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Olenginski LT, Attionu SK, Henninger EN, LeBlanc RM, Longhini AP, Dayie TK. Hepatitis B Virus Epsilon (ε) RNA Element: Dynamic Regulator of Viral Replication and Attractive Therapeutic Target. Viruses 2023; 15:1913. [PMID: 37766319 PMCID: PMC10534774 DOI: 10.3390/v15091913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 09/01/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
Hepatitis B virus (HBV) chronically infects millions of people worldwide, which underscores the importance of discovering and designing novel anti-HBV therapeutics to complement current treatment strategies. An underexploited but attractive therapeutic target is ε, a cis-acting regulatory stem-loop RNA situated within the HBV pregenomic RNA (pgRNA). The binding of ε to the viral polymerase protein (P) is pivotal, as it triggers the packaging of pgRNA and P, as well as the reverse transcription of the viral genome. Consequently, small molecules capable of disrupting this interaction hold the potential to inhibit the early stages of HBV replication. The rational design of such ligands necessitates high-resolution structural information for the ε-P complex or its individual components. While these data are currently unavailable for P, our recent structural elucidation of ε through solution nuclear magnetic resonance spectroscopy marks a significant advancement in this area. In this review, we provide a brief overview of HBV replication and some of the therapeutic strategies to combat chronic HBV infection. These descriptions are intended to contextualize our recent experimental efforts to characterize ε and identify ε-targeting ligands, with the ultimate goal of developing novel anti-HBV therapeutics.
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Affiliation(s)
- Lukasz T. Olenginski
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA (R.M.L.)
- Department of Biochemistry, University of Colorado, Boulder, CO 80309, USA
| | - Solomon K. Attionu
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA (R.M.L.)
| | - Erica N. Henninger
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA (R.M.L.)
| | - Regan M. LeBlanc
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA (R.M.L.)
| | - Andrew P. Longhini
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA (R.M.L.)
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Theodore K. Dayie
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA (R.M.L.)
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Olenginski LT, Kasprzak WK, Bergonzo C, Shapiro BA, Dayie TK. Conformational Dynamics of the Hepatitis B Virus Pre-genomic RNA on Multiple Time Scales: Implications for Viral Replication. J Mol Biol 2022; 434:167633. [PMID: 35595167 DOI: 10.1016/j.jmb.2022.167633] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 04/28/2022] [Accepted: 05/07/2022] [Indexed: 12/30/2022]
Abstract
Human hepatitis B virus (HBV) replication is initiated by the binding of the viral polymerase (P) to epsilon (ε), an ≈85-nucleotide (nt) cis-acting regulatory stem-loop RNA located at the 5'-end of the pre-genomic RNA (pgRNA). This interaction triggers P and pgRNA packaging and protein-primed reverse transcription and is therefore an attractive therapeutic target. Our recent nuclear magnetic resonance (NMR) structure of ε provides a useful starting point toward a detailed understanding of HBV replication, and hints at the functional importance of ε dynamics. Here, we present a detailed description of ε motions on the ps to ns and μs to ms time scales by NMR spin relaxation and relaxation dispersion, respectively. We also carried out molecular dynamics simulations to provide additional insight into ε conformational dynamics. These data outline a series of complex motions on multiple time scales within ε. Moreover, these motions occur in mostly conserved nucleotides from structural regions (i.e., priming loop, pseudo-triloop, and U43 bulge) that biochemical and mutational studies have shown to be essential for P binding, P-pgRNA packaging, protein-priming, and DNA synthesis. Taken together, our work implicates RNA dynamics as an integral feature that governs HBV replication.
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Affiliation(s)
- Lukasz T Olenginski
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
| | - Wojciech K Kasprzak
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Christina Bergonzo
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and University of Maryland, Rockville, MD 20850, USA
| | - Bruce A Shapiro
- RNA Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Theodore K Dayie
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA.
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Dörnbrack K, Beck J, Nassal M. Relaxing the restricted structural dynamics in the human hepatitis B virus RNA encapsidation signal enables replication initiation in vitro. PLoS Pathog 2022; 18:e1010362. [PMID: 35259189 PMCID: PMC8903280 DOI: 10.1371/journal.ppat.1010362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 02/10/2022] [Indexed: 11/18/2022] Open
Abstract
Hepadnaviruses, including hepatitis B virus (HBV) as a major human pathogen, replicate their tiny 3 kb DNA genomes by capsid-internal protein-primed reverse transcription of a pregenomic (pg) RNA. Initiation requires productive binding of the viral polymerase, P protein, to a 5´ proximal bipartite stem-loop, the RNA encapsidation signal ε. Then a residue in the central ε bulge directs the covalent linkage of a complementary dNMP to a Tyr sidechain in P protein´s Terminal Protein (TP) domain. After elongation by two or three nucleotides (nt) the TP-linked DNA oligo is transferred to a 3´ proximal acceptor, enabling full-length minus-strand DNA synthesis. No direct structural data are available on hepadnaviral initiation complexes but their cell-free reconstitution with P protein and ε RNA (Dε) from duck HBV (DHBV) provided crucial mechanistic insights, including on a major conformational rearrangement in the apical Dε part. Analogous cell-free systems for human HBV led at most to P—ε binding but no detectable priming. Here we demonstrate that local relaxation of the highly basepaired ε upper stem, by mutation or via synthetic split RNAs, enables ε-dependent in vitro priming with full-length P protein from eukaryotic translation extract yet also, and without additional macromolecules, with truncated HBV miniP proteins expressed in bacteria. Using selective 2-hydroxyl acylation analyzed by primer extension (SHAPE) we confirm that upper stem destabilization correlates with in vitro priming competence and show that the supposed bulge-closing basepairs are largely unpaired even in wild-type ε. We define the two 3´ proximal nt of this extended bulge as main initiation sites and provide evidence for a Dε-like opening of the apical ε part upon P protein binding. Beyond new HBV-specific basic aspects our novel in vitro priming systems should facilitate the development of high-throughput screens for priming inhibitors targeting this highly virus-specific process. Chronic hepatitis B virus (HBV) infection puts >250 million people at an increased risk for severe liver disease. Current treatments can control but rarely cure infection. HBV features a 3,200 bp DNA genome, generated by reverse transcription of a pregenomic (pg) RNA. To initiate DNA synthesis the viral polymerase, P protein, employs a stem-loop on pgRNA, ε, to covalently link a defined first nucleotide to its Terminal Protein (TP) domain. This protein-priming is highly virus-specific yet poorly understood. More is known for duck HBV (DHBV) where, different from HBV, protein-priming was successfully reconstituted in vitro years ago. One insight was that gaining priming-competence involves opening of the apical stem in DHBV ε RNA (Dε); in HBV ε the more extensive basepairing might restrict such dynamics. Here we relaxed these constraints by identifying functional but less stably folded, including split, HBV ε variants. Several such variants supported in vitro priming, including in a simple two-component-system employing a shortened recombinant P protein. Amongst other data the new cell-free systems yielded a first view on a major conformational change in HBV ε RNA bound to P protein, highlighting the importance of RNA dynamics for the human virus. Beyond furthering basic understanding our data should facilitate screening for protein-priming inhibitors as new anti-HBV agents.
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Affiliation(s)
- Katharina Dörnbrack
- Department of Internal Medicine II/Molecular Biology, University Hospital Freiburg, Freiburg, Germany
| | - Jürgen Beck
- Department of Internal Medicine II/Molecular Biology, University Hospital Freiburg, Freiburg, Germany
- * E-mail: (JB); , (MN)
| | - Michael Nassal
- Department of Internal Medicine II/Molecular Biology, University Hospital Freiburg, Freiburg, Germany
- * E-mail: (JB); , (MN)
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Conservation in the Iron Responsive Element Family. Genes (Basel) 2021; 12:genes12091365. [PMID: 34573347 PMCID: PMC8466369 DOI: 10.3390/genes12091365] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 08/27/2021] [Accepted: 08/27/2021] [Indexed: 12/24/2022] Open
Abstract
Iron responsive elements (IREs) are mRNA stem-loop targets for translational control by the two iron regulatory proteins IRP1 and IRP2. They are found in the untranslated regions (UTRs) of genes that code for proteins involved in iron metabolism. There are ten “classic” IRE types that define the conserved secondary and tertiary structure elements necessary for proper IRP binding, and there are 83 published “IRE-like” sequences, most of which depart from the established IRE model. Here are structurally-guided discussions regarding the essential features of an IRE and what is important for IRE family membership.
