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Kersten C, Archambault P, Köhler LP. Assessment of Nucleobase Protomeric and Tautomeric States in Nucleic Acid Structures for Interaction Analysis and Structure-Based Ligand Design. J Chem Inf Model 2024. [PMID: 38766733 DOI: 10.1021/acs.jcim.4c00520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
With increasing interest in RNA as a therapeutic and a potential target, the role of RNA structures has become more important. Even slight changes in nucleobases, such as modifications or protomeric and tautomeric states, can have a large impact on RNA structure and function, while local environments in turn affect protonation and tautomerization. In this work, the application of empirical tools for pKa and tautomer prediction for RNA modifications was elucidated and compared with ab initio quantum mechanics (QM) methods and expanded toward macromolecular RNA structures, where QM is no longer feasible. In this regard, the Protonate3D functionality within the molecular operating environment (MOE) was expanded for nucleobase protomer and tautomer predictions and applied to reported examples of altered protonation states depending on the local environment. Overall, observations of nonstandard protomers and tautomers were well reproduced, including structural C+G:C(A) and A+GG motifs, several mismatches, and protonation of adenosine or cytidine as the general acid in nucleolytic ribozymes. Special cases, such as cobalt hexamine-soaked complexes or the deprotonation of guanosine as the general base in nucleolytic ribozymes, proved to be challenging. The collected set of examples shall serve as a starting point for the development of further RNA protonation prediction tools, while the presented Protonate3D implementation already delivers reasonable protonation predictions for RNA and DNA macromolecules. For cases where higher accuracy is needed, like following catalytic pathways of ribozymes, incorporation of QM-based methods can build upon the Protonate3D-generated starting structures. Likewise, this protonation prediction can be used for structure-based RNA-ligand design approaches.
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Affiliation(s)
- Christian Kersten
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128 Mainz, Germany
- Institute for Quantitative and Computational Biosciences, Johannes Gutenberg-University, BioZentrum I, Hanns-Dieter-Hüsch.Weg 15, 55128 Mainz, Germany
| | - Philippe Archambault
- Chemical Computing Group, 910-1010 Sherbrooke W., Montreal, Quebec, Canada H3A 2R7
| | - Luca P Köhler
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128 Mainz, Germany
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2
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Błaszczyk L, Ryczek M, Das B, Mateja-Pluta M, Bejger M, Śliwiak J, Nakatani K, Kiliszek A. Antisense RNA C9orf72 hexanucleotide repeat associated with amyotrophic lateral sclerosis and frontotemporal dementia forms a triplex-like structure and binds small synthetic ligand. Nucleic Acids Res 2024:gkae376. [PMID: 38738637 DOI: 10.1093/nar/gkae376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 04/05/2024] [Accepted: 04/26/2024] [Indexed: 05/14/2024] Open
Abstract
The abnormal expansion of GGGGCC/GGCCCC hexanucleotide repeats (HR) in C9orf72 is associated with amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Structural polymorphisms of HR result in the multifactorial pathomechanism of ALS/FTD. Consequently, many ongoing studies are focused at developing therapies targeting pathogenic HR RNA. One of them involves small molecules blocking sequestration of important proteins, preventing formation of toxic nuclear foci. However, rational design of potential therapeutics is hindered by limited number of structural studies of RNA-ligand complexes. We determined the crystal structure of antisense HR RNA in complex with ANP77 ligand (1.1 Å resolution) and in the free form (0.92 and 1.5 Å resolution). HR RNA folds into a triplex structure composed of four RNA chains. ANP77 interacted with two neighboring single-stranded cytosines to form pseudo-canonical base pairs by adopting sandwich-like conformation and adjusting the position of its naphthyridine units to the helical twist of the RNA. In the unliganded structure, the cytosines formed a peculiar triplex i-motif, assembled by trans C•C+ pair and a third cytosine located at the Hoogsteen edge of the C•C+ pair. These results extend our knowledge of the structural polymorphisms of HR and can be used for rational design of small molecules targeting disease-related RNAs.
