyanine-guanidiniocarbonyl-pyrrole Conjugate. Molecules 2020; 25:molecules25194470. [PMID: 33003366 PMCID: PMC7583847 DOI: 10.3390/molecules25194470] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 09/25/2020] [Accepted: 09/27/2020] [Indexed: 11/16/2022] Open
Abstract
Two novel isosteric conjugates of guanidiniocarbonyl-pyrrole and 6-bromo-TO (thiazole orange) were prepared, differing only in linker connectivity to cyanine (benzothiazole nitrogen vs. quinoline nitrogen). The quinoline analog was significantly more susceptible to aggregation in an aqueous medium, which resulted in induced circular dichroism (ICD; λ = 450-550 nm) recognition between A-T(U) and G-C basepair containing polynucleotides. The benzothiazole-isostere showed pronounced (four-fold) fluorimetric selectivity toward ds-RNA in comparison to any ds-DNA, at variance to its quinoline-analogue fluorescence being weakly selective to GC-DNA. Preliminary screening on human tumor and normal lung cell lines showed that both dyes very efficiently enter living cells and accumulate in mitochondria, causing moderate cytotoxic effects, and thus could be considered as lead compounds toward novel theragnostic mitochondrial dyes.
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Affiliation(s)
- Tamara Šmidlehner
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (T.Š.); (M.K.)
| | - Marta Košćak
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (T.Š.); (M.K.)
| | - Ksenija Božinović
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia; (K.B.); (D.M.)
| | - Dragomira Majhen
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia; (K.B.); (D.M.)
| | - Carsten Schmuck
- Institute of Organic Chemistry, University of Duisburg-Essen, 45141 Essen, Germany;
| | - Ivo Piantanida
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (T.Š.); (M.K.)
- Correspondence: ; Tel.: +385-1-4571-326
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17
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Niu D, Zhao Y, Zhang W. Temperature stress response: A novel important function of Dermatophagoides farinae allergens. Exp Parasitol 2020; 218:108003. [PMID: 32980317 DOI: 10.1016/j.exppara.2020.108003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 08/13/2020] [Accepted: 09/18/2020] [Indexed: 11/19/2022]
Abstract
Dermatophagoides farinae, an important pathogen, has multiple allergens. However, their expression under physiological conditions are not understood. Our previous RNA-seq showed that allergens of D. farinae were up-regulated under temperature stress, implying that they may be involved in stress response. Here, we performed a comprehensive study. qRT-PCR detection indicated that 26 of the 34 allergens showed differential expression. Der f1 had the most abundant basic expression quantity. Der f 28.0201 (HSP70) and Der f3 had the same regulation pattern in 9 highly expressed transcripts, which only up-regulated at 41 °C and 43 °C, but Der f 28.0201 showed stronger regulation than Der f 3 (19.88-fold vs 6.02-fold). Whereas Der f 1, 2, 7, 21, 22, 27, and 30 were up-regulated under both heat and cold stress, and Der f 27 showed the strongest regulation ability among them. Der f 27 showed more significant up-regulation than Der f 28.0201 under heat stress (23.59-fold vs 19.88-fold), and Der f27 had more obvious up-regulation under cold than heat stress (30.70-fold vs 23.59-fold). The expression of Der f 27, 28.0201 and 1, and D. farinae survival rates significantly decreased following RNAi, indicating the upregulation of these allergens under temperature stress conferred thermo-tolerance or cold-tolerance to D. farinae. In this study, we described for the first time that these allergens have temperature-stress response functions. This new scientific discovery has important clinical value for revealing the more frequent and serious allergic diseases caused by D. farinae during the change of seasons.
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Affiliation(s)
- DongLing Niu
- Department of Pathogen Biology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, 710061, China
| | - YaE Zhao
- Department of Pathogen Biology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, 710061, China.
| | - WanYu Zhang
- Department of Pathogen Biology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, 710061, China
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18
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Wacquiez A, Coste F, Kut E, Gaudon V, Trapp S, Castaing B, Marc D. Structure and Sequence Determinants Governing the Interactions of RNAs with Influenza A Virus Non-Structural Protein NS1. Viruses 2020; 12:E947. [PMID: 32867106 PMCID: PMC7552008 DOI: 10.3390/v12090947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 08/17/2020] [Accepted: 08/25/2020] [Indexed: 11/16/2022] Open
Abstract
The non-structural protein NS1 of influenza A viruses is an RNA-binding protein of which its activities in the infected cell contribute to the success of the viral cycle, notably through interferon antagonism. We have previously shown that NS1 strongly binds RNA aptamers harbouring virus-specific sequence motifs (Marc et al., Nucleic Acids Res. 41, 434-449). Here, we started out investigating the putative role of one particular virus-specific motif through the phenotypic characterization of mutant viruses that were genetically engineered from the parental strain WSN. Unexpectedly, our data did not evidence biological importance of the putative binding of NS1 to this specific motif (UGAUUGAAG) in the 3'-untranslated region of its own mRNA. Next, we sought to identify specificity determinants in the NS1-RNA interaction through interaction assays in vitro with several RNA ligands and through solving by X-ray diffraction the 3D structure of several complexes associating NS1's RBD with RNAs of various affinities. Our data show that the RBD binds the GUAAC motif within double-stranded RNA helices with an apparent specificity that may rely on the sequence-encoded ability of the RNA to bend its axis. On the other hand, we showed that the RBD binds to the virus-specific AGCAAAAG motif when it is exposed in the apical loop of a high-affinity RNA aptamer, probably through a distinct mode of interaction that still requires structural characterization. Our data are consistent with more than one mode of interaction of NS1's RBD with RNAs, recognizing both structure and sequence determinants.
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MESH Headings
- 3' Untranslated Regions
- Animals
- Aptamers, Nucleotide/chemistry
- Aptamers, Nucleotide/metabolism
- Base Sequence
- Cell Line
- Humans
- Influenza A Virus, H1N1 Subtype/chemistry
- Influenza A Virus, H7N1 Subtype/chemistry
- Models, Molecular
- Nucleic Acid Conformation
- Protein Binding
- Protein Domains
- RNA/chemistry
- RNA/metabolism
- RNA, Double-Stranded/chemistry
- RNA, Double-Stranded/metabolism
- RNA, Messenger/chemistry
- RNA, Messenger/metabolism
- RNA, Viral/chemistry
- RNA, Viral/metabolism
- RNA-Binding Proteins/chemistry
- RNA-Binding Proteins/metabolism
- SELEX Aptamer Technique
- Viral Nonstructural Proteins/chemistry
- Viral Nonstructural Proteins/metabolism
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Affiliation(s)
- Alan Wacquiez
- Equipe 3IMo, UMR1282 Infectiologie et Santé Publique, INRAE, F-37380 Nouzilly, France; (A.W.); (E.K.); (S.T.)
- UMR1282 Infectiologie et Santé Publique, Université de Tours, F-37000 Tours, France
- Centre de Biophysique Moléculaire, UPR4301 CNRS, rue Charles Sadron, CEDEX 02, 45071 Orléans, France; (F.C.); (V.G.)
| | - Franck Coste
- Centre de Biophysique Moléculaire, UPR4301 CNRS, rue Charles Sadron, CEDEX 02, 45071 Orléans, France; (F.C.); (V.G.)
| | - Emmanuel Kut
- Equipe 3IMo, UMR1282 Infectiologie et Santé Publique, INRAE, F-37380 Nouzilly, France; (A.W.); (E.K.); (S.T.)
- UMR1282 Infectiologie et Santé Publique, Université de Tours, F-37000 Tours, France
| | - Virginie Gaudon
- Centre de Biophysique Moléculaire, UPR4301 CNRS, rue Charles Sadron, CEDEX 02, 45071 Orléans, France; (F.C.); (V.G.)
| | - Sascha Trapp
- Equipe 3IMo, UMR1282 Infectiologie et Santé Publique, INRAE, F-37380 Nouzilly, France; (A.W.); (E.K.); (S.T.)
- UMR1282 Infectiologie et Santé Publique, Université de Tours, F-37000 Tours, France
| | - Bertrand Castaing
- Centre de Biophysique Moléculaire, UPR4301 CNRS, rue Charles Sadron, CEDEX 02, 45071 Orléans, France; (F.C.); (V.G.)
| | - Daniel Marc
- Equipe 3IMo, UMR1282 Infectiologie et Santé Publique, INRAE, F-37380 Nouzilly, France; (A.W.); (E.K.); (S.T.)
- UMR1282 Infectiologie et Santé Publique, Université de Tours, F-37000 Tours, France
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19
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Thuy-Boun AS, Thomas JM, Grajo HL, Palumbo CM, Park S, Nguyen LT, Fisher AJ, Beal PA. Asymmetric dimerization of adenosine deaminase acting on RNA facilitates substrate recognition. Nucleic Acids Res 2020; 48:7958-7972. [PMID: 32597966 PMCID: PMC7641318 DOI: 10.1093/nar/gkaa532] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 06/09/2020] [Accepted: 06/24/2020] [Indexed: 12/20/2022] Open
Abstract
Adenosine deaminases acting on RNA (ADARs) are enzymes that convert adenosine to inosine in duplex RNA, a modification that exhibits a multitude of effects on RNA structure and function. Recent studies have identified ADAR1 as a potential cancer therapeutic target. ADARs are also important in the development of directed RNA editing therapeutics. A comprehensive understanding of the molecular mechanism of the ADAR reaction will advance efforts to develop ADAR inhibitors and new tools for directed RNA editing. Here we report the X-ray crystal structure of a fragment of human ADAR2 comprising its deaminase domain and double stranded RNA binding domain 2 (dsRBD2) bound to an RNA duplex as an asymmetric homodimer. We identified a highly conserved ADAR dimerization interface and validated the importance of these sequence elements on dimer formation via gel mobility shift assays and size exclusion chromatography. We also show that mutation in the dimerization interface inhibits editing in an RNA substrate-dependent manner for both ADAR1 and ADAR2.