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LeBlanc RM, Kasprzak WK, Longhini AP, Olenginski LT, Abulwerdi F, Ginocchio S, Shields B, Nyman J, Svirydava M, Del Vecchio C, Ivanic J, Schneekloth JS, Shapiro BA, Dayie TK, Le Grice SFJ. Structural insights of the conserved "priming loop" of hepatitis B virus pre-genomic RNA. J Biomol Struct Dyn 2021; 40:9761-9773. [PMID: 34155954 PMCID: PMC10167916 DOI: 10.1080/07391102.2021.1934544] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 05/20/2021] [Indexed: 12/16/2022]
Abstract
Initiation of protein-primed (-) strand DNA synthesis in hepatitis B virus (HBV) requires interaction of the viral polymerase with a cis-acting regulatory signal, designated epsilon (ε), located at the 5'-end of its pre-genomic RNA (pgRNA). Binding of polymerase to ε is also necessary for pgRNA encapsidation. While the mechanistic basis of this interaction remains elusive, mutagenesis studies suggest its internal 6-nt "priming loop" provides an important structural contribution. ε might therefore be considered a promising target for small molecule interventions to complement current nucleoside-analog based anti-HBV therapies. An ideal prerequisite to any RNA-directed small molecule strategy would be a detailed structural description of this important element. Herein, we present a solution NMR structure for HBV ε which, in combination with molecular dynamics and docking simulations, reports on a flexible ligand "pocket", reminiscent of those observed in proteins. We also demonstrate the binding of the selective estrogen receptor modulators (SERMs) Raloxifene, Bazedoxifene, and a de novo derivative to the priming loop.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Regan M. LeBlanc
- Basic Research Laboratory, National Cancer Institute, Frederick, MD, USA
- Vertex Pharmaceuticals, Boston, MA, USA
| | - Wojciech K. Kasprzak
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Andrew P. Longhini
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, USA
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Lukasz T. Olenginski
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, USA
| | - Fardokht Abulwerdi
- Basic Research Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Stefano Ginocchio
- Basic Research Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Brigit Shields
- RNA Biology Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Julie Nyman
- Basic Research Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Maryia Svirydava
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, USA
| | | | - Joseph Ivanic
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | | | - Bruce A. Shapiro
- RNA Biology Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Theodore Kwaku Dayie
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, USA
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Olenginski LT, Dayie TK. Quantifying the effects of long-range 13C- 13C dipolar coupling on measured relaxation rates in RNA. JOURNAL OF BIOMOLECULAR NMR 2021; 75:203-211. [PMID: 33914223 PMCID: PMC8131303 DOI: 10.1007/s10858-021-00368-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 04/05/2021] [Indexed: 06/12/2023]
Abstract
Selective stable isotope labeling has transformed structural and dynamics analysis of RNA by NMR spectroscopy. These methods can remove 13C-13C dipolar couplings that complicate 13C relaxation analyses. While these phenomena are well documented for sites with adjacent 13C nuclei (e.g. ribose C1'), less is known about so-called isolated sites (e.g. adenosine C2). To investigate and quantify the effects of long-range (> 2 Å) 13C-13C dipolar interactions on RNA dynamics, we simulated adenosine C2 relaxation rates in uniformly [U-13C/15N]-ATP or selectively [2-13C]-ATP labeled RNAs. Our simulations predict non-negligible 13C-13C dipolar contributions from adenosine C4, C5, and C6 to C2 longitudinal (R1) relaxation rates in [U-13C/15N]-ATP labeled RNAs. Moreover, these contributions increase at higher magnetic fields and molecular weights to introduce discrepancies that exceed 50%. This will become increasingly important at GHz fields. Experimental R1 measurements in the 61 nucleotide human hepatitis B virus encapsidation signal ε RNA labeled with [U-13C/15N]-ATP or [2-13C]-ATP corroborate these simulations. Thus, in the absence of selectively labeled samples, long-range 13C-13C dipolar contributions must be explicitly taken into account when interpreting adenosine C2 R1 rates in terms of motional models for large RNAs.
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Affiliation(s)
- Lukasz T Olenginski
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD, 20742, USA
| | - Theodore K Dayie
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD, 20742, USA.
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Becette OB, Zong G, Chen B, Taiwo KM, Case DA, Dayie TK. Solution NMR readily reveals distinct structural folds and interactions in doubly 13C- and 19F-labeled RNAs. SCIENCE ADVANCES 2020; 6:6/41/eabc6572. [PMID: 33028531 PMCID: PMC7541061 DOI: 10.1126/sciadv.abc6572] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 08/18/2020] [Indexed: 06/10/2023]
Abstract
RNAs form critical components of biological processes implicated in human diseases, making them attractive for small-molecule therapeutics. Expanding the sites accessible to nuclear magnetic resonance (NMR) spectroscopy will provide atomic-level insights into RNA interactions. Here, we present an efficient strategy to introduce 19F-13C spin pairs into RNA by using a 5-fluorouridine-5'-triphosphate and T7 RNA polymerase-based in vitro transcription. Incorporating the 19F-13C label in two model RNAs produces linewidths that are twice as sharp as the commonly used 1H-13C spin pair. Furthermore, the high sensitivity of the 19F nucleus allows for clear delineation of helical and nonhelical regions as well as GU wobble and Watson-Crick base pairs. Last, the 19F-13C label enables rapid identification of a small-molecule binding pocket within human hepatitis B virus encapsidation signal epsilon (hHBV ε) RNA. We anticipate that the methods described herein will expand the size limitations of RNA NMR and aid with RNA-drug discovery efforts.
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Affiliation(s)
- Owen B Becette
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20782, USA
| | - Guanghui Zong
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20782, USA
| | - Bin Chen
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20782, USA
| | - Kehinde M Taiwo
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20782, USA
| | - David A Case
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - T Kwaku Dayie
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20782, USA.
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Chemo-enzymatic synthesis of [2-13C, 7-15 N]-ATP for facile NMR analysis of RNA. MONATSHEFTE FUR CHEMIE 2020. [DOI: 10.1007/s00706-020-02667-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Ebrahimi P, Kaur S, Baronti L, Petzold K, Chen AA. A two-dimensional replica-exchange molecular dynamics method for simulating RNA folding using sparse experimental restraints. Methods 2019; 162-163:96-107. [PMID: 31059830 DOI: 10.1016/j.ymeth.2019.05.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 04/26/2019] [Accepted: 05/01/2019] [Indexed: 10/26/2022] Open
Abstract
We present a 2D replica exchange protocol incorporating secondary structure information to dramatically improve 3D RNA folding using molecular dynamics simulations. We show that incorporating base-pairing restraints into all-atom, explicit solvent simulations enables the accurate recapitulation of the global tertiary fold for 4 representative RNAs ranging in length from 24 to 68 nt. This method can potentially utilize base-pairing information from a wide variety of experimental inputs to predict complex RNA tertiary folds including pseudoknots, multi-loop junctions, and non-canonical interactions.
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Affiliation(s)
- Parisa Ebrahimi
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA
| | - Simi Kaur
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA
| | - Lorenzo Baronti
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Katja Petzold
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Alan A Chen
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA; The RNA Institute, University at Albany, State University of New York, Albany, NY, USA.