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Affiliation(s)
- Leszek Błaszczyk
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704, Poland
| | - Marcin Ryczek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704, Poland
| | - Bimolendu Das
- Department of Regulatory Bioorganic Chemistry, SANKEN (The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan
| | - Martyna Mateja-Pluta
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704, Poland
| | - Magdalena Bejger
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704, Poland
| | - Joanna Śliwiak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704, Poland
| | - Kazuhiko Nakatani
- Department of Regulatory Bioorganic Chemistry, SANKEN (The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan
| | - Agnieszka Kiliszek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704, Poland
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3
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Fedotova MV, Chuev GN. The Three-Dimensional Reference Interaction Site Model Approach as a Promising Tool for Studying Hydrated Viruses and Their Complexes with Ligands. Int J Mol Sci 2024; 25:3697. [PMID: 38612508 PMCID: PMC11011341 DOI: 10.3390/ijms25073697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/14/2024] Open
Abstract
Viruses are the most numerous biological form living in any ecosystem. Viral diseases affect not only people but also representatives of fauna and flora. The latest pandemic has shown how important it is for the scientific community to respond quickly to the challenge, including critically assessing the viral threat and developing appropriate measures to counter this threat. Scientists around the world are making enormous efforts to solve these problems. In silico methods, which allow quite rapid obtention of, in many cases, accurate information in this field, are effective tools for the description of various aspects of virus activity, including virus-host cell interactions, and, thus, can provide a molecular insight into the mechanism of virus functioning. The three-dimensional reference interaction site model (3D-RISM) seems to be one of the most effective and inexpensive methods to compute hydrated viruses, since the method allows us to provide efficient calculations of hydrated viruses, remaining all molecular details of the liquid environment and virus structure. The pandemic challenge has resulted in a fast increase in the number of 3D-RISM calculations devoted to hydrated viruses. To provide readers with a summary of this literature, we present a systematic overview of the 3D-RISM calculations, covering the period since 2010. We discuss various biophysical aspects of the 3D-RISM results and demonstrate capabilities, limitations, achievements, and prospects of the method using examples of viruses such as influenza, hepatitis, and SARS-CoV-2 viruses.
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Affiliation(s)
- Marina V. Fedotova
- G.A. Krestov Institute of Solution Chemistry, The Russian Academy of Sciences, Akademicheskaya St., 1, 153045 Ivanovo, Russia
| | - Gennady N. Chuev
- Institute of Theoretical and Experimental Biophysics, The Russian Academy of Sciences, Institutskaya St., 142290 Pushchino, Russia
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4
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Wang K, Yin Z, Sang C, Xia W, Wang Y, Sun T, Xu X. Geometric deep learning for the prediction of magnesium-binding sites in RNA structures. Int J Biol Macromol 2024; 262:130150. [PMID: 38365157 DOI: 10.1016/j.ijbiomac.2024.130150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/24/2024] [Accepted: 02/11/2024] [Indexed: 02/18/2024]
Abstract
Magnesium ions (Mg2+) are essential for the folding, functional expression, and structural stability of RNA molecules. However, predicting Mg2+-binding sites in RNA molecules based solely on RNA structures is still challenging. The molecular surface, characterized by a continuous shape with geometric and chemical properties, is important for RNA modelling and carries essential information for understanding the interactions between RNAs and Mg2+ ions. Here, we propose an approach named RNA-magnesium ion surface interaction fingerprinting (RMSIF), a geometric deep learning-based conceptual framework to predict magnesium ion binding sites in RNA structures. To evaluate the performance of RMSIF, we systematically enumerated decoy Mg2+ ions across a full-space grid within the range of 2 to 10 Å from the RNA molecule and made predictions accordingly. Visualization techniques were used to validate the prediction results and calculate success rates. Comparative assessments against state-of-the-art methods like MetalionRNA, MgNet, and Metal3DRNA revealed that RMSIF achieved superior success rates and accuracy in predicting Mg2+-binding sites. Additionally, in terms of the spatial distribution of Mg2+ ions within the RNA structures, a majority were situated in the deep grooves, while a minority occupied the shallow grooves. Collectively, the conceptual framework developed in this study holds promise for advancing insights into drug design, RNA co-transcriptional folding, and structure prediction.
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Affiliation(s)
- Kang Wang
- Department of Physics, Zhejiang University of Science and Technology, Hangzhou 310008, China
| | - Zuode Yin
- Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology, Changzhou 213001, China
| | - Chunjiang Sang
- Department of Physics, Zhejiang University of Science and Technology, Hangzhou 310008, China
| | - Wentao Xia
- Department of Physics, Zhejiang University of Science and Technology, Hangzhou 310008, China
| | - Yan Wang
- Department of Physics, Zhejiang University of Science and Technology, Hangzhou 310008, China
| | - Tingting Sun
- Department of Physics, Zhejiang University of Science and Technology, Hangzhou 310008, China.
| | - Xiaojun Xu
- Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology, Changzhou 213001, China.