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Affiliation(s)
| | - Justin M Thomas
- Department of Chemistry, University of California, Davis, CA, USA
| | - Herra L Grajo
- Department of Chemistry, University of California, Davis, CA, USA
| | - Cody M Palumbo
- Department of Chemistry, University of California, Davis, CA, USA
| | - SeHee Park
- Department of Chemistry, University of California, Davis, CA, USA
| | - Luan T Nguyen
- Department of Chemistry, University of California, Davis, CA, USA
| | - Andrew J Fisher
- Department of Chemistry, University of California, Davis, CA, USA
- Department of Molecular and Cellular Biology, University of California, Davis, CA, USA
| | - Peter A Beal
- Department of Chemistry, University of California, Davis, CA, USA
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20
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Lichtenberg SS, Laisney J, Elhaj Baddar Z, Tsyusko OV, Palli SR, Levard C, Masion A, Unrine JM. Comparison of Nanomaterials for Delivery of Double-Stranded RNA in Caenorhabditis elegans. J Agric Food Chem 2020; 68:7926-7934. [PMID: 32610013 DOI: 10.1021/acs.jafc.0c02840] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
RNA interference is a promising crop protection technology that has seen rapid development in the past several years. Here, we investigated polyamino acid biopolymers, inorganic nanomaterials, and hybrid organic-inorganic nanomaterials for delivery of dsRNA and efficacy of gene knockdown using the model nematode Caenorhabditis elegans. Using an oral route of delivery, we are able to approximate how nanomaterials will be delivered in the environment. Of the materials investigated, only Mg-Al layered double-hydroxide nanoparticles were effective at gene knockdown in C. elegans, reducing marker gene expression to 66.8% of that of the control at the lowest tested concentration. In addition, we identified previously unreported injuries to the mouthparts of C. elegans associated with the use of a common cell-penetrating peptide, poly-l-arginine. Our results will allow the pursuit of further research into promising materials for dsRNA delivery and also allow for the exclusion of those with little efficacy or deleterious effects.
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Affiliation(s)
- Stuart S Lichtenberg
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, Kentucky 40546, United States
| | - Jerome Laisney
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, Kentucky 40546, United States
| | - Zeinah Elhaj Baddar
- Department of Entomology, University of Kentucky, Lexington, Kentucky 40546, United States
| | - Olga V Tsyusko
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, Kentucky 40546, United States
| | - Subba R Palli
- Department of Entomology, University of Kentucky, Lexington, Kentucky 40546, United States
| | - Clement Levard
- CNRS, Aix-Marseille Univ., IRD, INRAE, Coll France, CEREGE, Europole Arbois,check BP 80, Aix en Provence 13545, France
| | - Armand Masion
- CNRS, Aix-Marseille Univ., IRD, INRAE, Coll France, CEREGE, Europole Arbois,check BP 80, Aix en Provence 13545, France
| | - Jason M Unrine
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, Kentucky 40546, United States
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21
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Elhaj Baddar Z, Gurusamy D, Laisney J, Tripathi P, Palli SR, Unrine JM. Polymer-Coated Hydroxyapatite Nanocarrier for Double-Stranded RNA Delivery. J Agric Food Chem 2020; 68:6811-6818. [PMID: 32491848 DOI: 10.1021/acs.jafc.0c02182] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Conventional synthetic insecticides have limited success due to insect resistance and negative effects on off-target biota and the environment. Although RNA interference (RNAi) is a tool that is becoming more widely utilized in pest control products, naked dsRNA has limited success in most taxa. Nanocarriers have shown promising results in enhancing the efficacy of this tool. In this study, we used a layer-by-layer electrostatic assembly where we synthesized poly(acrylic acid) (PAA)-coated hydroxyapatite (HA) nanoparticles (PAA-HA NPs) as inorganic nanocarriers, which were then coated with a layer of a cationic poly(amino acid), 10 kDa poly-l-arginine (PLR10), to allow for binding of a layer of negatively charged dsRNA. Binding of PLR10-PAA-HA NPs to dsRNA was found to increase as the mass ratio of NPs to dsRNA increased. In vitro studies with transgenic SF9 cells (from Spodoptera frugiperda) expressing the firefly luciferase gene showed a significant gene silencing (35% decrease) at a 5:1 NP-to-dsRNA ratio, while naked dsRNA was ineffective at gene silencing. There was a significant concentration-response relationship in knockdown; however, cytotoxicity was observed at higher concentrations. Confocal microscopy studies showed that dsRNA from PLR10-PAA-HA NPs was not localized within endosomes, while naked dsRNA appeared to be entrapped within the endosomes. Overall, polymer-functionalized HA nanocarriers enabled dsRNA to elicit gene knockdown in cells, whereas naked dsRNA was not effective in causing gene knockdown.
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Affiliation(s)
- Zeinah Elhaj Baddar
- Department of Entomology, University of Kentucky, Lexington, Kentucky 40546, United States
| | - Dhandapani Gurusamy
- Department of Entomology, University of Kentucky, Lexington, Kentucky 40546, United States
| | - Jérôme Laisney
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, Kentucky 40546, United States
| | - Priyanka Tripathi
- Department of Entomology, University of Kentucky, Lexington, Kentucky 40546, United States
| | - Subba R Palli
- Department of Entomology, University of Kentucky, Lexington, Kentucky 40546, United States
| | - Jason M Unrine
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, Kentucky 40546, United States
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22
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Gao Y, Vasic R, Song Y, Teng R, Liu C, Gbyli R, Biancon G, Nelakanti R, Lobben K, Kudo E, Liu W, Ardasheva A, Fu X, Wang X, Joshi P, Lee V, Dura B, Viero G, Iwasaki A, Fan R, Xiao A, Flavell RA, Li HB, Tebaldi T, Halene S. m 6A Modification Prevents Formation of Endogenous Double-Stranded RNAs and Deleterious Innate Immune Responses during Hematopoietic Development. Immunity 2020; 52:1007-1021.e8. [PMID: 32497523 PMCID: PMC7408742 DOI: 10.1016/j.immuni.2020.05.003] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 02/19/2020] [Accepted: 05/08/2020] [Indexed: 01/02/2023]
Abstract
N6-methyladenosine (m6A) is the most abundant RNA modification, but little is known about its role in mammalian hematopoietic development. Here, we show that conditional deletion of the m6A writer METTL3 in murine fetal liver resulted in hematopoietic failure and perinatal lethality. Loss of METTL3 and m6A activated an aberrant innate immune response, mediated by the formation of endogenous double-stranded RNAs (dsRNAs). The aberrantly formed dsRNAs were long, highly m6A modified in their native state, characterized by low folding energies, and predominantly protein coding. We identified coinciding activation of pattern recognition receptor pathways normally tasked with the detection of foreign dsRNAs. Disruption of the aberrant immune response via abrogation of downstream Mavs or Rnasel signaling partially rescued the observed hematopoietic defects in METTL3-deficient cells in vitro and in vivo. Our results suggest that m6A modification protects against endogenous dsRNA formation and a deleterious innate immune response during mammalian hematopoietic development.
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Affiliation(s)
- Yimeng Gao
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Stem Cell Center and Yale RNA Center, Yale University School of Medicine, New Haven, CT 06520, USA.
| | - Radovan Vasic
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Stem Cell Center and Yale RNA Center, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Yuanbin Song
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Stem Cell Center and Yale RNA Center, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Rhea Teng
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Stem Cell Center and Yale RNA Center, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Chengyang Liu
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Stem Cell Center and Yale RNA Center, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Rana Gbyli
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Stem Cell Center and Yale RNA Center, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Giulia Biancon
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Stem Cell Center and Yale RNA Center, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Raman Nelakanti
- Department of Genetics and Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Kirsten Lobben
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Stem Cell Center and Yale RNA Center, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Eriko Kudo
- Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA; Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Wei Liu
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Stem Cell Center and Yale RNA Center, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Anastasia Ardasheva
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Stem Cell Center and Yale RNA Center, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Xiaoying Fu
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Stem Cell Center and Yale RNA Center, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Xiaman Wang
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Stem Cell Center and Yale RNA Center, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Poorval Joshi
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Stem Cell Center and Yale RNA Center, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Veronica Lee
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Stem Cell Center and Yale RNA Center, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Burak Dura
- Yale Stem Cell Center and Yale RNA Center, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Biomedical Engineering and Yale Cancer Center, Yale University, New Haven, CT 06520, USA
| | - Gabriella Viero
- Institute of Biophysics, CNR Unit at Trento, Povo Trento 38123, Italy
| | - Akiko Iwasaki
- Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA; Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Rong Fan
- Yale Stem Cell Center and Yale RNA Center, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Biomedical Engineering and Yale Cancer Center, Yale University, New Haven, CT 06520, USA
| | - Andrew Xiao
- Department of Genetics and Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Richard A Flavell
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
| | - Hua-Bing Li
- Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Shanghai Jiao Tong University School of Medicine-Yale Institute for Immune Metabolism, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
| | - Toma Tebaldi
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Stem Cell Center and Yale RNA Center, Yale University School of Medicine, New Haven, CT 06520, USA.
| | - Stephanie Halene
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Stem Cell Center and Yale RNA Center, Yale University School of Medicine, New Haven, CT 06520, USA.
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23
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Patra MC, Batool M, Haseeb M, Choi S. A Computational Probe into the Structure and Dynamics of the Full-Length Toll-Like Receptor 3 in a Phospholipid Bilayer. Int J Mol Sci 2020; 21:ijms21082857. [PMID: 32325904 PMCID: PMC7215789 DOI: 10.3390/ijms21082857] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 04/14/2020] [Accepted: 04/16/2020] [Indexed: 02/07/2023] Open
Abstract
Toll-like receptor 3 (TLR3) provides the host with antiviral defense by initiating an immune signaling cascade for the production of type I interferons. The X-ray structures of isolated TLR3 ectodomain (ECD) and transmembrane (TM) domains have been reported; however, the structure of a membrane-solvated, full-length receptor remains elusive. We investigated an all-residue TLR3 model embedded inside a phospholipid bilayer using molecular dynamics simulations. The TLR3-ECD exhibited a ~30°–35° tilt on the membrane due to the electrostatic interaction between the N-terminal subdomain and phospholipid headgroups. Although the movement of dsRNA did not affect the dimer integrity of TLR3, its sugar-phosphate backbone was slightly distorted with the orientation of the ECD. TM helices exhibited a noticeable tilt and curvature but maintained a consistent crossing angle, avoiding the hydrophobic mismatch with the bilayer. Residues from the αD helix and the CD and DE loops of the Toll/interleukin-1 receptor (TIR) domains were partially absorbed into the lower leaflet of the bilayer. We found that the previously unknown TLR3-TIR dimerization interface could be stabilized by the reciprocal contact between αC and αD helices of one subunit and the αC helix and the BB loop of the other. Overall, the present study can be helpful to understand the signaling-competent form of TLR3 in physiological environments.