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Bergonzo C, Grishaev A. Maximizing accuracy of RNA structure in refinement against residual dipolar couplings. JOURNAL OF BIOMOLECULAR NMR 2019; 73:117-139. [PMID: 31049778 DOI: 10.1007/s10858-019-00236-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Accepted: 02/12/2019] [Indexed: 06/09/2023]
Abstract
Structural information about ribonucleic acid (RNA) is lagging behind that of proteins, in part due to its high charge and conformational variability. Molecular dynamics (MD) has played an important role in describing RNA structure, complementing information from both nuclear magnetic resonance (NMR), or X-ray crystallography. We examine the impact of the choice of the empirical force field for RNA structure refinement using cross-validation against residual dipolar couplings (RDCs) as structural accuracy reporter. Four force fields, representing both the state-of-the art in RNA simulation and the most popular selections in NMR structure determination, are compared for a prototypical A-RNA helix. RNA structural accuracy is also evaluated as a function of both density and nature of input NMR data including RDCs, anisotropic chemical shifts, and distance restraints. Our results show a complex interplay between the experimental restraints and the force fields indicating two best-performing choices: high-fidelity refinement in explicit solvent, and the conformational database-derived potentials. Accuracy of RNA models closely tracks the density of 1-bond C-H RDCs, with other data types having beneficial, but smaller effects. At lower RDC density, or when refining against NOEs only, the two selected force fields are capable of accurately describing RNA helices with little or no experimental RDC data, making them available for the higher order structure assembly or better quantification of the intramolecular dynamics. Unrestrained simulations of simple RNA motifs with state-of-the art MD force fields appear to capture the flexibility inherent in nucleic acids while also maintaining a good agreement with the experimental observables.
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Affiliation(s)
- Christina Bergonzo
- National Institute of Standards and Technology and Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD, 20850, USA
| | - Alexander Grishaev
- National Institute of Standards and Technology and Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD, 20850, USA.
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Chakraborty D, Ghosh S. The epsilon motif of hepatitis B virusRNAexhibits a potassium‐dependent ribonucleolytic activity. FEBS J 2017; 284:1184-1203. [DOI: 10.1111/febs.14050] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 01/21/2017] [Accepted: 02/22/2017] [Indexed: 12/01/2022]
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12
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Effect of mutations on internal dynamics of an RNA hairpin from hepatitis B virus. Biophys Chem 2016; 218:7-13. [DOI: 10.1016/j.bpc.2016.08.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 08/12/2016] [Accepted: 08/12/2016] [Indexed: 12/21/2022]
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13
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Nelissen FHT, Tessari M, Wijmenga SS, Heus HA. Stable isotope labeling methods for DNA. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2016; 96:89-108. [PMID: 27573183 DOI: 10.1016/j.pnmrs.2016.06.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 06/02/2016] [Accepted: 06/02/2016] [Indexed: 06/06/2023]
Abstract
NMR is a powerful method for studying proteins and nucleic acids in solution. The study of nucleic acids by NMR is far more challenging than for proteins, which is mainly due to the limited number of building blocks and unfavorable spectral properties. For NMR studies of DNA molecules, (site specific) isotope enrichment is required to facilitate specific NMR experiments and applications. Here, we provide a comprehensive review of isotope-labeling strategies for obtaining stable isotope labeled DNA as well as specifically stable isotope labeled building blocks required for enzymatic DNA synthesis.
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Affiliation(s)
- Frank H T Nelissen
- Institute for Molecules and Materials, Radboud University, 6525 AJ Nijmegen, The Netherlands.
| | - Marco Tessari
- Institute for Molecules and Materials, Radboud University, 6525 AJ Nijmegen, The Netherlands.
| | - Sybren S Wijmenga
- Institute for Molecules and Materials, Radboud University, 6525 AJ Nijmegen, The Netherlands.
| | - Hans A Heus
- Institute for Molecules and Materials, Radboud University, 6525 AJ Nijmegen, The Netherlands.
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14
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Juneja A, Villa A, Nilsson L. Elucidating the Relation between Internal Motions and Dihedral Angles in an RNA Hairpin Using Molecular Dynamics. J Chem Theory Comput 2015; 10:3532-40. [PMID: 26588317 DOI: 10.1021/ct500203m] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Molecular dynamics simulations were performed to characterize the internal motions of the ribonucleic acid apical stem loop of human hepatitis B virus. The NMR relaxation rates calculated directly from the trajectory are in good agreement with the experiment. Calculated order parameters follow the experimental pattern. Order parameters lower than 0.8 are observed for nucleotides that are weakly hydrogen bonded to their base pair partner, unpaired, or part of the loop. These residues show slow decay of the internal correlation functions of their base and sugar C-H vectors. Concerted motions around backbone dihedral angles influence the amplitude of motion of the sugar and base C-H vectors. The order parameters for base C-H vectors are also affected by the fluctuation of the glycosidic dihedral angle.
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Affiliation(s)
- Alok Juneja
- Department of Biosciences and Nutrition, Center of Biosciences, Karolinska Institutet , SE-141 83 Huddinge, Sweden
| | - Alessandra Villa
- Department of Biosciences and Nutrition, Center of Biosciences, Karolinska Institutet , SE-141 83 Huddinge, Sweden
| | - Lennart Nilsson
- Department of Biosciences and Nutrition, Center of Biosciences, Karolinska Institutet , SE-141 83 Huddinge, Sweden
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15
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Nelissen FHT, Heus HA, Wijmenga SS. Production of Homogeneous Recombinant RNA Using a tRNA Scaffold and Hammerhead Ribozymes. Methods Mol Biol 2015; 1316:33-44. [PMID: 25967051 DOI: 10.1007/978-1-4939-2730-2_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Bacterial overproduction of recombinant RNA using a tRNA scaffold yields large amounts of chimeric RNA. For structural and functional characterizations of the RNA it is often necessary to remove the scaffold. Here we describe an efficient and facile method to release the RNA of interest from the tRNA scaffold by selective cleavage using cis-acting hammerhead ribozymes. After cleavage, the RNA of interest is purified to homogeneity using standard chromatographic and electrophoretic methods. Up to 5 mg of highly pure end-product RNA can be obtained from a single liter of bacterial culture.
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Affiliation(s)
- Frank H T Nelissen
- Biophysical Chemistry, Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525AJ, Nijmegen, The Netherlands
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16
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Taxilaga-Zetina O, Pliego-Pastrana P, Carbajal-Tinoco MD. RNA pseudo-knots simulated with a one-bead coarse-grained model. J Chem Phys 2014; 140:115106. [PMID: 24655208 DOI: 10.1063/1.4868650] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
We present a revised version of a Monte Carlo simulation model for RNA molecules that was introduced in a previous communication [O. Taxilaga-Zetina, P. Pliego-Pastrana, and M. D. Carbajal-Tinoco, Phys. Rev. E 81, 041914 (2010)]. The basic model consists of a series of knowledge-based pair potentials that were obtained from the statistical analysis of large RNAs belonging to the Protein Data Bank. These effective interactions are then used to dress a polymeric chain that reproduces relatively simple secondary structures (e.g., small hairpins). In order to describe more complicated three-dimensional structures such as pseudo-knots, here we include orientational information for the interaction between nucleotides forming hydrogen bonds, as in the case of the Watson-Crick base pairs. As a result, the simulated molecules obtained through the modified model are now consistent with their corresponding experimental configurations.
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Affiliation(s)
- Oscar Taxilaga-Zetina
- Departamento de Física, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 14-740, 07000 México D.F., Mexico
| | - Patricia Pliego-Pastrana
- Área Académica de Matemáticas y Física, ICBI, Universidad Autónoma del Estado de Hidalgo, Carr. Pachuca Tulancingo Km 4.5, 42182 Pachuca Hgo., Mexico
| | - Mauricio D Carbajal-Tinoco
- Departamento de Física, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 14-740, 07000 México D.F., Mexico
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van der Werf R, Wijmenga SS, Heus HA, Olsthoorn RC. Structural and thermodynamic signatures that define pseudotriloop RNA hairpins. RNA (NEW YORK, N.Y.) 2013; 19:1833-9. [PMID: 24158793 PMCID: PMC3884659 DOI: 10.1261/rna.039636.113] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Pseudotriloop (PTL) structures in RNAs have been recognized as essential elements in RNA folding and recognition of proteins. PTL structures are derived from hexaloops by formation of a cross-loop base pair leaving a triloop and 3' bulged out residue. Despite their common presence and functional importance, insufficient structural and thermodynamic data are available that can be used to predict formation of PTLs from sequence alone. Using NMR spectroscopy and UV-melting data we established factors that contribute to the formation and stability of PTL structures derived from hepatitis B virus and human foamy virus. The NMR data show that, besides the cross-loop base pair, also a 3' pyrimidine bulge and a G-C loop-closing base pair are primary determinants of PTL formation. By changing the G-C closing base pair into C-G, the PTL switches into a hexaloop. Comparison of these rules with regular triloop hairpins and PTLs from other sources is discussed as well as the conservation of a PTL in human foamy virus and other spumaretroviruses.