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5
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Chen CC, Han J, Chinn CA, Rounds JS, Li X, Nikan M, Myszka M, Tong L, Passalacqua LFM, Bredy T, Wood MA, Luptak A. Inhibition of Cpeb3 ribozyme elevates CPEB3 protein expression and polyadenylation of its target mRNAs and enhances object location memory. eLife 2024; 13:e90116. [PMID: 38319152 PMCID: PMC10919898 DOI: 10.7554/elife.90116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 02/05/2024] [Indexed: 02/07/2024] Open
Abstract
A self-cleaving ribozyme that maps to an intron of the cytoplasmic polyadenylation element-binding protein 3 (Cpeb3) gene is thought to play a role in human episodic memory, but the underlying mechanisms mediating this effect are not known. We tested the activity of the murine sequence and found that the ribozyme's self-scission half-life matches the time it takes an RNA polymerase to reach the immediate downstream exon, suggesting that the ribozyme-dependent intron cleavage is tuned to co-transcriptional splicing of the Cpeb3 mRNA. Our studies also reveal that the murine ribozyme modulates maturation of its harboring mRNA in both cultured cortical neurons and the hippocampus: inhibition of the ribozyme using an antisense oligonucleotide leads to increased CPEB3 protein expression, which enhances polyadenylation and translation of localized plasticity-related target mRNAs, and subsequently strengthens hippocampal-dependent long-term memory. These findings reveal a previously unknown role for self-cleaving ribozyme activity in regulating experience-induced co-transcriptional and local translational processes required for learning and memory.
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Affiliation(s)
- Claire C Chen
- Department of Pharmaceutical Sciences, University of California, IrvineIrvineUnited States
| | - Joseph Han
- Department of Neurobiology and Behavior, Center for the Neurobiology of Learning and Memory, University of California, IrvineIrvineUnited States
| | - Carlene A Chinn
- Department of Neurobiology and Behavior, Center for the Neurobiology of Learning and Memory, University of California, IrvineIrvineUnited States
| | - Jacob S Rounds
- Department of Neurobiology and Behavior, Center for the Neurobiology of Learning and Memory, University of California, IrvineIrvineUnited States
| | - Xiang Li
- Department of Neurobiology and Behavior, Center for the Neurobiology of Learning and Memory, University of California, IrvineIrvineUnited States
| | | | - Marie Myszka
- Department of Chemistry, University of California, IrvineIrvineUnited States
| | - Liqi Tong
- Institute for Memory Impairments and Neurological Disorders, University of California, IrvineIrvineUnited States
| | - Luiz FM Passalacqua
- Department of Pharmaceutical Sciences, University of California, IrvineIrvineUnited States
| | - Timothy Bredy
- Department of Neurobiology and Behavior, Center for the Neurobiology of Learning and Memory, University of California, IrvineIrvineUnited States
| | - Marcelo A Wood
- Department of Neurobiology and Behavior, Center for the Neurobiology of Learning and Memory, University of California, IrvineIrvineUnited States
| | - Andrej Luptak
- Department of Pharmaceutical Sciences, University of California, IrvineIrvineUnited States
- Department of Chemistry, University of California, IrvineIrvineUnited States
- Department of Molecular Biology and Biochemistry, University of California, IrvineIrvineUnited States
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6
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Kläge D, Müller E, Hartig JS. A comparative survey of the influence of small self-cleaving ribozymes on gene expression in human cell culture. RNA Biol 2024; 21:1-11. [PMID: 38146121 PMCID: PMC10761166 DOI: 10.1080/15476286.2023.2296203] [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] [Accepted: 12/13/2023] [Indexed: 12/27/2023] Open
Abstract
Self-cleaving ribozymes are versatile tools for synthetic biologists when it comes to controlling gene expression. Up to date, 12 different classes are known, and over the past decades more and more details about their structure, cleavage mechanisms and natural environments have been uncovered. However, when these motifs are applied to mammalian gene expression constructs, the outcome can often be unexpected. A variety of factors, such as surrounding sequences and positioning of the ribozyme influences the activity and hence performance of catalytic RNAs. While some information about the efficiency of individual ribozymes (each tested in specific contexts) is known, general trends obtained from standardized, comparable experiments are lacking, complicating decisions such as which ribozyme to choose and where to insert it into the target mRNA. In many cases, application-specific optimization is required, which can be very laborious. Here, we systematically compared different classes of ribozymes within the 3'-UTR of a given reporter gene. We then examined position-dependent effects of the best-performing ribozymes. Moreover, we tested additional variants of already widely used hammerhead ribozymes originating from various organisms. We were able to identify functional structures suited for aptazyme design and generated highly efficient hammerhead ribozyme variants originating from the human genome. The present dataset will aide decisions about how to apply ribozymes for affecting gene expression as well as for developing ribozyme-based switches for controlling gene expression in human cells.