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24
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Chernikov IV, Gladkikh DV, Karelina UA, Meschaninova MI, Ven’yaminova AG, Vlassov VV, Chernolovskaya EL. Trimeric Small Interfering RNAs and Their Cholesterol-Containing Conjugates Exhibit Improved Accumulation in Tumors, but Dramatically Reduced Silencing Activity. Molecules 2020; 25:molecules25081877. [PMID: 32325757 PMCID: PMC7221888 DOI: 10.3390/molecules25081877] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 04/16/2020] [Accepted: 04/16/2020] [Indexed: 12/15/2022] Open
Abstract
Cholesterol derivatives of nuclease-resistant, anti-MDR1 small-interfering RNAs were designed to contain a 2’-OMe-modified 21-bp siRNA and a 63-bp TsiRNA in order to investigate their accumulation and silencing activity in vitro and in vivo. The results showed that increasing the length of the RNA duplex in such a conjugate increases its biological activity when delivered using a transfection agent. However, the efficiency of accumulation in human drug-resistant KB-8-5 cells during delivery in vitro in a carrier-free mode was reduced as well as efficiency of target gene silencing. TsiRNAs demonstrated a similar biodistribution in KB-8-5 xenograft tumor-bearing SCID mice with more efficient accumulation in organs and tumors than cholesterol-conjugated canonical siRNAs; however, this accumulation did not provide a silencing effect. The lack of correlation between the accumulation in the organ and the silencing activity of cholesterol conjugates of siRNAs of different lengths can be attributed to the fact that trimeric Ch-TsiRNA lags mainly in the intercellular space and does not penetrate sufficiently into the cytoplasm of the cell. Increased accumulation in the organs and in the tumor, by itself, shows that using siRNA with increased molecular weight is an effective approach to control biodistribution and delivery to the target organ.
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25
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Kim KH, Hwang J, Kim JH, Son KP, Jang Y, Kim M, Kang SJ, Lee JO, Kang JY, Choi BS. Structural and biophysical properties of RIG-I bound to dsRNA with G-U wobble base pairs. RNA Biol 2020; 17:325-334. [PMID: 31852354 PMCID: PMC6999645 DOI: 10.1080/15476286.2019.1700034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 11/14/2019] [Accepted: 11/15/2019] [Indexed: 10/25/2022] Open
Abstract
Retinoic acid-inducible gene I (RIG-I) is responsible for innate immunity via the recognition of short double-stranded RNAs in the cytosol. With the clue that G-U wobble base pairs in the influenza A virus's RNA promoter region are responsible for RIG-I activation, we determined the complex structure of RIG-I ΔCARD and a short hairpin RNA with G-U wobble base pairs by X-ray crystallography. Interestingly, the overall helical backbone trace was not affected by the presence of the wobble base pairs; however, the base pair inclination and helical axis angle changed upon RIG-I binding. NMR spectroscopy revealed that RIG-I binding renders the flexible base pair of the influenza A virus's RNA promoter region between the two G-U wobble base pairs even more flexible. Binding to RNA with wobble base pairs resulted in a more flexible RIG-I complex. This flexible complex formation correlates with the entropy-favoured binding of RIG-I and RNA, which results in tighter binding affinity and RIG-I activation. This study suggests that the structure and dynamics of RIG-I are tailored to the binding of specific RNA sequences with different flexibility.
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Affiliation(s)
- Ki-Hun Kim
- Department of Chemistry, KAIST, Daejeon, Republic of Korea
| | - Jihyun Hwang
- Department of Chemistry, KAIST, Daejeon, Republic of Korea
| | - Jin Hong Kim
- Department of Chemistry, KAIST, Daejeon, Republic of Korea
| | - Kyung-Pyo Son
- Department of Biological Sciences, KAIST, Daejeon, Republic of Korea
| | - Yejin Jang
- Virus Research and Testing Group, Therapeutics and Biotechnology Division, KRICT, Daejeon, Republic of Korea
| | - Meehyein Kim
- Virus Research and Testing Group, Therapeutics and Biotechnology Division, KRICT, Daejeon, Republic of Korea
| | - Suk-Jo Kang
- Department of Biological Sciences, KAIST, Daejeon, Republic of Korea
| | - Jie-Oh Lee
- Department of Chemistry, KAIST, Daejeon, Republic of Korea
| | - Jin Young Kang
- Department of Chemistry, KAIST, Daejeon, Republic of Korea
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26
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Ban Ž, Griesbeck S, Tomić S, Nitsch J, Marder TB, Piantanida I. A Quadrupolar Bis-Triarylborane Chromophore as a Fluorimetric and Chirooptic Probe for Simultaneous and Selective Sensing of DNA, RNA and Proteins. Chemistry 2020; 26:2195-2203. [PMID: 31756013 PMCID: PMC7065195 DOI: 10.1002/chem.201903936] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 11/21/2019] [Indexed: 12/29/2022]
Abstract
A water-soluble tetracationic quadrupolar bis-triarylborane chromophore showed strong binding to ds-DNA, ds-RNA, ss-RNA, as well as to the naturally most abundant protein, BSA. The novel dye can distinguish between DNA/RNA and BSA by fluorescence emission separated by Δ ν ˜ =3600 cm-1 , allowing for the simultaneous quantification of DNA/RNA and protein (BSA) in a mixture. The applicability of such fluorimetric differentiation in vitro was demonstrated, strongly supporting a protein-like target as a dominant binding site of 1 in cells. Moreover, our dye also bound strongly to ss-RNA, with the unusual rod-like structure of the dye, decorated by four positive charges at its termini and having a hydrophobic core, acting as a spindle for wrapping A, C and U ss-RNAs, but not poly G, the latter preserving its secondary structure. To the best of our knowledge, such unmatched, multifaceted binding activity of a small molecule toward DNA, RNA, and proteins and the selectivity of its fluorimetric and chirooptic response makes the quadrupolar bis-triarylborane a novel chromophore/fluorophore moiety for biochemical applications.
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Affiliation(s)
- Željka Ban
- Division of Organic Chemistry and BiochemistryRuder Boškovic InstituteZagrebCroatia
| | - Stefanie Griesbeck
- Institut für Anorganische Chemie andInstitute for Sustainable Chemistry & Catalysis with BoronJulius-Maximilians-Universität Würzburg97074WürzburgGermany
| | - Sanja Tomić
- Division of Organic Chemistry and BiochemistryRuder Boškovic InstituteZagrebCroatia
| | - Jörn Nitsch
- Institut für Anorganische Chemie andInstitute for Sustainable Chemistry & Catalysis with BoronJulius-Maximilians-Universität Würzburg97074WürzburgGermany
| | - Todd B. Marder
- Institut für Anorganische Chemie andInstitute for Sustainable Chemistry & Catalysis with BoronJulius-Maximilians-Universität Würzburg97074WürzburgGermany
| | - Ivo Piantanida
- Division of Organic Chemistry and BiochemistryRuder Boškovic InstituteZagrebCroatia
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27
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Fu H, Zhang C, Qiang XW, Yang YJ, Dai L, Tan ZJ, Zhang XH. Opposite Effects of High-Valent Cations on the Elasticities of DNA and RNA Duplexes Revealed by Magnetic Tweezers. Phys Rev Lett 2020; 124:058101. [PMID: 32083903 DOI: 10.1103/physrevlett.124.058101] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 01/16/2020] [Indexed: 06/10/2023]
Abstract
We report that trivalent cobalt hexammine cations decrease the persistence length, stretching modulus, helical density, and size of plectonemes formed under torque of DNA but increase those of RNA. Divalent magnesium cations, however, decrease the persistence lengths, contour lengths, and sizes of plectonemes while increasing the helical densities of both DNA and RNA. The experimental results are explained by different binding modes of the cations on DNA and RNA in our all-atom molecular dynamics simulations. The significant variations of the helical densities and structures of DNA and RNA duplexes induced by high-valent cations may affect interactions of the duplexes with proteins.
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Affiliation(s)
- Hang Fu
- College of Life Sciences, the Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan 430072, China
| | - Chen Zhang
- College of Life Sciences, the Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan 430072, China
| | - Xiao-Wei Qiang
- Center for Theoretical Physics and Key Laboratory of Artificial Micro & Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Ya-Jun Yang
- College of Life Sciences, the Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan 430072, China
| | - Liang Dai
- Department of Physics, City University of Hong Kong, Hong Kong 999077, China
| | - Zhi-Jie Tan
- Center for Theoretical Physics and Key Laboratory of Artificial Micro & Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Xing-Hua Zhang
- College of Life Sciences, the Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan 430072, China
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28
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Mizuuchi R, Usui K, Ichihashi N. Structural transition of replicable RNAs during in vitro evolution with Qβ replicase. RNA 2020; 26:83-90. [PMID: 31690585 PMCID: PMC6913131 DOI: 10.1261/rna.073106.119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 10/26/2019] [Indexed: 06/10/2023]
Abstract
Single-stranded RNAs (ssRNAs) are utilized as genomes in some viruses and also in experimental models of ancient life-forms, owing to their simplicity. One of the largest problems for ssRNA replication is the formation of double-stranded RNA (dsRNA), a dead-end product for ssRNA replication. A possible strategy to avoid dsRNA formation is to create strong intramolecular secondary structures of ssRNA. To design ssRNAs that efficiently replicate by Qβ replicase with minimum dsRNA formation, we previously proposed the "fewer unpaired GC rule." According to this rule, ssRNAs that have fewer unpaired G and C bases in the secondary structure should efficiently replicate with less dsRNA formation. However, the validity of this rule still needs to be examined, especially for longer ssRNAs. Here, we analyze nine long ssRNAs that successively appeared during an in vitro evolution of replicable ssRNA by Qβ replicase and examine whether this rule can explain the structural transitions of the RNAs. We found that these ssRNAs improved their template abilities step-by-step with decreasing dsRNA formation as mutations accumulated. We then examine the secondary structures of all the RNAs by a chemical modification method. The analysis of the structures revealed that the probabilities of unpaired G and C bases tended to decrease gradually in the course of evolution. The decreases were caused by the local structural changes around the mutation sites in most of the cases. These results support the validity of the "fewer unpaired GC rule" to efficiently design replicable ssRNAs by Qβ replicase, useful for more complex ssRNA replication systems.