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Affiliation(s)
- Ramon van der Werf
- Leiden Institute of Chemistry, University of Leiden, 2333 CC Leiden, The Netherlands
- Institute for Molecules and Materials, Radboud University Nijmegen, 6525 AJ Nijmegen, The Netherlands
- Department of Radiology, Erasmus Medical Centre, 3015 CE Rotterdam, The Netherlands
| | - Sybren S. Wijmenga
- Institute for Molecules and Materials, Radboud University Nijmegen, 6525 AJ Nijmegen, The Netherlands
| | - Hans A. Heus
- Institute for Molecules and Materials, Radboud University Nijmegen, 6525 AJ Nijmegen, The Netherlands
| | - René C.L. Olsthoorn
- Leiden Institute of Chemistry, University of Leiden, 2333 CC Leiden, The Netherlands
- Corresponding authorE-mail
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18
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Aptamer-based therapeutics: new approaches to combat human viral diseases. Pharmaceuticals (Basel) 2013; 6:1507-42. [PMID: 24287493 PMCID: PMC3873675 DOI: 10.3390/ph6121507] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Revised: 11/12/2013] [Accepted: 11/15/2013] [Indexed: 12/18/2022] Open
Abstract
Viruses replicate inside the cells of an organism and continuously evolve to contend with an ever-changing environment. Many life-threatening diseases, such as AIDS, SARS, hepatitis and some cancers, are caused by viruses. Because viruses have small genome sizes and high mutability, there is currently a lack of and an urgent need for effective treatment for many viral pathogens. One approach that has recently received much attention is aptamer-based therapeutics. Aptamer technology has high target specificity and versatility, i.e., any viral proteins could potentially be targeted. Consequently, new aptamer-based therapeutics have the potential to lead a revolution in the development of anti-infective drugs. Additionally, aptamers can potentially bind any targets and any pathogen that is theoretically amenable to rapid targeting, making aptamers invaluable tools for treating a wide range of diseases. This review will provide a broad, comprehensive overview of viral therapies that use aptamers. The aptamer selection process will be described, followed by an explanation of the potential for treating virus infection by aptamers. Recent progress and prospective use of aptamers against a large variety of human viruses, such as HIV-1, HCV, HBV, SCoV, Rabies virus, HPV, HSV and influenza virus, with particular focus on clinical development of aptamers will also be described. Finally, we will discuss the challenges of advancing antiviral aptamer therapeutics and prospects for future success.
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19
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Feng H, Chen P, Zhao F, Nassal M, Hu K. Evidence for multiple distinct interactions between hepatitis B virus P protein and its cognate RNA encapsidation signal during initiation of reverse transcription. PLoS One 2013; 8:e72798. [PMID: 23977352 PMCID: PMC3748129 DOI: 10.1371/journal.pone.0072798] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Accepted: 07/11/2013] [Indexed: 12/27/2022] Open
Abstract
Replication of hepatitis B virus (HBV) via protein-primed reverse transcription is initiated by binding of the viral P protein to the conserved ε stem-loop on the pregenomic (pg) RNA. This triggers encapsidation of the complex and the ε-templated synthesis of a short P protein-linked DNA oligonucleotide (priming) for subsequent minus-strand DNA extension. ε consists of a lower and upper stem, a bulge containing the priming template, and an apical loop. The nonhelical subelements are considered important for DNA synthesis and pgRNA packaging whereas the role of the upper stem is not well characterized. Priming itself could until recently not be addressed because in vitro generated HBV P - ε complexes showed no activity. Focussing on the four A residues at the base and tip of the upper ε stem and the two U residues in the loop we first investigated the impact of 24 mutations on viral DNA accumulation in transfected cells. While surprisingly many mutations were tolerated, further analyzing the negatively acting mutations, including in a new cell-free priming system, revealed divergent position-related impacts on pgRNA packaging, priming activity and possibly initiation site selection. This genetic separability implies that the ε RNA undergoes multiple distinct interactions with P protein as pgRNA encapsidation and replication initiation progress, and that the strict conservation of ε in nature may reflect its optimal adaptation to comply with all of them. The data further define the most attractive mutants for future studies, including as decoys for interference with HBV replication.
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Affiliation(s)
- Hui Feng
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Ping Chen
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Fei Zhao
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Michael Nassal
- University Hospital Freiburg, Department of Internal Medicine II/Molecular Biology, Freiburg, Germany
- * E-mail: (MN); (KH)
| | - Kanghong Hu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- Biomedical Center, Hubei University of Technology, Wuhan, China
- * E-mail: (MN); (KH)
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20
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van der Werf RM, Tessari M, Wijmenga SS. Nucleic acid helix structure determination from NMR proton chemical shifts. JOURNAL OF BIOMOLECULAR NMR 2013; 56:95-112. [PMID: 23564038 DOI: 10.1007/s10858-013-9725-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Accepted: 03/27/2013] [Indexed: 05/12/2023]
Abstract
We present a method for de novo derivation of the three-dimensional helix structure of nucleic acids using non-exchangeable proton chemical shifts as sole source of experimental restraints. The method is called chemical shift de novo structure derivation protocol employing singular value decomposition (CHEOPS) and uses iterative singular value decomposition to optimize the structure in helix parameter space. The correct performance of CHEOPS and its range of application are established via an extensive set of structure derivations using either simulated or experimental chemical shifts as input. The simulated input data are used to assess in a defined manner the effect of errors or limitations in the input data on the derived structures. We find that the RNA helix parameters can be determined with high accuracy. We finally demonstrate via three deposited RNA structures that experimental proton chemical shifts suffice to derive RNA helix structures with high precision and accuracy. CHEOPS provides, subject to further development, new directions for high-resolution NMR structure determination of nucleic acids.
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Affiliation(s)
- Ramon M van der Werf
- Department of Biophysical Chemistry, Institute of Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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21
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Fonville JM, Swart M, Vokáčová Z, Sychrovský V, Šponer JE, Šponer J, Hilbers CW, Bickelhaupt FM, Wijmenga SS. Chemical shifts in nucleic acids studied by density functional theory calculations and comparison with experiment. Chemistry 2012; 18:12372-87. [PMID: 22899588 DOI: 10.1002/chem.201103593] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Indexed: 11/10/2022]
Abstract
NMR chemical shifts are highly sensitive probes of local molecular conformation and environment and form an important source of structural information. In this study, the relationship between the NMR chemical shifts of nucleic acids and the glycosidic torsion angle, χ, has been investigated for the two commonly occurring sugar conformations. We have calculated by means of DFT the chemical shifts of all atoms in the eight DNA and RNA mono-nucleosides as a function of these two variables. From the DFT calculations, structures and potential energy surfaces were determined by using constrained geometry optimizations at the BP86/TZ2P level of theory. The NMR parameters were subsequently calculated by single-point calculations at the SAOP/TZ2P level of theory. Comparison of the (1)H and (13)C NMR shifts calculated for the mono-nucleosides with the shifts determined by NMR spectroscopy for nucleic acids demonstrates that the theoretical shifts are valuable for the characterization of nucleic acid conformation. For example, a clear distinction can be made between χ angles in the anti and syn domains. Furthermore, a quantitative determination of the χ angle in the syn domain is possible, in particular when (13)C and (1)H chemical shift data are combined. The approximate linear dependence of the C1' shift on the χ angle in the anti domain provides a good estimate of the angle in this region. It is also possible to derive the sugar conformation from the chemical shift information. The DFT calculations reported herein were performed on mono-nucleosides, but examples are also provided to estimate intramolecularly induced shifts as a result of hydrogen bonding, polarization effects, or ring-current effects.