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Affiliation(s)
- Dennis Kläge
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Konstanz, Germany
| | - Elisabeth Müller
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Konstanz, Germany
| | - Jörg S. Hartig
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Konstanz, Germany
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7
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Li J, Takeda M, Imahatakenaka M, Ikeda M. Identification of dihydroorotate dehydrogenase inhibitor, vidofludimus, as a potent and novel inhibitor for influenza virus. J Med Virol 2024; 96:e29372. [PMID: 38235544 DOI: 10.1002/jmv.29372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 12/14/2023] [Accepted: 12/25/2023] [Indexed: 01/19/2024]
Abstract
Influenza A virus (IAV) infection causes respiratory disease. Recently, infection of IAV H5N1 among mammals are reported in farmed mink. Therefore, to discover antivirals against IAV, we screened a compound library by using the RNA-dependent RNA polymerase (RdRp) assay system derived from H5N1 IAV including a drug-resistant PA mutant (I38T) and a viral polymerase activity enhancing PB2 mutant (T271A). Upon screening, we found vidofludimus can be served as a potential inhibitor for IAV. Vidofludimus an orally active inhibitor for dihydroorotate dehydrogenase (DHODH), a key enzyme for the cellular de novo pyrimidine biosynthesis pathway. We found that vidofludimus exerted antiviral activity against wild-type and drug-resistant mutant IAV, with effective concentrations (EC50 ) of 2.10 and 2.11 μM, respectively. The anti-IAV activity of vidofludimus was canceled by the treatment of uridine or cytidine through pyrimidine salvage synthesis pathway, or orotic acid through pyrimidine de novo synthesis pathway. This indicated that the main target of vidofludimus is DHODH in IAV RdRp expressing cells. We also produced recombinant seasonal IAV H1N1 virion and influenza B virus (IBV) RdRp assay system and confirmed vidofludimus also carried highly antiviral activity against seasonal IAV and IBV. Vidofludimus is a candidate drug for the future threat of IAV H5N1 infection among humans as well as seasonal influenza virus infection.
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Affiliation(s)
- Jiazhou Li
- Division of Biological Information Technology, Joint Research Center for Human Retrovirus Infection, Kagoshima University, Kagoshima, Japan
| | - Midori Takeda
- Division of Biological Information Technology, Joint Research Center for Human Retrovirus Infection, Kagoshima University, Kagoshima, Japan
| | - Mikiko Imahatakenaka
- Division of Biological Information Technology, Joint Research Center for Human Retrovirus Infection, Kagoshima University, Kagoshima, Japan
| | - Masanori Ikeda
- Division of Biological Information Technology, Joint Research Center for Human Retrovirus Infection, Kagoshima University, Kagoshima, Japan
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8
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Kretsch RC, Andersen ES, Bujnicki JM, Chiu W, Das R, Luo B, Masquida B, McRae EK, Schroeder GM, Su Z, Wedekind JE, Xu L, Zhang K, Zheludev IN, Moult J, Kryshtafovych A. RNA target highlights in CASP15: Evaluation of predicted models by structure providers. Proteins 2023; 91:1600-1615. [PMID: 37466021 PMCID: PMC10792523 DOI: 10.1002/prot.26550] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/16/2023] [Accepted: 06/26/2023] [Indexed: 07/20/2023]
Abstract
The first RNA category of the Critical Assessment of Techniques for Structure Prediction competition was only made possible because of the scientists who provided experimental structures to challenge the predictors. In this article, these scientists offer a unique and valuable analysis of both the successes and areas for improvement in the predicted models. All 10 RNA-only targets yielded predictions topologically similar to experimentally determined structures. For one target, experimentalists were able to phase their x-ray diffraction data by molecular replacement, showing a potential application of structure predictions for RNA structural biologists. Recommended areas for improvement include: enhancing the accuracy in local interaction predictions and increased consideration of the experimental conditions such as multimerization, structure determination method, and time along folding pathways. The prediction of RNA-protein complexes remains the most significant challenge. Finally, given the intrinsic flexibility of many RNAs, we propose the consideration of ensemble models.
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Affiliation(s)
- Rachael C. Kretsch
- Biophysics Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Ebbe S. Andersen
- Interdisciplinary Nanoscience Center and Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Janusz M. Bujnicki
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Wah Chiu
- Biophysics Program, Stanford University School of Medicine, Stanford, CA, USA
- Department of Bioengineering and James H. Clark Center, Stanford University, Stanford, CA, USA
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Rhiju Das
- Biophysics Program, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford, CA, USA
| | - Bingnan Luo
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610044, Sichuan, China
| | - Benoît Masquida
- UMR 7156, CNRS – Universite de Strasbourg, Strasbourg, France
| | - Ewan K.S. McRae
- Center for RNA Therapeutics, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Griffin M. Schroeder
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY, 14642, USA
- Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY, 14642, USA
| | - Zhaoming Su
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610044, Sichuan, China
| | - Joseph E. Wedekind
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY, 14642, USA
- Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY, 14642, USA
| | - Lily Xu
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Kaiming Zhang
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Ivan N. Zheludev
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - John Moult
- Department of Cell Biology and Molecular Genetics, Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland, USA
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9
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Banna HA, Das NK, Ojha M, Koirala D. Advances in chaperone-assisted RNA crystallography using synthetic antibodies. BBA ADVANCES 2023; 4:100101. [PMID: 37655005 PMCID: PMC10466895 DOI: 10.1016/j.bbadva.2023.100101] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 07/13/2023] [Accepted: 08/17/2023] [Indexed: 09/02/2023] Open
Abstract
RNA molecules play essential roles in many biological functions, from gene expression regulation, cellular growth, and metabolism to catalysis. They frequently fold into three-dimensional structures to perform their functions. Therefore, determining RNA structure represents a key step for understanding the structure-function relationships and developing RNA-targeted therapeutics. X-ray crystallography remains a method of choice for determining high-resolution RNA structures, but it has been challenging due to difficulties associated with RNA crystallization and phasing. Several natural and synthetic RNA binding proteins have been used to facilitate RNA crystallography. Having unique properties to help crystal packing and phasing, synthetic antibody fragments, specifically the Fabs, have emerged as promising RNA crystallization chaperones, and so far, over a dozen of RNA structures have been solved using this strategy. Nevertheless, multiple steps in this approach need to be improved, including the recombinant expression of these anti-RNA Fabs, to warrant the full potential of these synthetic Fabs as RNA crystallization chaperones. This review highlights the nuts and bolts and recent advances in the chaperone-assisted RNA crystallography approach, specifically emphasizing the Fab antibody fragments as RNA crystallization chaperones.