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Affiliation(s)
- Ryo Mizuuchi
- Komaba Institute for Science, The University of Tokyo, Meguro, Tokyo 153-8902, Japan
- JST, PRESTO, Kawaguchi, Saitama 332-0012, Japan
| | - Kimihito Usui
- Japan Science and Technology Agency, Suita, Osaka, 565-0871, Japan
| | - Norikazu Ichihashi
- Komaba Institute for Science, The University of Tokyo, Meguro, Tokyo 153-8902, Japan
- Department of Life Science, Graduate School of Arts and Science, The University of Tokyo, Meguro-ku, Tokyo, 153-8902, Japan
- Universal Biology Institute, The University of Tokyo, Meguro-ku, Tokyo, 153-8902, Japan
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29
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Ren X, Linehan MM, Iwasaki A, Pyle AM. RIG-I Recognition of RNA Targets: The Influence of Terminal Base Pair Sequence and Overhangs on Affinity and Signaling. Cell Rep 2019; 29:3807-3815.e3. [PMID: 31851914 DOI: 10.1016/j.celrep.2019.11.052] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Revised: 09/24/2019] [Accepted: 11/13/2019] [Indexed: 12/25/2022] Open
Abstract
Within the complex environment of the human cell, the RIG-I innate immune receptor must detect the presence of double-stranded viral RNA molecules and differentiate them from a diversity of host RNA molecules. In an ongoing effort to understand the molecular basis for RIG-I target specificity, here, we evaluate the ability of this sensor to respond to triphosphorylated, double-stranded RNA molecules that contain all possible terminal base pairs and common mismatches. In addition, we test the response to duplexes with various types of 5' and 3' overhangs. We conducted quantitative measurements of RNA ligand affinity, then tested RNA variants for their ability to stimulate the RIG-I-dependent interferon response in cells and in whole animals. The resulting data provide insights into the design of RNA therapeutics that prevent RIG-I activation, and they provide valuable insights into the mechanisms of evasion by deadly pathogens such as the Ebola and Marburg viruses.
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Affiliation(s)
- Xiaoming Ren
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA
| | - Melissa M Linehan
- Department of Immunobiology, Yale University, New Haven, CT 06520, USA
| | - Akiko Iwasaki
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA; Department of Immunobiology, Yale University, New Haven, CT 06520, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA
| | - Anna Marie Pyle
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA.
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30
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Abstract
The mechanical properties of double-stranded RNA (dsRNA) are involved in many of its biological functions and are relevant for future nanotechnology applications. DsRNA must tightly bend to fit inside viral capsids or deform upon the interaction with proteins that regulate gene silencing or the immune response against viral attacks. However, the question of how the nucleotide sequence affects the global mechanical properties of dsRNA has so far remained largely unexplored. Here, we have employed state-of-the-art atomistic molecular dynamics simulations to unveil the mechanical response of different RNA duplexes to an external force. Our results reveal that, similarly to dsDNA, the mechanical properties of dsRNA are highly sequence-dependent. However, we find that the nucleotide sequence affects in a strikingly different manner the stretching and twisting response of RNA and DNA duplexes under force. We find that the elastic response of dsRNA is dominated by the local high flexibility of pyrimidine-purine steps. Moreover, the flexibility of pyrimidine-purine steps is independent of the sequence context, and the global flexibility of the duplex reasonably scales with the number of this kind of base-pair dinucleotides. We conclude that disparities of the mechanical response of dinucleotides are responsible for the differences observed in the mechanical properties of RNA and DNA duplexes.
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Affiliation(s)
- Alberto Marin-Gonzalez
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Cantoblanco, Madrid, Spain.
| | - J G Vilhena
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain. and Department of Physics, University of Basel, Klingelbergstrasse 82, CH 4056 Basel, Switzerland
| | - Fernando Moreno-Herrero
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Cantoblanco, Madrid, Spain.
| | - Ruben Perez
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain. and Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, E-28049 Madrid, Spain
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31
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Abstract
The biological functions of RNA range from gene regulation through catalysis and depend critically on its structure and flexibility. Conformational variations of flexible, non-base-paired components, including RNA hinges, bulges, or single-stranded tails, are well documented. Recent work has also identified variations in the structure of ubiquitous, base-paired duplexes found in almost all functional RNAs. Duplexes anchor the structures of folded RNAs, and their surface features are recognized by partner molecules. To date, no consistent picture has been obtained that describes the range of conformations assumed by RNA duplexes. Here, we apply wide angle, solution X-ray scattering (WAXS) to quantify these variations, by sampling length scales characteristic of helical geometries under different solution conditions. To identify the radius, helical rise, twist, and length of dsRNA helices, we exploit molecular dynamics generated structures, explicit solvent models, and ensemble optimization methods. Our results quantify the substantial and salt-dependent deviations of double-stranded (ds) RNA duplexes from the assumed canonical A-form conformation. Recent experiments underscore the need to properly describe the structures of RNA duplexes when interpreting the salt dependence of RNA conformations.
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Affiliation(s)
- Yen-Lin Chen
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853
| | - Lois Pollack
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853
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32
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Xu S, Ci Y, Wang L, Yang Y, Zhang L, Xu C, Qin C, Shi L. Zika virus NS3 is a canonical RNA helicase stimulated by NS5 RNA polymerase. Nucleic Acids Res 2019; 47:8693-8707. [PMID: 31361901 PMCID: PMC6895266 DOI: 10.1093/nar/gkz650] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 07/10/2019] [Accepted: 07/16/2019] [Indexed: 01/19/2023] Open
Abstract
Zika virus is a positive single-strand RNA virus whose replication involved RNA unwinding and synthesis. ZIKV NS3 contains a helicase domain, but its enzymatic activity is not fully characterized. Here, we established a dsRNA unwinding assay based on the FRET effect to study the helicase activity of ZIKV NS3, which provided kinetic information in real time. We found that ZIKV NS3 specifically unwound dsRNA/dsDNA with a 3' overhang in the 3' to 5' direction. The RNA unwinding ability of NS3 significantly decreased when the duplex was longer than 18 base pairs. The helicase activity of NS3 depends on ATP hydrolysis and binding to RNA. Mutations in the ATP binding region or the RNA binding region of NS3 impair its helicase activity, thus blocking viral replication in the cell. Furthermore, we showed that ZIKV NS5 interacted with NS3 and stimulated its helicase activity. Disrupting NS3-NS5 interaction resulted in a defect in viral replication, revealing the tight coupling of RNA unwinding and synthesis. We suggest that NS3 helicase activity is stimulated by NS5; thus, viral replication can be carried out efficiently. Our work provides a molecular mechanism of ZIKV NS3 unwinding and novel insights into ZIKV replication.
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MESH Headings
- Adenosine Triphosphate/chemistry
- Adenosine Triphosphate/metabolism
- Animals
- Binding Sites
- Chlorocebus aethiops
- Cloning, Molecular
- Cricetulus
- Epithelial Cells/virology
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Gene Expression
- Gene Expression Regulation, Viral
- Genetic Vectors/chemistry
- Genetic Vectors/metabolism
- Kinetics
- Models, Molecular
- Protein Binding
- Protein Conformation, alpha-Helical
- Protein Conformation, beta-Strand
- Protein Interaction Domains and Motifs
- Protein Structure, Tertiary
- RNA Helicases/chemistry
- RNA Helicases/genetics
- RNA Helicases/metabolism
- RNA, Double-Stranded/chemistry
- RNA, Double-Stranded/genetics
- RNA, Double-Stranded/metabolism
- RNA, Viral/chemistry
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Serine Endopeptidases/chemistry
- Serine Endopeptidases/genetics
- Serine Endopeptidases/metabolism
- Substrate Specificity
- Vero Cells
- Viral Nonstructural Proteins/chemistry
- Viral Nonstructural Proteins/genetics
- Viral Nonstructural Proteins/metabolism
- Zika Virus/genetics
- Zika Virus/metabolism
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Affiliation(s)
- Shan Xu
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
| | - Yali Ci
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
| | - Leijie Wang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
| | - Yang Yang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
| | - Leiliang Zhang
- Institute of Pathogen Biology, Chinese Academy of Medical Sciences, Beijing, China
| | - Caimin Xu
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
| | - Chengfeng Qin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Lei Shi
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
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33
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Naskar S, Joshi H, Chakraborty B, Seeman NC, Maiti PK. Atomic structures of RNA nanotubes and their comparison with DNA nanotubes. Nanoscale 2019; 11:14863-14878. [PMID: 31355845 DOI: 10.1039/c9nr00786e] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We present a computational framework to model RNA based nanostructures and study their microscopic structures. We model hexagonal nanotubes made of 6 dsRNA (RNTs) connected by double crossover (DX) at different positions. Using several hundred nano-second (ns) long all-atom molecular dynamics simulations, we study the atomic structure, conformational change and elastic properties of RNTs in the presence of explicit water and ions. Based on several structural quantities such as root mean square deviation (RMSD) and root mean square fluctuation (RMSF), we find that the RNTs are almost as stable as DNA nanotubes (DNTs). Although the central portion of the RNTs maintain its cylindrical shape, both the terminal regions open up to give rise to a gating like behavior which can play a crucial role in drug delivery. From the bending angle distribution, we observe that the RNTs are more flexible than DNTs. The calculated persistence length of the RNTs is in the micron range which is an order of magnitude higher than that of a single dsRNA. The stretch modulus of the RNTs from the contour length distribution is in the range of 4-7 nN depending on the sequence. The calculated persistence length and stretch modulus are in the same range of values as in the case of DNTs. To understand the structural properties of RNTs at the individual base-pair level we have also calculated all the helicoidal parameters and analyzed the relative flexibility and rigidity of RNTs having a different sequence. These findings emphasized the fascinating properties of RNTs which will expedite further theoretical and experimental studies in this field.