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Affiliation(s)
- Judith M Fonville
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
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Skov J, Gaudin M, Podbevšek P, Olsthoorn RC, Petersen M. The subgenomic promoter of brome mosaic virus folds into a stem-loop structure capped by a pseudo-triloop that is structurally similar to the triloop of the genomic promoter. RNA (NEW YORK, N.Y.) 2012; 18:992-1000. [PMID: 22393035 PMCID: PMC3334706 DOI: 10.1261/rna.029918.111] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
In brome mosaic virus, both the replication of the genomic (+)-RNA strands and the transcription of the subgenomic RNA are carried out by the viral replicase. The production of (-)-RNA strands is dependent on the formation of an AUA triloop in the stem-loop C (SLC) hairpin in the 3'-untranslated region of the (+)-RNA strands. Two alternate hypotheses have been put forward for the mechanism of subgenomic RNA transcription. One posits that transcription commences by recognition of at least four key nucleotides in the subgenomic promoter by the replicase. The other posits that subgenomic transcription starts by binding of the replicase to a hairpin formed by the subgenomic promoter that resembles the minus strand promoter hairpin SLC. In this study, we have determined the three-dimensional structure of the subgenomic promoter hairpin using NMR spectroscopy. The data show that the hairpin is stable at 30°C and that it forms a pseudo-triloop structure with a transloop base pair and a nucleotide completely excluded from the helix. The transloop base pair is capped by an AUA triloop that possesses an extremely well packed structure very similar to that of the AUA triloop of SLC, including the formation of a so-called clamped-adenine motif. The similarities of the NMR structures of the hairpins required for genomic RNA and subgenomic RNA synthesis show that the replicase recognizes structure rather than sequence-specific motifs in both promoters.
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Affiliation(s)
- Joan Skov
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, 5230 Odense M, Denmark
| | - Mathieu Gaudin
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, 5230 Odense M, Denmark
| | - Peter Podbevšek
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, 5230 Odense M, Denmark
| | - René C.L. Olsthoorn
- Department of Molecular Genetics, Leiden Institute of Chemistry, Leiden University, 2300 RA Leiden, The Netherlands
| | - Michael Petersen
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, 5230 Odense M, Denmark
- Corresponding author.E-mail .
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Nelissen FHT, Leunissen EHP, van de Laar L, Tessari M, Heus HA, Wijmenga SS. Fast production of homogeneous recombinant RNA--towards large-scale production of RNA. Nucleic Acids Res 2012; 40:e102. [PMID: 22457065 PMCID: PMC3401473 DOI: 10.1093/nar/gks292] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
In the past decades, RNA molecules have emerged as important players in numerous cellular processes. To understand these processes at the molecular and atomic level, large amounts of homogeneous RNA are required for structural, biochemical and pharmacological investigations. Such RNAs are generally obtained from laborious and costly in vitro transcriptions or chemical synthesis. In 2007, a recombinant RNA technology has been described for the constitutive production of large amounts of recombinant RNA in Escherichia coli using a tRNA-scaffold approach. We demonstrate a general applicable extension to the described approach by introducing the following improvements: (i) enhanced transcription of large recombinant RNAs by T7 RNA polymerase (high transcription rates, versatile), (ii) efficient and facile excision of the RNA of interest from the tRNA-scaffold by dual cis-acting hammerhead ribozyme mediated cleavage and (iii) rapid purification of the RNA of interest employing anion-exchange chromatography or affinity chromatography followed by denaturing polyacrylamide gel electrophoresis. These improvements in the existing method pave the tRNA-scaffold approach further such that any (non-)structured product RNA of a defined length can cost-efficiently be obtained in (multi-)milligram quantities without in vitro enzymatic manipulations.
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Affiliation(s)
- Frank H T Nelissen
- Department of Biophysical Chemistry, Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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In vitro epsilon RNA-dependent protein priming activity of human hepatitis B virus polymerase. J Virol 2012; 86:5134-50. [PMID: 22379076 DOI: 10.1128/jvi.07137-11] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Hepatitis B virus (HBV) replicates its DNA genome through reverse transcription of a pregenomic RNA (pgRNA) by using a multifunctional polymerase (HP). A critical function of HP is its specific recognition of a viral RNA signal termed ε (Hε) located on pgRNA, which is required for specific packaging of pgRNA into viral nucleocapsids and initiation of viral reverse transcription. HP initiates reverse transcription by using itself as a protein primer (protein priming) and Hε as the obligatory template. We have purified HP from human cells that retained Hε binding activity in vitro. Furthermore, HP purified as a complex with Hε, but not HP alone, displayed in vitro protein priming activity. While the HP-Hε interaction in vitro and in vivo required the Hε internal bulge, but not its apical loop, and was not significantly affected by the cap-Hε distance, protein priming required both the Hε apical loop and internal bulge, as well as a short distance between the cap and Hε, mirroring the requirements for RNA packaging. These studies have thus established new HBV protein priming and RNA binding assays that should greatly facilitate the dissection of the requirements and molecular mechanisms of HP-Hε interactions, RNA packaging, and protein priming.
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25
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Chen A, Brown C. Distinct families of cis-acting RNA replication elements epsilon from hepatitis B viruses. RNA Biol 2012; 9:130-6. [PMID: 22418844 PMCID: PMC3346311 DOI: 10.4161/rna.18649] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The hepadnavirus encapsidation signal, epsilon (ε), is an RNA structure located at the 5′ end of the viral pregenomic RNA. It is essential for viral replication and functions in polymerase protein binding and priming. This structure could also have potential regulatory roles in controlling the expression of viral replicative proteins. In addition to its structure, the primary sequence of this RNA element has crucial functional roles in the viral lifecycle. Although the ε elements in hepadnaviruses share common critical functions, there are some significant differences in mammalian and avian hepadnaviruses, which include both sequence and structural variations.
Here we present several covariance models for ε elements from the Hepadnaviridae. The model building included experimentally determined data from previous studies using chemical probing and NMR analysis. These models have sufficient similarity to comprise a clan. The clan has in common a highly conserved overall structure consisting of a lower-stem, bulge, upper-stem and apical-loop.
The models differ in functionally critical regions—notably the two types of avian ε elements have a tetra-loop (UGUU) including a non-canonical UU base pair, while the hepatitis B virus (HBV) epsilon has a tri-loop (UGU). The avian epsilon elements have a less stable dynamic structure in the upper stem. Comparisons between these models and all other Rfam models, and searches of genomes, showed these structures are specific to the Hepadnaviridae. Two family models and the clan are available from the Rfam database.
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Affiliation(s)
- Augustine Chen
- Biochemistry and Genetics Otago; University of Otago; Dunedin, New Zealand
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26
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Feng H, Beck J, Nassal M, Hu KH. A SELEX-screened aptamer of human hepatitis B virus RNA encapsidation signal suppresses viral replication. PLoS One 2011; 6:e27862. [PMID: 22125633 PMCID: PMC3220704 DOI: 10.1371/journal.pone.0027862] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Accepted: 10/26/2011] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND The specific interaction between hepatitis B virus (HBV) polymerase (P protein) and the ε RNA stem-loop on pregenomic (pg) RNA is crucial for viral replication. It triggers both pgRNA packaging and reverse transcription and thus represents an attractive antiviral target. RNA decoys mimicking ε in P protein binding but not supporting replication might represent novel HBV inhibitors. However, because generation of recombinant enzymatically active HBV polymerase is notoriously difficult, such decoys have as yet not been identified. METHODOLOGY/PRINCIPAL FINDINGS Here we used a SELEX approach, based on a new in vitro reconstitution system exploiting a recombinant truncated HBV P protein (miniP), to identify potential ε decoys in two large ε RNA pools with randomized upper stem. Selection of strongly P protein binding RNAs correlated with an unexpected strong enrichment of A residues. Two aptamers, S6 and S9, displayed particularly high affinity and specificity for miniP in vitro, yet did not support viral replication when part of a complete HBV genome. Introducing S9 RNA into transiently HBV producing HepG2 cells strongly suppressed pgRNA packaging and DNA synthesis, indicating the S9 RNA can indeed act as an ε decoy that competitively inhibits P protein binding to the authentic ε signal on pgRNA. CONCLUSIONS/SIGNIFICANCE This study demonstrates the first successful identification of human HBV ε aptamers by an in vitro SELEX approach. Effective suppression of HBV replication by the S9 aptamer provides proof-of-principle for the ability of ε decoy RNAs to interfere with viral P-ε complex formation and suggests that S9-like RNAs may further be developed into useful therapeutics against chronic hepatitis B.