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Affiliation(s)
- Hasan Al Banna
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD 21250, USA
| | - Naba Krishna Das
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD 21250, USA
| | - Manju Ojha
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD 21250, USA
| | - Deepak Koirala
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD 21250, USA
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10
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Fang R, Chen X, Shen J, Wang B. Targeted mRNA demethylation in Arabidopsis using plant m6A editor. PLANT METHODS 2023; 19:81. [PMID: 37559087 PMCID: PMC10413771 DOI: 10.1186/s13007-023-01053-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 07/14/2023] [Indexed: 08/11/2023]
Abstract
BACKGROUND N6-methyladenosine (m6A) is an important epigenetic modification involved in RNA stability and translation regulation. Manipulating the expression of RNA m6A methyltransferases or demethylases makes it difficult to study the effect of specific RNA methylation. RESULTS In this study, we report the development of Plant m6A Editors (PMEs) using dLwaCas13a (from L. wadei) and human m6A demethylase ALKBH5 catalytic domain. PMEs specifically demethylates m6A of targeted mRNAs (WUS, STM, FT, SPL3 and SPL9) to increase mRNAs stability. In addition, we discovered that a double ribozyme system can significantly improve the efficiency of RNA editing. CONCLUSION PMEs specifically demethylates m6A of targeted mRNAs to increase mRNAs stability, suggesting that this engineered tool is instrumental for biotechnological applications.
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Affiliation(s)
- Ruiqiu Fang
- Institute of Maize and Featured Upland Crops, Zhejiang Academy of Agricultural Sciences, Dongyang, 322100, Zhejiang, China.
| | - Xiaolong Chen
- Institute of Maize and Featured Upland Crops, Zhejiang Academy of Agricultural Sciences, Dongyang, 322100, Zhejiang, China
| | - Jie Shen
- Department of Life Sciences, Changzhi University, Changzhi, 046011, Shanxi, China
| | - Bin Wang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, Zhejiang, China.
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11
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Thiyagarajah K, Basic M, Hildt E. Cellular Factors Involved in the Hepatitis D Virus Life Cycle. Viruses 2023; 15:1687. [PMID: 37632029 PMCID: PMC10459925 DOI: 10.3390/v15081687] [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: 06/30/2023] [Revised: 07/30/2023] [Accepted: 08/01/2023] [Indexed: 08/27/2023] Open
Abstract
Hepatitis D virus (HDV) is a defective RNA virus with a negative-strand RNA genome encompassing less than 1700 nucleotides. The HDV genome encodes only for one protein, the hepatitis delta antigen (HDAg), which exists in two forms acting as nucleoproteins. HDV depends on the envelope proteins of the hepatitis B virus as a helper virus for packaging its ribonucleoprotein complex (RNP). HDV is considered the causative agent for the most severe form of viral hepatitis leading to liver fibrosis/cirrhosis and hepatocellular carcinoma. Many steps of the life cycle of HDV are still enigmatic. This review gives an overview of the complete life cycle of HDV and identifies gaps in knowledge. The focus is on the description of cellular factors being involved in the life cycle of HDV and the deregulation of cellular pathways by HDV with respect to their relevance for viral replication, morphogenesis and HDV-associated pathogenesis. Moreover, recent progress in antiviral strategies targeting cellular structures is summarized in this article.
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Affiliation(s)
| | | | - Eberhard Hildt
- Paul-Ehrlich-Institute, Department of Virology, D-63225 Langen, Germany; (K.T.); (M.B.)