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Affiliation(s)
- Supriyo Naskar
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India.
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34
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Pajak A, Laine I, Clemente P, El-Fissi N, Schober FA, Maffezzini C, Calvo-Garrido J, Wibom R, Filograna R, Dhir A, Wedell A, Freyer C, Wredenberg A. Defects of mitochondrial RNA turnover lead to the accumulation of double-stranded RNA in vivo. PLoS Genet 2019; 15:e1008240. [PMID: 31365523 PMCID: PMC6668790 DOI: 10.1371/journal.pgen.1008240] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 06/11/2019] [Indexed: 12/02/2022] Open
Abstract
The RNA helicase SUV3 and the polynucleotide phosphorylase PNPase are involved in the degradation of mitochondrial mRNAs but their roles in vivo are not fully understood. Additionally, upstream processes, such as transcript maturation, have been linked to some of these factors, suggesting either dual roles or tightly interconnected mechanisms of mitochondrial RNA metabolism. To get a better understanding of the turn-over of mitochondrial RNAs in vivo, we manipulated the mitochondrial mRNA degrading complex in Drosophila melanogaster models and studied the molecular consequences. Additionally, we investigated if and how these factors interact with the mitochondrial poly(A) polymerase, MTPAP, as well as with the mitochondrial mRNA stabilising factor, LRPPRC. Our results demonstrate a tight interdependency of mitochondrial mRNA stability, polyadenylation and the removal of antisense RNA. Furthermore, disruption of degradation, as well as polyadenylation, leads to the accumulation of double-stranded RNAs, and their escape out into the cytoplasm is associated with an altered immune-response in flies. Together our results suggest a highly organised and inter-dependable regulation of mitochondrial RNA metabolism with far reaching consequences on cellular physiology. Although a number of factors have been implemented in the turnover of mitochondrial (mt) DNA-derived transcripts, their exact functions and interplay with one another is not entirely clear. Several of these factors have been proposed to co-ordinately regulate both transcript maturation, as well as degradation, but the order of events during mitochondrial RNA turnover is less well understood. Using a range of different genetically modified Drosophila melanogaster models, we studied the involvement of the RNA helicase SUV3, the polynucleotide phosphorylase PNPase, the leucine-rich pentatricopeptide repeat motif-containing protein LRPPRC, and the mitochondrial RNA poly(A) polymerase MTPAP, in stabilisation, polyadenylation, and degradation of mitochondrial transcripts. Our results show a tight collaborative activity of these factors in vivo and reveal a clear hierarchical order of events leading to mitochondrial mRNA maturation. Furthermore, we demonstrate that the loss of SUV3, PNPase, or MTPAP leads to the accumulation of mitochondrial-derived antisense RNA in the cytoplasm of cells, which is associated with an altered immune-response in flies.
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Affiliation(s)
- Aleksandra Pajak
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Isabelle Laine
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Paula Clemente
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Najla El-Fissi
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Florian A. Schober
- Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Camilla Maffezzini
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Javier Calvo-Garrido
- Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Rolf Wibom
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Roberta Filograna
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Ashish Dhir
- Centre for Genomic and Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Anna Wedell
- Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Christoph Freyer
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
- * E-mail: (CF); (AW)
| | - Anna Wredenberg
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
- * E-mail: (CF); (AW)
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35
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Ho V, Yong HY, Chevrier M, Narang V, Lum J, Toh YX, Lee B, Chen J, Tan EY, Luo D, Fink K. RIG-I Activation by a Designer Short RNA Ligand Protects Human Immune Cells against Dengue Virus Infection without Causing Cytotoxicity. J Virol 2019; 93:e00102-19. [PMID: 31043531 PMCID: PMC6600207 DOI: 10.1128/jvi.00102-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 04/23/2019] [Indexed: 12/25/2022] Open
Abstract
Virus-derived double-stranded RNA (dsRNA) molecules containing a triphosphate group at the 5' end are natural ligands of retinoic acid-inducible gene I (RIG-I). The cellular pathways and proteins induced by RIG-I are an essential part of the innate immune response against viral infections. Starting from a previously published RNA scaffold (3p10L), we characterized an optimized small dsRNA hairpin (called 3p10LG9, 25 nucleotides [nt] in length) as a highly efficient RIG-I activator. Dengue virus (DENV) infection in cell lines and primary human skin cells could be prevented and restricted through 3p10LG9-mediated activation of RIG-I. This antiviral effect was RIG-I and interferon signal dependent. The effect was temporary and was reversed above a saturating concentration of RIG-I ligand. This finding revealed an effective feedback loop that controls potentially damaging inflammatory effects of the RIG-I response, at least in immune cells. Our results show that the small RIG-I activator 3p10LG9 can confer short-term protection against DENV and can be further explored as an antiviral treatment in humans.IMPORTANCE Short hairpin RNA ligands that activate RIG-I induce antiviral responses in infected cells and prevent or control viral infections. Here, we characterized a new short hairpin RNA molecule with high efficacy in antiviral gene activation and showed that this molecule is able to control dengue virus infection. We demonstrate how structural modifications of minimal RNA ligands can lead to increased potency and a wider window of RIG-I-activating concentrations before regulatory mechanisms kick in at high concentrations. We also show that minimal RNA ligands induce an effective antiviral response in human skin dendritic cells and macrophages, which are the target cells of initial infection after the mosquito releases virus into the skin. Using short hairpin RNA as RIG-I ligands could therefore be explored as antiviral therapy.
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Affiliation(s)
- Victor Ho
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Hui Yee Yong
- School of Biological Sciences, Nanyang Technological University, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Marion Chevrier
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore
| | - Vipin Narang
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore
| | - Josephine Lum
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore
| | - Ying-Xiu Toh
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore
| | - Bernett Lee
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore
| | - Jinmiao Chen
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore
| | - Ern Yu Tan
- Department of General Surgery, Tan Tock Seng Hospital, Singapore
| | - Dahai Luo
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Katja Fink
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
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36
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Abstract
Adenovirus Virus-Associated (VA) RNAs are the first discovered viral noncoding RNAs. By mimicking double-stranded RNAs (dsRNAs), the exceptionally abundant, multifunctional VA RNAs sabotage host machineries that sense, transport, process, or edit dsRNAs. How VA-I suppresses PKR activation despite its strong dsRNA character, and inhibits the crucial antiviral kinase to promote viral translation, remains largely unknown. Here, we report a 2.7 Å crystal structure of VA-I RNA. The acutely bent VA-I features an unusually structured apical loop, a wobble-enriched, coaxially stacked apical and tetra-stems necessary and sufficient for PKR inhibition, and a central domain pseudoknot that resembles codon-anticodon interactions and prevents PKR activation by VA-I. These global and local structural features collectively define VA-I as an archetypal PKR inhibitor made of RNA. The study provides molecular insights into how viruses circumnavigate cellular rules of self vs non-self RNAs to not only escape, but further compromise host innate immunity.
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Affiliation(s)
- Iris V Hood
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, 50 South Drive, Room 4503, Bethesda, MD, 20892, USA
| | - Jackson M Gordon
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, 50 South Drive, Room 4503, Bethesda, MD, 20892, USA
| | - Charles Bou-Nader
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, 50 South Drive, Room 4503, Bethesda, MD, 20892, USA
| | - Frances E Henderson
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, 50 South Drive, Room 4503, Bethesda, MD, 20892, USA
| | - Soheila Bahmanjah
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, 50 South Drive, Room 4503, Bethesda, MD, 20892, USA
| | - Jinwei Zhang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, 50 South Drive, Room 4503, Bethesda, MD, 20892, USA.
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37
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Zhong C, Smith NA, Zhang D, Goodfellow S, Zhang R, Shan W, Wang MB. Full-Length Hairpin RNA Accumulates at High Levels in Yeast but Not in Bacteria and Plants. Genes (Basel) 2019; 10:E458. [PMID: 31208028 PMCID: PMC6627737 DOI: 10.3390/genes10060458] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 06/12/2019] [Accepted: 06/12/2019] [Indexed: 12/15/2022] Open
Abstract
Hairpin-structured (hp) RNA has been widely used to induce RNA interference (RNAi) in plants and animals, and an in vivo expression system for hpRNA is important for large-scale RNAi applications. Bacterial expression systems have so far been developed for in vivo expression of hpRNA or double-stranded (ds) RNA, but the structure of the resulting RNAi molecules has remained unclear. Here we report that long hpRNAs expressed in the bacteria Escherichia coli and Sinorhizobium meliloti were largely processed into shorter dsRNA fragments with no or few full-length molecules being present. A loss-of-function mutation in the dsRNA-processing enzyme RNase III, in the widely used E. coli HT115 strain, did not prevent the processing of hpRNA. Consistent with previous observations in plants, the loop sequence of long hpRNA expressed in Agrobacterium-infiltrated Nicotiana benthamiana leaves was excised, leaving no detectable levels of full-length hpRNA molecule. In contrast to bacteria and plants, long hpRNAs expressed in the budding yeast Saccharomyces cerevisiae accumulated as intact, full-length molecules. RNA extracted from hpRNA-expressing yeast cells was shown to be capable of inducing RNAi against a β-glucuronidase (GUS) reporter gene in tobacco leaves when applied topically on leaf surfaces. Our results indicate that yeast can potentially be used to express full-length hpRNA molecules for RNAi and perhaps other structured RNAs that are important in biological applications.
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Affiliation(s)
- Chengcheng Zhong
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling 712100, China.
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture and Food, Canberra, ACT 2601, Australia.
- College of Plant Protection, Northwest A&F University, Yangling 712100, China.
| | - Neil A Smith
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture and Food, Canberra, ACT 2601, Australia.
| | - Daai Zhang
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture and Food, Canberra, ACT 2601, Australia.
| | - Simon Goodfellow
- School of Chemistry and Molecular Bioscience, University of Wollongong, NSW 2522, Australia.
| | - Ren Zhang
- School of Chemistry and Molecular Bioscience, University of Wollongong, NSW 2522, Australia.
| | - Weixing Shan
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling 712100, China.