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Affiliation(s)
- Hui Feng
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Jürgen Beck
- University Hospital Freiburg, Internal Medicine II/Molecular Biology, Freiburg, Germany
| | - Michael Nassal
- University Hospital Freiburg, Internal Medicine II/Molecular Biology, Freiburg, Germany
| | - Kang-hong Hu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
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Homs M, Buti M, Quer J, Jardí R, Schaper M, Tabernero D, Ortega I, Sanchez A, Esteban R, Rodriguez-Frias F. Ultra-deep pyrosequencing analysis of the hepatitis B virus preCore region and main catalytic motif of the viral polymerase in the same viral genome. Nucleic Acids Res 2011; 39:8457-71. [PMID: 21742757 PMCID: PMC3201856 DOI: 10.1093/nar/gkr451] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Hepatitis B virus (HBV) pregenomic RNA contains a hairpin structure (ε) located in the preCore region, essential for viral replication. ε stability is enhanced by the presence of preCore variants and ε is recognized by the HBV polymerase (Pol). Mutations in the retrotranscriptase domain (YMDD) of Pol are associated with treatment resistance. The aim of this study was to analyze the preCore region and YMDD motif by ultra-deep pyrosequencing (UDPS). To evaluate the UDPS error rate, an internal control sequence was inserted in the amplicon. A newly developed technique enabled simultaneous analysis of the preCore region and Pol in the same viral genome, as well as the conserved sequence of the internal control. Nucleotide errors in HindIII yielded a UDPS error rate <0.05%. UDPS study confirmed the possibility of simultaneous detection of preCore and YMDD mutations, and demonstrated the complexity of the HBV quasispecies and cooperation between viruses. Thermodynamic stability of the ε signal was found to be the main constraint for selecting main preCore mutations. Analysis of ε-signal variability suggested the essential nature of the ε structural motif and that certain nucleotides may be involved in ε signal functions.
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Affiliation(s)
- Maria Homs
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto Carlos III Corsega 180, 08036, Barcelona, Department of Biochemistry, Department of Hepatology, Hospital Vall d’Hebron, Universitat Autònoma de Barcelona Passeig Vall d'Hebron 119–129, 08035, Barcelona and Statistics and Bioinformatics Unit, Research Institut, Hospital Vall d’Hebron Passeig Vall d'Hebron 119–129, 08035, Barcelona, Spain
| | - Maria Buti
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto Carlos III Corsega 180, 08036, Barcelona, Department of Biochemistry, Department of Hepatology, Hospital Vall d’Hebron, Universitat Autònoma de Barcelona Passeig Vall d'Hebron 119–129, 08035, Barcelona and Statistics and Bioinformatics Unit, Research Institut, Hospital Vall d’Hebron Passeig Vall d'Hebron 119–129, 08035, Barcelona, Spain
| | - Josep Quer
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto Carlos III Corsega 180, 08036, Barcelona, Department of Biochemistry, Department of Hepatology, Hospital Vall d’Hebron, Universitat Autònoma de Barcelona Passeig Vall d'Hebron 119–129, 08035, Barcelona and Statistics and Bioinformatics Unit, Research Institut, Hospital Vall d’Hebron Passeig Vall d'Hebron 119–129, 08035, Barcelona, Spain
| | - Rosendo Jardí
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto Carlos III Corsega 180, 08036, Barcelona, Department of Biochemistry, Department of Hepatology, Hospital Vall d’Hebron, Universitat Autònoma de Barcelona Passeig Vall d'Hebron 119–129, 08035, Barcelona and Statistics and Bioinformatics Unit, Research Institut, Hospital Vall d’Hebron Passeig Vall d'Hebron 119–129, 08035, Barcelona, Spain
| | - Melanie Schaper
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto Carlos III Corsega 180, 08036, Barcelona, Department of Biochemistry, Department of Hepatology, Hospital Vall d’Hebron, Universitat Autònoma de Barcelona Passeig Vall d'Hebron 119–129, 08035, Barcelona and Statistics and Bioinformatics Unit, Research Institut, Hospital Vall d’Hebron Passeig Vall d'Hebron 119–129, 08035, Barcelona, Spain
| | - David Tabernero
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto Carlos III Corsega 180, 08036, Barcelona, Department of Biochemistry, Department of Hepatology, Hospital Vall d’Hebron, Universitat Autònoma de Barcelona Passeig Vall d'Hebron 119–129, 08035, Barcelona and Statistics and Bioinformatics Unit, Research Institut, Hospital Vall d’Hebron Passeig Vall d'Hebron 119–129, 08035, Barcelona, Spain
| | - Israel Ortega
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto Carlos III Corsega 180, 08036, Barcelona, Department of Biochemistry, Department of Hepatology, Hospital Vall d’Hebron, Universitat Autònoma de Barcelona Passeig Vall d'Hebron 119–129, 08035, Barcelona and Statistics and Bioinformatics Unit, Research Institut, Hospital Vall d’Hebron Passeig Vall d'Hebron 119–129, 08035, Barcelona, Spain
| | - Alex Sanchez
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto Carlos III Corsega 180, 08036, Barcelona, Department of Biochemistry, Department of Hepatology, Hospital Vall d’Hebron, Universitat Autònoma de Barcelona Passeig Vall d'Hebron 119–129, 08035, Barcelona and Statistics and Bioinformatics Unit, Research Institut, Hospital Vall d’Hebron Passeig Vall d'Hebron 119–129, 08035, Barcelona, Spain
| | - Rafael Esteban
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto Carlos III Corsega 180, 08036, Barcelona, Department of Biochemistry, Department of Hepatology, Hospital Vall d’Hebron, Universitat Autònoma de Barcelona Passeig Vall d'Hebron 119–129, 08035, Barcelona and Statistics and Bioinformatics Unit, Research Institut, Hospital Vall d’Hebron Passeig Vall d'Hebron 119–129, 08035, Barcelona, Spain
| | - Francisco Rodriguez-Frias
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto Carlos III Corsega 180, 08036, Barcelona, Department of Biochemistry, Department of Hepatology, Hospital Vall d’Hebron, Universitat Autònoma de Barcelona Passeig Vall d'Hebron 119–129, 08035, Barcelona and Statistics and Bioinformatics Unit, Research Institut, Hospital Vall d’Hebron Passeig Vall d'Hebron 119–129, 08035, Barcelona, Spain
- *To whom correspondence should be addressed. Tel: 0034 932746991; Fax: 0034 932746831;
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A high level of mutation tolerance in the multifunctional sequence encoding the RNA encapsidation signal of an avian hepatitis B virus and slow evolution rate revealed by in vivo infection. J Virol 2011; 85:9300-13. [PMID: 21752921 DOI: 10.1128/jvi.05005-11] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
In all hepadnaviruses, protein-primed reverse transcription of the pregenomic RNA (pgRNA) is initiated by binding of the viral polymerase, P protein, to the ε RNA element. Universally, ε consists of a lower stem and an upper stem, separated by a bulge, and an apical loop. Complex formation triggers pgRNA encapsidation and the ε-templated synthesis of a DNA oligonucleotide (priming) that serves to generate minus-strand DNA. In vitro systems for duck hepatitis B virus (DHBV) yielded important insights into the priming mechanism, yet their relevance in infection is largely unexplored. Moreover, additional functions encoded in the DHBV ε (Dε) sequence could affect in vivo fitness. We therefore assessed the in vivo performances of five recombinant DHBVs bearing multiple mutations in the upper Dε stem. Three variants with only modestly reduced in vitro replication competence established chronic infection in ducks. From one variant but not another, three adapted new variants emerged upon passaging, as demonstrated by increased relative fitness in coinfections with wild-type DHBV. All three showed enhanced priming and replication competence in vitro, and in one, DHBV e antigen (DHBeAg) production was restored. Pronounced impacts on other Dε functions were not detected; however, gradual, synergistic contributions to overall performance are suggested by the fact of none of the variants reaching the in vivo fitness of wild-type virus. These data shed more light on the P-Dε interaction, define important criteria for the design of future in vivo evolution experiments, and suggest that the upper Dε stem sequences provided an evolutionary playground for DHBV to optimize in vivo fitness.