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12
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Chen CC, Han J, Chinn CA, Rounds JS, Li X, Nikan M, Myszka M, Tong L, Passalacqua LFM, Bredy TW, Wood MA, Lupták A. Inhibition of CPEB3 ribozyme elevates CPEB3 protein expression and polyadenylation of its target mRNAs, and enhances object location memory. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.07.543953. [PMID: 37333407 PMCID: PMC10274809 DOI: 10.1101/2023.06.07.543953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
A self-cleaving ribozyme that maps to an intron of the cytoplasmic polyadenylation element binding protein 3 (CPEB3) gene is thought to play a role in human episodic memory, but the underlying mechanisms mediating this effect are not known. We tested the activity of the murine sequence and found that the ribozyme's self-scission half-life matches the time it takes an RNA polymerase to reach the immediate downstream exon, suggesting that the ribozyme-dependent intron cleavage is tuned to co-transcriptional splicing of the CPEB3 mRNA. Our studies also reveal that the murine ribozyme modulates maturation of its harboring mRNA in both cultured cortical neurons and the hippocampus: inhibition of the ribozyme using an antisense oligonucleotide leads to increased CPEB3 protein expression, which enhances polyadenylation and translation of localized plasticity-related target mRNAs, and subsequently strengthens hippocampal-dependent long-term memory. These findings reveal a previously unknown role for self-cleaving ribozyme activity in regulating experience-induced co-transcriptional and local translational processes required for learning and memory.
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Affiliation(s)
- Claire C. Chen
- Department of Pharmaceutical Sciences, University of California–Irvine, Irvine, California 92697, United States
| | - Joseph Han
- Department of Neurobiology and Behavior, Center for the Neurobiology of Learning and Memory, University of California–Irvine, Irvine, California 92697, United States
| | - Carlene A. Chinn
- Department of Neurobiology and Behavior, Center for the Neurobiology of Learning and Memory, University of California–Irvine, Irvine, California 92697, United States
| | - Jacob S. Rounds
- Department of Neurobiology and Behavior, Center for the Neurobiology of Learning and Memory, University of California–Irvine, Irvine, California 92697, United States
| | - Xiang Li
- Department of Neurobiology and Behavior, Center for the Neurobiology of Learning and Memory, University of California–Irvine, Irvine, California 92697, United States
| | - Mehran Nikan
- Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Marie Myszka
- Department of Chemistry, University of California–Irvine, Irvine, California 92697, United States
| | - Liqi Tong
- Institute for Memory Impairments and Neurological Disorders, University of California–Irvine, Irvine, California 92697, United States
| | - Luiz F. M. Passalacqua
- Department of Pharmaceutical Sciences, University of California–Irvine, Irvine, California 92697, United States
| | - Timothy W. Bredy
- Department of Neurobiology and Behavior, Center for the Neurobiology of Learning and Memory, University of California–Irvine, Irvine, California 92697, United States
| | - Marcelo A. Wood
- Department of Neurobiology and Behavior, Center for the Neurobiology of Learning and Memory, University of California–Irvine, Irvine, California 92697, United States
| | - Andrej Lupták
- Department of Pharmaceutical Sciences, University of California–Irvine, Irvine, California 92697, United States
- Department of Chemistry, University of California–Irvine, Irvine, California 92697, United States
- Department of Molecular Biology and Biochemistry, University of California–Irvine, Irvine, California 92697, United States
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13
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Gamper H, McCormick C, Makhamreh A, Wanunu M, Rouhanifard SH, Hou YM. Enzymatic synthesis of RNA standards for mapping and quantifying RNA modifications in sequencing analysis. Methods Enzymol 2023; 692:127-153. [PMID: 37925177 DOI: 10.1016/bs.mie.2023.04.024] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2023]
Abstract
Synthesis of RNA standards that contain an internal site-specific modification is important for mapping and quantification of the modified nucleotide in sequencing analysis. While RNA containing a site-specific modification can be readily synthesized by solid-state coupling for less than 100-mer nucleotides, longer RNA must be synthesized by enzymatic ligation in the presence of a DNA splint. However, long RNAs have structural heterogeneity, and those generated by in vitro transcription have 3'-end sequence heterogeneity, which together substantially reduce the yield of ligation. Here we describe a method of 3-part splint ligation that joins an in vitro transcribed left-arm RNA, an in vitro transcribed right-arm RNA, and a chemically synthesized modification-containing middle RNA, with an efficiency higher than previously reported. We report that the improved efficiency is largely attributed to the inclusion of a pair of DNA disruptors proximal to the ligation sites, and to a lesser extent to the homogeneous processing of the 3'-end of the left-arm RNA. The yields of the ligated long RNA are sufficiently high to afford purification to homogeneity for practical RNA research. We also verify the sequence accuracy at each ligation junction by nanopore sequencing.