- College of Agronomy, Northwest A&F University, Yangling 712100, China.
| | - Ming-Bo Wang
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture and Food, Canberra, ACT 2601, Australia.
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Abstract
Recent investigations documented that plants can uptake and process externally applied double-stranded RNAs (dsRNAs), hairpin RNAs (hpRNAs), and small interfering RNAs (siRNAs) designed to silence important genes of plant pathogenic viruses, fungi, or insects. The exogenously applied RNAs spread locally and systemically, move into the pathogens, and induce RNA interference-mediated plant pathogen resistance. Recent findings also provided examples of plant transgene and endogene post-transcriptional down-regulation by complementary dsRNAs or siRNAs applied onto the plant surfaces. Understanding the plant perception and processing of exogenous RNAs could result in the development of novel biotechnological approaches for crop protection. This review summarizes and discusses the emerging studies reporting on exogenous RNA applications for down-regulation of essential fungal and insect genes, targeting of plant viruses, or suppression of plant transgenes and endogenes for increased resistance and changed phenotypes. We also analyze the current understanding of dsRNA uptake mechanisms and dsRNA stability in plant environments.
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Affiliation(s)
- Alexandra S Dubrovina
- Laboratory of Biotechnology, Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, 690022 Vladivostok, Russia.
| | - Konstantin V Kiselev
- Laboratory of Biotechnology, Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, 690022 Vladivostok, Russia.
- Far Eastern Federal University, The School of Natural Sciences, 690090 Vladivostok, Russia.
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39
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Bou-Nader C, Gordon JM, Henderson FE, Zhang J. The search for a PKR code-differential regulation of protein kinase R activity by diverse RNA and protein regulators. RNA 2019; 25:539-556. [PMID: 30770398 PMCID: PMC6467004 DOI: 10.1261/rna.070169.118] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The interferon-inducible protein kinase R (PKR) is a key component of host innate immunity that restricts viral replication and propagation. As one of the four eIF2α kinases that sense diverse stresses and direct the integrated stress response (ISR) crucial for cell survival and proliferation, PKR's versatile roles extend well beyond antiviral defense. Targeted by numerous host and viral regulators made of RNA and proteins, PKR is subject to multiple layers of endogenous control and external manipulation, driving its rapid evolution. These versatile regulators include not only the canonical double-stranded RNA (dsRNA) that activates the kinase activity of PKR, but also highly structured viral, host, and artificial RNAs that exert a full spectrum of effects. In this review, we discuss our deepening understanding of the allosteric mechanism that connects the regulatory and effector domains of PKR, with an emphasis on diverse structured RNA regulators in comparison to their protein counterparts. Through this analysis, we conclude that much of the mechanistic details that underlie this RNA-regulated kinase await structural and functional elucidation, upon which we can then describe a "PKR code," a set of structural and chemical features of RNA that are both descriptive and predictive for their effects on PKR.
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Affiliation(s)
- Charles Bou-Nader
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland 20892, USA
| | - Jackson M Gordon
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland 20892, USA
| | - Frances E Henderson
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland 20892, USA
| | - Jinwei Zhang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland 20892, USA
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40
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Kim SSY, Sze L, Liu C, Lam KP. The stress granule protein G3BP1 binds viral dsRNA and RIG-I to enhance interferon-β response. J Biol Chem 2019; 294:6430-6438. [PMID: 30804210 PMCID: PMC6484135 DOI: 10.1074/jbc.ra118.005868] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 02/07/2019] [Indexed: 12/24/2022] Open
Abstract
RIG-I senses viral RNA in the cytosol and initiates host innate immune response by triggering the production of type 1 interferon. A recent RNAi knockdown screen yielded close to hundred host genes whose products affected viral RNA-induced IFN-β production and highlighted the complexity of the antiviral response. The stress granule protein G3BP1, known to arrest mRNA translation, was identified as a regulator of RIG-I-induced IFN-β production. How G3BP1 functions in RIG-I signaling is not known, however. Here, we overexpress G3BP1 with RIG-I in HEK293T cells and found that G3BP1 significantly enhances RIG-I-induced ifn-b mRNA synthesis. More importantly, we demonstrate that G3BP1 binds RIG-I and that this interaction involves the C-terminal RGG domain of G3BP1. Confocal microscopy studies also show G3BP1 co-localization with RIG-I and with infecting vesicular stomatitis virus in Cos-7 cells. Interestingly, immunoprecipitation studies using biotin-labeled viral dsRNA or poly(I·C) and cell lysate-derived or in vitro translated G3BP1 indicated that G3BP1 could directly bind these substrates and again via its RGG domain. Computational modeling further revealed a juxtaposed interaction between G3BP1 RGG and RIG-I RNA-binding domains. Together, our data reveal G3BP1 as a critical component of RIG-I signaling and possibly acting as a co-sensor to promote RIG-I recognition of pathogenic RNA.
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Affiliation(s)
- Susana Soo-Yeon Kim
- From the Immunology Group, Bioprocessing Technology Institute, Agency for Science, Technology & Research (A*STAR), Singapore,
| | - Lynette Sze
- From the Immunology Group, Bioprocessing Technology Institute, Agency for Science, Technology & Research (A*STAR), Singapore
| | - ChengCheng Liu
- From the Immunology Group, Bioprocessing Technology Institute, Agency for Science, Technology & Research (A*STAR), Singapore,
| | - Kong-Peng Lam
- From the Immunology Group, Bioprocessing Technology Institute, Agency for Science, Technology & Research (A*STAR), Singapore,
- the Department of Microbiology & Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, and
- School of Biological Sciences, Nanyang Technological University, Singapore
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41
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Grabowska M, Grześkowiak BF, Szutkowski K, Wawrzyniak D, Głodowicz P, Barciszewski J, Jurga S, Rolle K, Mrówczyński R. Nano-mediated delivery of double-stranded RNA for gene therapy of glioblastoma multiforme. PLoS One 2019; 14:e0213852. [PMID: 30889203 PMCID: PMC6424419 DOI: 10.1371/journal.pone.0213852] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 03/03/2019] [Indexed: 11/18/2022] Open
Abstract
Glioblastoma multiforme (GBM) is the most common type of malignant gliomas, characterized by genetic instability, intratumoral histopathological variability and unpredictable clinical behavior. Disappointing results in the treatment of gliomas with surgery, radiation and chemotherapy have fueled a search for new therapeutic targets and treatment modalities. Here we report new approach towards RNA interference therapy of glioblastoma multiforme based on the magnetic nanoparticles delivery of the double-stranded RNA (dsRNA) with homological sequences to mRNA of tenascin-C (TN-C), named ATN-RNA. The obtained nanocomposite consisted of polyethyleneimine (PEI) coated magnetic nanoparticles conjugated to the dsRNA show high efficiency in ATN-RNA delivery, resulting not only in significant TN-C expression level suppressesion, but also impairing the tumor cells migration. Moreover, synthesized nanomaterials show high contrast properties in magnetic resonance imaging (MRI) and low cytotoxicity combining with lack of induction of interferon response. We believe that the present work is a successful combination of effective, functional, non-immunostimulatory dsRNA delivery system based on magnetic nanoparticles with high potential for further application in GBM therapy.
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Affiliation(s)
- Małgorzata Grabowska
- Department of Molecular Neurooncology, Institute of Bioorganic Chemistry Polish Academy of Science, Poznan, Poland
| | | | - Kosma Szutkowski
- NanoBioMedical Centre, Adam Mickiewicz University in Poznan, Poznan, Poland
| | - Dariusz Wawrzyniak
- Department of Molecular Neurooncology, Institute of Bioorganic Chemistry Polish Academy of Science, Poznan, Poland
| | - Paweł Głodowicz
- Department of Molecular Neurooncology, Institute of Bioorganic Chemistry Polish Academy of Science, Poznan, Poland
| | - Jan Barciszewski
- Department of Epigenetics, Institute of Bioorganic Chemistry Polish Academy of Science, Poznan, Poland
| | - Stefan Jurga
- NanoBioMedical Centre, Adam Mickiewicz University in Poznan, Poznan, Poland
| | - Katarzyna Rolle
- Department of Molecular Neurooncology, Institute of Bioorganic Chemistry Polish Academy of Science, Poznan, Poland
- Centre for Advanced Technologies, Poznan, Poland
- * E-mail: (RM); (KR)
| | - Radosław Mrówczyński
- NanoBioMedical Centre, Adam Mickiewicz University in Poznan, Poznan, Poland
- * E-mail: (RM); (KR)
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42
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Lisowiec-Wachnicka J, Znosko BM, Pasternak A. Contribution of 3'T and 3'TT overhangs to the thermodynamic stability of model siRNA duplexes. Biophys Chem 2019; 246:35-39. [PMID: 30660935 PMCID: PMC6386172 DOI: 10.1016/j.bpc.2018.12.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 12/21/2018] [Accepted: 12/30/2018] [Indexed: 12/31/2022]
Abstract
Herein, we report comprehensive thermodynamic studies on 36 RNA/DNA duplexes designed as siRNA mimics to determine the energetic contribution of 3'T and 3'TT dangling ends. The thermodynamic effect induced by the presence of 3'T overhangs on the stability of RNA duplexes ranges from -0.28 to -0.92 kcal/mol and strongly depends on the type and orientation of the adjacent base pair. Further extension of the 3'-dangling end length, by a second T residue, results in additional stabilization of 0.14 to 0.21 kcal/mol. The results revealed that the thermodynamic contribution of 3'-dangling T and TT on RNA duplexes differs from the influence of 3'-dangling U and UU on RNA duplexes and 3'-dangling T and TT on DNA duplexes. This data suggests that using the contribution of 3'-dangling T values for RNA duplexes, instead of 3'-dangling T values for DNA duplexes or 3'-dangling U values for RNA duplexes, would improve the prediction of the stability of siRNA duplexes.
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Affiliation(s)
- Jolanta Lisowiec-Wachnicka
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Brent M Znosko
- Saint Louis University, 3501 Laclede Ave., St. Louis, MO 63103-2010, United States
| | - Anna Pasternak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704 Poznań, Poland.