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Cevec M, Thibaudeau C, Plavec J. NMR structure of the let-7 miRNA interacting with the site LCS1 of lin-41 mRNA from Caenorhabditis elegans. Nucleic Acids Res 2010; 38:7814-21. [PMID: 20660479 PMCID: PMC2995062 DOI: 10.1093/nar/gkq640] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
We have determined the 3D structure of a 34-nt RNA construct, herein named LCS1co, which mimics the interaction of let-7 microRNA (miRNA) to one of its complementary binding sites, LCS1, in the 3′-untranslated region of lin-41 mRNA by solution-state NMR spectroscopy. let-7 miRNAs control the timing of development of the nematode Caenorhabditis elegans and are highly conserved in mammals. The sequence and structure of the two conserved let-7 complementary sites, LCS1 and LCS2, in the 3′-untranslated region of lin-41 mRNA are important for a proper downregulation of lin-41. The high-resolution NMR structure reveals details of the binding of let-7 miRNA to lin-41 mRNA which involves formation of a complex with non-canonical structural elements within the seed region. LCS1co exhibits a stem-loop structure with two stems, an asymmetric internal loop and an adenine bulge. Comparison with the NMR solution-state structure of the let-7:lin-41 complex involving the LCS2-binding site shows that conformational freedom of the asymmetric internal loop of LCS1co correlates with a smaller bend between the upper and lower stems in comparison to the well-defined asymmetric loop of LCS2co.
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Affiliation(s)
- Mirko Cevec
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, Slovenia
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30
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Ampt KAM, van der Werf RM, Nelissen FHT, Tessari M, Wijmenga SS. The unstable part of the apical stem of duck hepatitis B virus epsilon shows enhanced base pair opening but not pico- to nanosecond dynamics and is essential for reverse transcriptase binding. Biochemistry 2009; 48:10499-508. [PMID: 19817488 DOI: 10.1021/bi9011385] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Hepatitis B virus (HBV) replication starts with binding of reverse transcriptase (RT) to the apical stem-loop region of epsilon, a conserved element of the RNA pregenome. For duck HBV, an in vitro replication system has provided molecular details of this interaction. Further insights can be obtained from the structure and dynamics of the duck and human apical stem-loops. Previously, we reported these for the human apical stem-loop. Here, we present the same for the duck counterpart. Unlike its human counterpart, the duck apical stem is unstable in its middle/upper part and contains noncanonical base pairs. This dynamics study is the first of an unstable RNA-DNA stem. Similar to the human stem, the duck apical stem comprises two helical segments with a bend angle of ca. 10 degrees , separated by a nonpaired mobile U residue. It is capped by a well-structured conserved UGUU loop with two residues mobile on the pico- to nanosecond time scale, one of which is involved in RT binding. Remarkably, the unstable middle/upper part of the stem does not show enhanced pico- to nanosecond time scale dynamics. Instead, adenine dispersion relaxation studies indicate enhanced millisecond time scale dynamics involving base pair opening. It can then be concluded that base pair opening is essential for epsilon-RT binding, because stabilization of the stem abolishes binding. We hypothesize that binding occurs by conformational capture of bases in the base pair open state. The unstable secondary structure of the apical stem-loop makes duck epsilon-RT binding unusual in light of recent classifications of RNA target interactions that assume stable secondary structures.
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Affiliation(s)
- Kirsten A M Ampt
- Biophysical Chemistry, Institute of Molecules and Materials, Radboud University of Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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31
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32
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Hu J, Lin L. RNA-protein interactions in hepadnavirus reverse transcription. Front Biosci (Landmark Ed) 2009; 14:1606-18. [PMID: 19273150 DOI: 10.2741/3328] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The small DNA genome of hepadnaviruses is replicated by reverse transcription via an RNA intermediate. This RNA "pregenome" contains important signals that control critical steps of viral replication, including RNA packaging, initiation of reverse transcription, and elongation of minus strand DNA, through specific interactions with the viral reverse transcriptase, the capsid protein, and host factors. In particular, the interaction between the viral reverse transcriptase and RNA pregenome requires a host chaperone complex composed of the heat shock protein 90 and its cochaperones.
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Affiliation(s)
- Jianming Hu
- Department of Microbiology and Immunology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA.
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33
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Ampt KAM, Ottink OM, Girard FC, Nelissen F, Tessari M, Wijmenga SS. 1H, 13C and 15N NMR assignments of Duck HBV apical stem loop of the epsilon encapsidation signal. BIOMOLECULAR NMR ASSIGNMENTS 2008; 2:159-162. [PMID: 19636894 DOI: 10.1007/s12104-008-9110-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2008] [Accepted: 07/28/2008] [Indexed: 05/28/2023]
Abstract
The replication of Hepatitis B virus is initiated by binding of its reverse transcriptase to the apical stem loop and primer loop of epsilon. Here, we present the (1)H/(13)C/(15)N NMR assignments of the bases and sugars of the 29 residues apical stem loop of Duck HBV epsilon.
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Affiliation(s)
- K A M Ampt
- Department of Biophysical Chemistry, Radboud University Nijmegen, Toernooiveld 1, 6525 ED, Nijmegen, The Netherlands
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34
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van der Werf RM, Girard FC, Nelissen F, Tessari M, Wijmenga SS. 1H, 13C and 15N NMR assignments of Duck HBV primer loop of the encapsidation signal epsilon. BIOMOLECULAR NMR ASSIGNMENTS 2008; 2:143-145. [PMID: 19636890 DOI: 10.1007/s12104-008-9106-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2008] [Accepted: 07/28/2008] [Indexed: 05/28/2023]
Abstract
The replication of the hepatitis B virus is initiated by binding of the viral reverse transcriptase protein complex to the apical stem loop of the epsilon element to place it next to the primer loop, from which a four nucleotide DNA primer is subsequently synthesized. Here, we present the (1)H/(13)C/(15)N NMR assignments of the bases and sugars of the 37 residues primer loop of Duck HBV epsilon (BMRB-entry 15786).
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Affiliation(s)
- R M van der Werf
- Department of Biophysical Chemistry, Radboud University Nijmegen, Toernooiveld 1, 6525 ED, Nijmegen, The Netherlands
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35
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Functional and structural dynamics of hepadnavirus reverse transcriptase during protein-primed initiation of reverse transcription: effects of metal ions. J Virol 2008; 82:5703-14. [PMID: 18400846 DOI: 10.1128/jvi.02760-07] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Reverse transcription in hepadnaviruses is primed by the viral reverse transcriptase (RT) (protein priming) and requires the interaction between the RT and a specific viral RNA template termed epsilon. Protein priming is resistant to a number of RT inhibitors that can block subsequent viral DNA elongation and likely requires a distinct "priming" conformation. Furthermore, protein priming may consist of two distinct stages, i.e., the attachment of the first deoxynucleotide to RT (initiation) and the subsequent addition of 2 or 3 deoxynucleotides (polymerization). In particular, a truncated duck hepatitis B virus RT (MiniRT2) is competent in initiation but defective in polymerization when tested in the presence of Mg(2+). Given the known effects of metal ions on the activities of various DNA and RNA polymerases, we tested if metal ions could affect hepadnavirus RT priming. We report here that Mn(2+), in comparison with Mg(2+), showed dramatic effects on the priming activity of MiniRT2 as well as the full-length RT. First and foremost, MiniRT2 exhibited full polymerization activity in the presence of Mn(2+), indicating that MiniRT2 contains all sequences essential for polymerization but is unable to transition from initiation to polymerization with Mg(2+). Second, the initiation activities of MiniRT2 and the full-length RT were much stronger with Mn(2+). Third, the nucleotide and template specificities during protein priming were decreased in the presence of Mn(2+). Fourth, polymerization was sensitive to inhibition by a pyrophosphate analog in the presence of Mn(2+) but not in the presence of Mg(2+). Finally, limited proteolysis provided direct evidence that the priming active MiniRT2 adopted distinct conformations depending on the presence of Mn(2+) versus that of Mg(2+) and that the transition from initiation to polymerization was accompanied by RT conformational change.