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Affiliation(s)
- Howard Gamper
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, United States
| | - Caroline McCormick
- Department of Bioengineering, Northeastern University, Boston, MA, United States
| | - Amr Makhamreh
- Department of Bioengineering, Northeastern University, Boston, MA, United States
| | - Meni Wanunu
- Department of Bioengineering, Northeastern University, Boston, MA, United States; Department of Physics, Northeastern University, Boston, MA, United States
| | - Sara H Rouhanifard
- Department of Bioengineering, Northeastern University, Boston, MA, United States
| | - Ya-Ming Hou
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, United States.
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14
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Schaffter SW, Wintenberg ME, Murphy TM, Strychalski EA. Design Approaches to Expand the Toolkit for Building Cotranscriptionally Encoded RNA Strand Displacement Circuits. ACS Synth Biol 2023; 12:1546-1561. [PMID: 37134273 DOI: 10.1021/acssynbio.3c00079] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Cotranscriptionally encoded RNA strand displacement (ctRSD) circuits are an emerging tool for programmable molecular computation, with potential applications spanning in vitro diagnostics to continuous computation inside living cells. In ctRSD circuits, RNA strand displacement components are continuously produced together via transcription. These RNA components can be rationally programmed through base pairing interactions to execute logic and signaling cascades. However, the small number of ctRSD components characterized to date limits circuit size and capabilities. Here, we characterize over 200 ctRSD gate sequences, exploring different input, output, and toehold sequences and changes to other design parameters, including domain lengths, ribozyme sequences, and the order in which gate strands are transcribed. This characterization provides a library of sequence domains for engineering ctRSD components, i.e., a toolkit, enabling circuits with up to 4-fold more inputs than previously possible. We also identify specific failure modes and systematically develop design approaches that reduce the likelihood of failure across different gate sequences. Lastly, we show the ctRSD gate design is robust to changes in transcriptional encoding, opening a broad design space for applications in more complex environments. Together, these results deliver an expanded toolkit and design approaches for building ctRSD circuits that will dramatically extend capabilities and potential applications.
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Affiliation(s)
- Samuel W Schaffter
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Molly E Wintenberg
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Terence M Murphy
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
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15
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Montagud-Martínez R, Márquez-Costa R, Rodrigo G. Programmable regulation of translation by harnessing the CRISPR-Cas13 system. Chem Commun (Camb) 2023; 59:2616-2619. [PMID: 36757178 DOI: 10.1039/d3cc00058c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The ability to control protein expression at both the transcriptional and post-transcriptional levels is instrumental for the cell to integrate multiple molecular signals and then reach high operational sophistication. Although challenging, fully artificial regulations at different levels are required for boosting systems and synthetic biology. Here, we report the development of a novel framework to regulate translation by repurposing the CRISPR-Cas13 immune system, which uses an RNA-guided ribonuclease. By exploiting a cell-free expression system for prototyping gene regulatory structures, our results demonstrate that CRISPR-dCas13a ribonucleoproteins (d means catalytically dead) can be programmed to repress or activate translation initiation. The performance assessment of the engineered systems also revealed guide RNA design principles. Moreover, we show that the system can work in vivo. This development complements the ability to regulate transcription with other CRISPR-Cas systems and offers potential applications.
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Affiliation(s)
- Roser Montagud-Martínez
- Institute for Integrative Systems Biology (I2SysBio), CSIC - University of Valencia, 46980, Paterna, Spain.
| | - Rosa Márquez-Costa
- Institute for Integrative Systems Biology (I2SysBio), CSIC - University of Valencia, 46980, Paterna, Spain.
| | - Guillermo Rodrigo
- Institute for Integrative Systems Biology (I2SysBio), CSIC - University of Valencia, 46980, Paterna, Spain.
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16
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General Strategies for RNA X-ray Crystallography. Molecules 2023; 28:molecules28052111. [PMID: 36903357 PMCID: PMC10004510 DOI: 10.3390/molecules28052111] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 02/22/2023] [Accepted: 02/22/2023] [Indexed: 02/27/2023] Open
Abstract
An extremely small proportion of the X-ray crystal structures deposited in the Protein Data Bank are of RNA or RNA-protein complexes. This is due to three main obstacles to the successful determination of RNA structure: (1) low yields of pure, properly folded RNA; (2) difficulty creating crystal contacts due to low sequence diversity; and (3) limited methods for phasing. Various approaches have been developed to address these obstacles, such as native RNA purification, engineered crystallization modules, and incorporation of proteins to assist in phasing. In this review, we will discuss these strategies and provide examples of how they are used in practice.