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43
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Abstract
PELDOR (pulsed electron-electron double resonance) is an established method to study intramolecular distances and can give evidence for conformational changes and flexibilities. However, it can also be used to study intermolecular interactions as for example oligerimization. Here, we used PELDOR to study the "end-to-end" stacking of small double-stranded (ds) RNAs. For this study, the dsRNA molecules were only singly labeled with the spin label TPA to avoid multispin effects and to measure only the intermolecular stacking interactions. It can be shown that small dsRNAs tend to assemble to rod-like structures due to π-π interactions between the base pairs at the end of the strands. On the one hand, these interactions can influence or complicate measurements aimed at the determining of the structure and dynamics of the dsRNA molecule itself. On the other hand, it can be interesting to study such intermolecular stacking interactions in more detail, as for example their dependence on ion concentration. We quantitatively determined the stacking probability as a function of the monovalent NaCl salt and the dsRNA concentration. From these data, the dissociation constant Kd was deduced and found to depend on the ratio between the NaCl salt and dsRNA concentrations. Additionally, the distances and distance distributions obtained predict a model for the stacking geometry of dsRNAs. Introducing a nucleotide overhangs at one end of the dsRNA molecule restricts the stacking to the other end, leading only to dimer formations. Introducing such an overhang at both ends of the dsRNA molecule fully suppresses stacking, as we demonstrate by PELDOR experiments quantitatively.
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Affiliation(s)
- Nicole Erlenbach
- Institute of Physical and Theoretical Chemistry, Center of Biomolecular Magnetic Resonance, Goethe University, D-60438 Frankfurt am Main, Germany
| | - Christian Grünewald
- Institute of Organic Chemistry and Chemical Biology, Goethe University, D-60438 Frankfurt am Main, Germany
| | - Bisera Krstic
- Institute of Physical and Theoretical Chemistry, Center of Biomolecular Magnetic Resonance, Goethe University, D-60438 Frankfurt am Main, Germany
| | - Alexander Heckel
- Institute of Organic Chemistry and Chemical Biology, Goethe University, D-60438 Frankfurt am Main, Germany
| | - Thomas F Prisner
- Institute of Physical and Theoretical Chemistry, Center of Biomolecular Magnetic Resonance, Goethe University, D-60438 Frankfurt am Main, Germany
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44
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Castellanos NL, Smagghe G, Sharma R, Oliveira EE, Christiaens O. Liposome encapsulation and EDTA formulation of dsRNA targeting essential genes increase oral RNAi-caused mortality in the Neotropical stink bug Euschistus heros. Pest Manag Sci 2019; 75:537-548. [PMID: 30094917 DOI: 10.1002/ps.5167] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 08/01/2018] [Accepted: 08/03/2018] [Indexed: 05/28/2023]
Abstract
BACKGROUND The Neotropical stink bug Euschistus heros is a major pest in soybean fields. Development of highly species-specific pesticides based on RNA interference (RNAi) could provide a new sustainable and environmentally friendly control strategy. RESULTS Here, the potential of RNAi as a pest control tool against E. heros was assessed. First, target gene selection using a microinjection approach was performed. Seven of the 15 candidate genes tested exhibited > 95% mortality after hemolymph injection of 27.5 ng dsRNA. Subsequently, dsRNA was administered orally using different formulations: naked dsRNA, liposome-encapsulated-dsRNA and dsRNA formulated with EDTA. Liposome-encapsulated dsRNA targeting vATPase A and muscle actin led to significant mortality after 14 days (45% and 42%, respectively), whereas EDTA-formulated dsRNA did so for only one of the target genes. Ex vivo analysis of the dsRNA stability in collected saliva indicated a strong dsRNA-degrading capacity by E. heros saliva, which could explain the need for dsRNA formulations. CONCLUSION The results demonstrate that continuous ingestion of dsRNA with EDTA or liposome-encapsulated dsRNA can prevent dsRNA from being degraded enzymatically and suggest great potential for using these formulations in dsRNA delivery to use RNAi as a functional genomics tool or for pest management of stink bugs. © 2018 Society of Chemical Industry.
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Affiliation(s)
- Nathaly L Castellanos
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
- Departamento de Entomologia, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Guy Smagghe
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Rohit Sharma
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Eugênio E Oliveira
- Departamento de Entomologia, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Olivier Christiaens
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
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45
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Okada S, Ueda H, Noda Y, Suzuki T. Transcriptome-wide identification of A-to-I RNA editing sites using ICE-seq. Methods 2018; 156:66-78. [PMID: 30578846 DOI: 10.1016/j.ymeth.2018.12.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 12/17/2018] [Accepted: 12/17/2018] [Indexed: 01/15/2023] Open
Abstract
In A-to-I RNA editing, adenosine is converted to inosine in double-stranded regions of RNAs. Inosine, an abundant epitranscriptomic mark, contributes to a wide range of biological processes by regulating gene expression post-transcriptionally. To understand the effect of A-to-I RNA editing on regulation of the epitranscriptome, accurate mapping of inosines is necessary. To this end, we established a biochemical method called inosine chemical erasing sequencing (ICE-seq) that enables unbiased and reliable identification of A-to-I RNA editing sites throughout the transcriptome. Here, we describe our updated protocol for ICE-seq in the human transcriptome.
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Affiliation(s)
- Shunpei Okada
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Hiroki Ueda
- Biological Data Science Division, Research Center for Advanced Science and Technology (RCAST), University of Tokyo, Tokyo 153-8904, Japan
| | - Yuta Noda
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.
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46
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Zheng J, Wang C, Chang MR, Devarkar SC, Schweibenz B, Crynen GC, Garcia-Ordonez RD, Pascal BD, Novick SJ, Patel SS, Marcotrigiano J, Griffin PR. HDX-MS reveals dysregulated checkpoints that compromise discrimination against self RNA during RIG-I mediated autoimmunity. Nat Commun 2018; 9:5366. [PMID: 30560918 PMCID: PMC6299088 DOI: 10.1038/s41467-018-07780-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 11/28/2018] [Indexed: 01/25/2023] Open
Abstract
Retinoic acid inducible gene-I (RIG-I) ensures immune surveillance of viral RNAs bearing a 5'-triphosphate (5'ppp) moiety. Mutations in RIG-I (C268F and E373A) lead to impaired ATPase activity, thereby driving hyperactive signaling associated with autoimmune diseases. Here we report, using hydrogen/deuterium exchange, mechanistic models for dysregulated RIG-I proofreading that ultimately result in the improper recognition of cellular RNAs bearing 7-methylguanosine and N1-2'-O-methylation (Cap1) on the 5' end. Cap1-RNA compromises its ability to stabilize RIG-I helicase and blunts caspase activation and recruitment domains (CARD) partial opening by threefold. RIG-I H830A mutation restores Cap1-helicase engagement as well as CARDs partial opening event to a level comparable to that of 5'ppp. However, E373A RIG-I locks the receptor in an ATP-bound state, resulting in enhanced Cap1-helicase engagement and a sequential CARDs stimulation. C268F mutation renders a more tethered ring architecture and results in constitutive CARDs signaling in an ATP-independent manner.
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MESH Headings
- Adenosine Triphosphatases/metabolism
- Autoimmunity/genetics
- Caspase Activation and Recruitment Domain/immunology
- DEAD Box Protein 58/chemistry
- DEAD Box Protein 58/genetics
- DEAD Box Protein 58/immunology
- DEAD Box Protein 58/metabolism
- Deuterium Exchange Measurement/methods
- Gain of Function Mutation
- Guanosine/analogs & derivatives
- Guanosine/chemistry
- Guanosine/immunology
- Guanosine/metabolism
- Immunity, Innate/genetics
- Interferon-Induced Helicase, IFIH1/immunology
- Interferon-Induced Helicase, IFIH1/metabolism
- Mass Spectrometry/methods
- Methylation
- Models, Molecular
- Mutagenesis, Site-Directed
- Protein Binding/genetics
- Protein Binding/immunology
- RNA Caps/chemistry
- RNA Caps/immunology
- RNA Caps/metabolism
- RNA, Double-Stranded/chemistry
- RNA, Double-Stranded/immunology
- RNA, Double-Stranded/metabolism
- RNA, Viral/immunology
- Receptors, Immunologic
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/immunology
- Recombinant Proteins/metabolism
- Signal Transduction/genetics
- Signal Transduction/immunology
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Affiliation(s)
- Jie Zheng
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, 33458, USA.
| | - Chen Wang
- Structural Virology Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Mi Ra Chang
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | - Swapnil C Devarkar
- Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, 08854, USA
| | - Brandon Schweibenz
- Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, 08854, USA
| | - Gogce C Crynen
- The Center for Computational Biology, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | - Ruben D Garcia-Ordonez
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | - Bruce D Pascal
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, 33458, USA
- Omics Informatics LLC, Honolulu, HI 96813, USA
| | - Scott J Novick
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | - Smita S Patel
- Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, 08854, USA
| | - Joseph Marcotrigiano
- Structural Virology Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Patrick R Griffin
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, 33458, USA.
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47
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Belashov IA, Crawford DW, Cavender CE, Dai P, Beardslee PC, Mathews DH, Pentelute BL, McNaughton BR, Wedekind JE. Structure of HIV TAR in complex with a Lab-Evolved RRM provides insight into duplex RNA recognition and synthesis of a constrained peptide that impairs transcription. Nucleic Acids Res 2018; 46:6401-6415. [PMID: 29961805 PMCID: PMC6061845 DOI: 10.1093/nar/gky529] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 05/23/2018] [Accepted: 05/25/2018] [Indexed: 12/22/2022] Open
Abstract
Natural and lab-evolved proteins often recognize their RNA partners with exquisite affinity. Structural analysis of such complexes can offer valuable insight into sequence-selective recognition that can be exploited to alter biological function. Here, we describe the structure of a lab-evolved RNA recognition motif (RRM) bound to the HIV-1 trans-activation response (TAR) RNA element at 1.80 Å-resolution. The complex reveals a trio of arginines in an evolved β2-β3 loop penetrating deeply into the major groove to read conserved guanines while simultaneously forming cation-π and salt-bridge contacts. The observation that the evolved RRM engages TAR within a double-stranded stem is atypical compared to most RRMs. Mutagenesis, thermodynamic analysis and molecular dynamics validate the atypical binding mode and quantify molecular contributions that support the exceptionally tight binding of the TAR-protein complex (KD,App of 2.5 ± 0.1 nM). These findings led to the hypothesis that the β2-β3 loop can function as a standalone TAR-recognition module. Indeed, short constrained peptides comprising the β2-β3 loop still bind TAR (KD,App of 1.8 ± 0.5 μM) and significantly weaken TAR-dependent transcription. Our results provide a detailed understanding of TAR molecular recognition and reveal that a lab-evolved protein can be reduced to a minimal RNA-binding peptide.