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36
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Nassal M. Hepatitis B viruses: reverse transcription a different way. Virus Res 2008; 134:235-49. [PMID: 18339439 DOI: 10.1016/j.virusres.2007.12.024] [Citation(s) in RCA: 282] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2007] [Revised: 11/28/2007] [Accepted: 12/05/2007] [Indexed: 02/07/2023]
Abstract
Hepatitis B virus (HBV), the causative agent of B-type hepatitis in humans, is the type member of the Hepadnaviridae, hepatotropic DNA viruses that replicate via reverse transcription. Beyond long-established differences to retroviruses in gene expression and overall replication strategy newer work has uncovered additional distinctions in the mechanism of reverse transcription per se. These include protein-priming by the unique extra terminal protein domain of the reverse transcriptase (RT) utilizing an RNA hairpin for de novo initiation of first strand DNA synthesis, and the strict dependence of this process on cellular chaperones. Recent in vitro reconstitution systems enabled first biochemical insights into this multifactorial reaction, complemented by high resolution structural information on the RNA, though not yet the protein, level. Genetic approaches have revealed long-distance interactions in the nucleic acid templates as an important factor enabling the puzzling template switches required to produce the relaxed circular (RC) DNA found in infectious virions. Finally, the failure of even potent HBV RT inhibitors to eliminate nuclear covalently closed circular (ccc) DNA, the functional equivalent of integrated proviral DNA, has spurred a renewed interest in the mechanism of cccDNA generation. These new developments are in the focus of this review.
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Affiliation(s)
- Michael Nassal
- University Hospital Freiburg, Internal Medicine 2/Molecular Biology, Hugstetter Str. 55, D-79106 Freiburg, Germany.
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37
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Cevec M, Thibaudeau C, Plavec J. Solution structure of a let-7 miRNA:lin-41 mRNA complex from C. elegans. Nucleic Acids Res 2008; 36:2330-7. [PMID: 18296482 PMCID: PMC2367737 DOI: 10.1093/nar/gkn088] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Let-7 microRNA (miRNA) regulates heterochronic genes in developmental timing of the nematode Caenorhabditis elegans. Binding of miRNA to messenger RNA (mRNA) and structural features of the complex are crucial for gene silencing. We herein present the NMR solution structure of a model mimicking the interaction of let-7 miRNA with its complementary site (LCS 2) in the 3' untranslated region (3'-UTR) of the lin-41 mRNA. A structural study was performed by NMR spectroscopy using NOE restraints, torsion angle restraints and residual dipolar couplings. The 33-nt RNA construct folds into a stem-loop structure that features two stem regions which are separated by an asymmetric internal loop. One of the stems comprises a GU wobble base pair, which does not alter its overall A-form RNA conformation. The asymmetric internal loop adopts a single, well-defined structure in which three uracils form a base triple, while two adenines form a base pair. The 3D structure of the construct gives insight into the structural aspects of interactions between let-7 miRNA and lin-41 mRNA.
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Affiliation(s)
- Mirko Cevec
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
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38
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Petzold K, Duchardt E, Flodell S, Larsson G, Kidd-Ljunggren K, Wijmenga S, Schleucher J. Conserved nucleotides in an RNA essential for hepatitis B virus replication show distinct mobility patterns. Nucleic Acids Res 2007; 35:6854-61. [PMID: 17933777 PMCID: PMC2175316 DOI: 10.1093/nar/gkm774] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The number of regulatory RNAs with identified non-canonical structures is increasing, and structural transitions often play a role in their biological function. This stimulates interest in internal motions of RNA, which can underlie structural transitions. Heteronuclear NMR relaxation measurements, which are commonly used to study internal motion, only report on local motions of few sites within the molecule. Here we have studied a 27-nt segment of the human hepatitis B virus (HBV) pregenomic RNA, which is essential for viral replication. We combined heteronuclear relaxation with the new off-resonance ROESY technique, which reports on internal motions of H,H contacts. Using off-resonance ROESY, we could for the first time detect motion of through-space H,H contacts, such as in intra-residue base-ribose contacts or inter-nucleotide contacts, both essential for NMR structure determination. Motions in non-canonical structure elements were found primarily on the sub-nanosecond timescale. Different patterns of mobility were observed among several mobile nucleotides. The most mobile nucleotides are highly conserved among different HBV strains, suggesting that their mobility patterns may be necessary for the RNA’s biological function.
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Affiliation(s)
- Katja Petzold
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-901 87 Umeå, Sweden
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39
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Stahl M, Beck J, Nassal M. Chaperones activate hepadnavirus reverse transcriptase by transiently exposing a C-proximal region in the terminal protein domain that contributes to epsilon RNA binding. J Virol 2007; 81:13354-64. [PMID: 17913810 PMCID: PMC2168843 DOI: 10.1128/jvi.01196-07] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
All hepatitis B viruses replicate by protein-primed reverse transcription, employing a specialized reverse transcriptase, P protein, that carries a unique terminal protein (TP) domain. To initiate reverse transcription, P protein must bind to a stem-loop, epsilon, on the pregenomic RNA template. TP then provides a Y residue for covalent attachment of the first nucleotide of an epsilon-templated DNA oligonucleotide (priming reaction) that serves to initiate full-length minus-strand DNA synthesis. epsilon binding requires the chaperone-dependent conversion of inactive P protein into an activated, metastable form designated P*. However, how P* differs structurally from P protein is not known. Here we used an in vitro reconstitution system for active duck hepatitis B virus P combined with limited proteolysis, site-specific antibodies, and defined P mutants to structurally compare nonactivated versus chaperone-activated versus primed P protein. The data show that Hsp70 action, under conditions identical to those required for functional activation, transiently exposes the C proximal TP region which is, probably directly, involved in epsilon RNA binding. Notably, after priming and epsilon RNA removal, a very similar new conformation appears stable without further chaperone activity; hence, the activation of P protein is triggered by energy-consuming chaperone action but may be completed by template RNA binding.
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Affiliation(s)
- Michael Stahl
- University Hospital Freiburg, Internal Med. II/Molecular Biology, Hugstetter Str. 55, D-79106 Freiburg, Germany
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40
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Getz M, Sun X, Casiano-Negroni A, Zhang Q, Al-Hashimi HM. NMR studies of RNA dynamics and structural plasticity using NMR residual dipolar couplings. Biopolymers 2007; 86:384-402. [PMID: 17594140 DOI: 10.1002/bip.20765] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
An increasing number of RNAs are being discovered that perform their functions by undergoing large changes in conformation in response to a variety of cellular signals, including recognition of proteins and small molecular targets, changes in temperature, and RNA synthesis itself. The measurement of NMR residual dipolar couplings (RDCs) in partially aligned systems is providing new insights into the structural plasticity of RNA through combined characterization of large-amplitude collective helix motions and local flexibility in noncanonical regions over a wide window of biologically relevant timescales (<milliseconds). Here, we review RDC methodology for studying RNA structural dynamics and survey what has been learnt thus far from application of these methods. Future methodological challenges are also identified.
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Affiliation(s)
- Melissa Getz
- Department of Chemistry, The University of Michigan, Ann Arbor, MI 48109, USA
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41
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Girard FC, Ottink OM, Ampt KA, Tessari M, Wijmenga SS. Thermodynamics and NMR studies on Duck, Heron and Human HBV encapsidation signals. Nucleic Acids Res 2007; 35:2800-11. [PMID: 17430968 PMCID: PMC1885660 DOI: 10.1093/nar/gkm131] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Hepatitis B virus (HBV) replication is initiated by binding of its reverse transcriptase (P) to the apical stem-loop (AL) and primer loop (PL) of epsilon, a highly conserved RNA element at the 5'-end of the RNA pregenome. Mutation studies on duck/heron and human in vitro systems have shown similarities but also differences between their P-epsilon interaction. Here, NMR and UV thermodynamic data on AL (and PL) from these three species are presented. The stabilities of the duck and heron ALs were found to be similar, and much lower than that of human. NMR data show that this low stability stems from an 11-nt internal bulge destabilizing the stem of heron AL. In duck, although structured at low temperature, this region also forms a weak point as its imino resonances broaden to disappearance between 30 and 35 degrees C well below the overall AL melting temperature. Surprisingly, the duck- and heron ALs were both found to be capped by a stable well-structured UGUU tetraloop. All avian ALs are expected to adhere to this because of their conserved sequence. Duck PL is stable and structured and, in view of sequence similarities, the same is expected for heron - and human PL.
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Affiliation(s)
| | | | | | | | - Sybren S. Wijmenga
- *To whom correspondence should be addressed +31 24 3653384/2678+31 24 3652112
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