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Affiliation(s)
- Ivan A Belashov
- Department of Biochemistry & Biophysics, Center for RNA Biology, and Center for AIDS Research, University of Rochester School of Medicine & Dentistry, Rochester, NY 14642, USA
| | - David W Crawford
- Department of Chemistry, Colorado State University, Fort Collins, CO 80523, USA
| | - Chapin E Cavender
- Department of Biochemistry & Biophysics, Center for RNA Biology, and Center for AIDS Research, University of Rochester School of Medicine & Dentistry, Rochester, NY 14642, USA
| | - Peng Dai
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Patrick C Beardslee
- Department of Chemistry, Colorado State University, Fort Collins, CO 80523, USA
| | - David H Mathews
- Department of Biochemistry & Biophysics, Center for RNA Biology, and Center for AIDS Research, University of Rochester School of Medicine & Dentistry, Rochester, NY 14642, USA
| | - Bradley L Pentelute
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02139, USA
| | - Brian R McNaughton
- Department of Chemistry, Colorado State University, Fort Collins, CO 80523, USA
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Joseph E Wedekind
- Department of Biochemistry & Biophysics, Center for RNA Biology, and Center for AIDS Research, University of Rochester School of Medicine & Dentistry, Rochester, NY 14642, USA
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48
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Lässig C, Lammens K, Gorenflos López JL, Michalski S, Fettscher O, Hopfner KP. Unified mechanisms for self-RNA recognition by RIG-I Singleton-Merten syndrome variants. eLife 2018; 7:e38958. [PMID: 30047865 PMCID: PMC6086658 DOI: 10.7554/elife.38958] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 07/24/2018] [Indexed: 12/13/2022] Open
Abstract
The innate immune sensor retinoic acid-inducible gene I (RIG-I) detects cytosolic viral RNA and requires a conformational change caused by both ATP and RNA binding to induce an active signaling state and to trigger an immune response. Previously, we showed that ATP hydrolysis removes RIG-I from lower-affinity self-RNAs (Lässig et al., 2015), revealing how ATP turnover helps RIG-I distinguish viral from self-RNA and explaining why a mutation in a motif that slows down ATP hydrolysis causes the autoimmune disease Singleton-Merten syndrome (SMS). Here we show that a different, mechanistically unexplained SMS variant, C268F, which is localized in the ATP-binding P-loop, can signal independently of ATP but is still dependent on RNA. The structure of RIG-I C268F in complex with double-stranded RNA reveals that C268F helps induce a structural conformation in RIG-I that is similar to that induced by ATP. Our results uncover an unexpected mechanism to explain how a mutation in a P-loop ATPase can induce a gain-of-function ATP state in the absence of ATP.
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Affiliation(s)
- Charlotte Lässig
- Department of BiochemistryLudwig-Maximilians-Universität MünchenMunichGermany
- Gene Center, Ludwig-Maximilians-Universität MünchenMunichGermany
| | - Katja Lammens
- Department of BiochemistryLudwig-Maximilians-Universität MünchenMunichGermany
- Gene Center, Ludwig-Maximilians-Universität MünchenMunichGermany
| | - Jacob Lucián Gorenflos López
- Department of BiochemistryLudwig-Maximilians-Universität MünchenMunichGermany
- Gene Center, Ludwig-Maximilians-Universität MünchenMunichGermany
| | - Sebastian Michalski
- Department of BiochemistryLudwig-Maximilians-Universität MünchenMunichGermany
- Gene Center, Ludwig-Maximilians-Universität MünchenMunichGermany
| | - Olga Fettscher
- Department of BiochemistryLudwig-Maximilians-Universität MünchenMunichGermany
- Gene Center, Ludwig-Maximilians-Universität MünchenMunichGermany
| | - Karl-Peter Hopfner
- Department of BiochemistryLudwig-Maximilians-Universität MünchenMunichGermany
- Gene Center, Ludwig-Maximilians-Universität MünchenMunichGermany
- Center for Integrated Protein Science MunichMunichGermany
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49
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Sheng P, Fields C, Aadland K, Wei T, Kolaczkowski O, Gu T, Kolaczkowski B, Xie M. Dicer cleaves 5'-extended microRNA precursors originating from RNA polymerase II transcription start sites. Nucleic Acids Res 2018; 46:5737-5752. [PMID: 29746670 PMCID: PMC6009592 DOI: 10.1093/nar/gky306] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 04/01/2018] [Accepted: 04/11/2018] [Indexed: 12/15/2022] Open
Abstract
MicroRNAs (miRNAs) are approximately 22 nucleotide (nt) long and play important roles in post-transcriptional regulation in both plants and animals. In animals, precursor (pre-) miRNAs are ∼70 nt hairpins produced by Drosha cleavage of long primary (pri-) miRNAs in the nucleus. Exportin-5 (XPO5) transports pre-miRNAs into the cytoplasm for Dicer processing. Alternatively, pre-miRNAs containing a 5' 7-methylguanine (m7G-) cap can be generated independently of Drosha and XPO5. Here we identify a class of m7G-capped pre-miRNAs with 5' extensions up to 39 nt long. The 5'-extended pre-miRNAs are transported by Exportin-1 (XPO1). Unexpectedly, a long 5' extension does not block Dicer processing. Rather, Dicer directly cleaves 5'-extended pre-miRNAs by recognizing its 3' end to produce mature 3p miRNA and extended 5p miRNA both in vivo and in vitro. The recognition of 5'-extended pre-miRNAs by the Dicer Platform-PAZ-Connector (PPC) domain can be traced back to ancestral animal Dicers, suggesting that this previously unrecognized Dicer reaction mode is evolutionarily conserved. Our work reveals additional genetic sources for small regulatory RNAs and substantiates Dicer's essential role in RNAi-based gene regulation.
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Affiliation(s)
- Peike Sheng
- Department of Biochemistry and Molecular Biology
- UF Health Cancer Center
| | | | - Kelsey Aadland
- Department of Microbiology & Cell Science, Institute of Food and Agricultural Sciences
| | - Tianqi Wei
- Department of Biochemistry and Molecular Biology
| | - Oralia Kolaczkowski
- Department of Microbiology & Cell Science, Institute of Food and Agricultural Sciences
| | - Tongjun Gu
- Interdisciplinary Center for Biotechnology Research
| | - Bryan Kolaczkowski
- Department of Microbiology & Cell Science, Institute of Food and Agricultural Sciences
- UF Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Mingyi Xie
- Department of Biochemistry and Molecular Biology
- UF Health Cancer Center
- UF Genetics Institute, University of Florida, Gainesville, FL 32610, USA
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50
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Spasic A, Kennedy SD, Needham L, Manoharan M, Kierzek R, Turner DH, Mathews DH. Molecular dynamics correctly models the unusual major conformation of the GAGU RNA internal loop and with NMR reveals an unusual minor conformation. RNA 2018; 24:656-672. [PMID: 29434035 PMCID: PMC5900564 DOI: 10.1261/rna.064527.117] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 01/19/2018] [Indexed: 05/08/2023]
Abstract
The RNA "GAGU" duplex, (5'GACGAGUGUCA)2, contains the internal loop (5'-GAGU-3')2 , which has two conformations in solution as determined by NMR spectroscopy. The major conformation has a loop structure consisting of trans-Watson-Crick/Hoogsteen GG pairs, A residues stacked on each other, U residues bulged outside the helix, and all sugars with a C2'-endo conformation. This differs markedly from the internal loops, (5'-GAGC-3')2, (5'-AAGU-3')2, and (5'-UAGG-3')2, which all have cis-Watson-Crick/Watson-Crick AG "imino" pairs flanked by cis-Watson-Crick/Watson-Crick canonical pairs resulting in maximal hydrogen bonding. Here, molecular dynamics was used to test whether the Amber force field (ff99 + bsc0 + OL3) approximates molecular interactions well enough to keep stable the unexpected conformation of the GAGU major duplex structure and the NMR structures of the duplexes containing (5'-GAGC-3')2, (5'-AAGU-3')2, and (5'-UAGG-3')2 internal loops. One-microsecond simulations were repeated four times for each of the duplexes starting in their NMR conformations. With the exception of (5'-UAGG-3')2, equivalent simulations were also run starting with alternative conformations. Results indicate that the Amber force field keeps the NMR conformations of the duplexes stable for at least 1 µsec. They also demonstrate an unexpected minor conformation for the (5'-GAGU-3')2 loop that is consistent with newly measured NMR spectra of duplexes with natural and modified nucleotides. Thus, unrestrained simulations led to the determination of the previously unknown minor conformation. The stability of the native (5'-GAGU-3')2 internal loop as compared to other loops can be explained by changes in hydrogen bonding and stacking as the flanking bases are changed.
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Affiliation(s)
- Aleksandar Spasic
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York 14642, USA
- Center for RNA Biology, University of Rochester Medical Center, Rochester, New York 14642, USA
| | - Scott D Kennedy
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York 14642, USA
| | - Laura Needham
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York 14642, USA
- Center for RNA Biology, University of Rochester Medical Center, Rochester, New York 14642, USA
| | - Muthiah Manoharan
- Department of Discovery, Alnylam Pharmaceuticals, Cambridge, Massachusetts 02142, USA
| | - Ryszard Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan Noskowskiego, Poland
| | - Douglas H Turner
- Center for RNA Biology, University of Rochester Medical Center, Rochester, New York 14642, USA
- Department of Chemistry, University of Rochester, Rochester, New York 14627-0216, USA
| | - David H Mathews
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York 14642, USA
- Center for RNA Biology, University of Rochester Medical Center, Rochester, New York 14642, USA
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, New York 14642, USA
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