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17
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Weissman B, Ekesan Ş, Lin HC, Gardezi S, Li NS, Giese TJ, McCarthy E, Harris ME, York DM, Piccirilli JA. Dissociative Transition State in Hepatitis Delta Virus Ribozyme Catalysis. J Am Chem Soc 2023; 145:2830-2839. [PMID: 36706353 PMCID: PMC10112047 DOI: 10.1021/jacs.2c10079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Ribonucleases and small nucleolytic ribozymes are both able to catalyze RNA strand cleavage through 2'-O-transphosphorylation, provoking the question of whether protein and RNA enzymes facilitate mechanisms that pass through the same or distinct transition states. Here, we report the primary and secondary 18O kinetic isotope effects for hepatitis delta virus ribozyme catalysis that reveal a dissociative, metaphosphate-like transition state in stark contrast to the late, associative transition states observed for reactions catalyzed by specific base, Zn2+ ions, or ribonuclease A. This new information provides evidence for a discrete ribozyme active site design that modulates the RNA cleavage pathway to pass through an altered transition state.
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Affiliation(s)
- Benjamin Weissman
- Department of Chemistry and Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, United States
| | - Şölen Ekesan
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine, Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Hsuan-Chun Lin
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Shahbaz Gardezi
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Nan-Sheng Li
- Department of Chemistry and Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, United States
| | - Timothy J Giese
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine, Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Erika McCarthy
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine, Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Michael E Harris
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Darrin M York
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine, Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Joseph A Piccirilli
- Department of Chemistry and Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, United States
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18
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Khalfi P, Kennedy PT, Majzoub K, Asselah T. Hepatitis D virus: Improving virological knowledge to develop new treatments. Antiviral Res 2023; 209:105461. [PMID: 36396025 DOI: 10.1016/j.antiviral.2022.105461] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 10/21/2022] [Accepted: 11/05/2022] [Indexed: 11/16/2022]
Abstract
Hepatitis delta virus (HDV), a satellite of hepatitis B virus (HBV), possesses the smallest viral genome known to infect animals. HDV needs HBV surface protein for secretion and entry into target liver cells. However, HBV is dispensable for HDV genome amplification, as it relies almost exclusively on cellular host factors for replication. HBV/HDV co-infections affect over 12 million people worldwide and constitute the most severe form of viral hepatitis. Co-infected individuals are at higher risk of developing liver cirrhosis and hepatocellular carcinoma compared to HBV mono-infected patients. Bulevirtide, an entry inhibitor, was conditionally approved in July 2020 in the European Union for adult patients with chronic hepatitis delta (CHD) and compensated liver disease. There are several drugs in development, including lonafarnib and interferon lambda, with different modes of action. In this review, we detail our current fundamental knowledge of HDV lifecycle and review antiviral treatments under development against this virus, outlining their respective mechanisms-of-action. Finally, we describe the antiviral effect these compounds are showing in ongoing clinical trials, discussing their promise and potential pitfalls for managing HDV infected patients.
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Affiliation(s)
- Pierre Khalfi
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS-UMR 5535, Montpellier 34293 cedex 5, France
| | - Patrick T Kennedy
- The Blizard Institute, Queen Mary University of London, The Royal London Hospital, Barts Health NHS Trust, London, UK
| | - Karim Majzoub
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS-UMR 5535, Montpellier 34293 cedex 5, France.
| | - Tarik Asselah
- Université de Paris, Cité CRI, INSERM UMR 1149, Department of Hepatology, AP-HP Hôpital Beaujon, Clichy, France.
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19
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Tseligka ED, Conzelmann S, Cambet Y, Schaer T, Negro F, Clément S. Identification of selective hepatitis delta virus ribozyme inhibitors by high-throughput screening of small molecule libraries. JHEP Rep 2022; 5:100652. [PMID: 36704052 PMCID: PMC9871325 DOI: 10.1016/j.jhepr.2022.100652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 11/24/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022] Open
Abstract
Background & Aims Chronic hepatitis delta is the most severe form of chronic viral hepatitis and is associated with faster progression towards cirrhosis, liver decompensation, and hepatocellular carcinoma. Hepatitis delta virus (HDV)'s tight dependency on hepatitis B virus and the host cell machinery for its life cycle limits the development of direct-acting antivirals. Thus, we aimed to identify compounds that could block HDV replication by targeting its antigenomic ribozyme. Methods We generated stable Huh7 human hepatoma cells expressing a reporter gene (Gaussia luciferase) either downstream (Gluc-2xRz) or upstream (2xRz-Gluc) of two HDV antigenomic ribozyme sequences. We performed high-throughput screening of three small molecule libraries. The secreted luciferase was measured as a readout of ribozyme inhibition upon addition of the molecules. Each plate was considered valid when the Z factor was >0.4. Specificity and toxicity evaluations were performed for the hits with a Z-score >5 and half-maximal inhibitory concentration was calculated by performing a dose-response experiment. Results A dose-dependent induction of luciferase expression was detected in Gluc-2xRz-transfected cells incubated with the antisense morpholino, suggesting that the catalytic activity of the ribozyme cloned downstream of the reporter gene was efficiently inhibited. Among the 6,644 compounds screened, we identified four compounds that showed a specific inhibitory effect on the HDV antigenomic ribozyme in Gluc-2xRz cells, i.e. three histone deacetylase inhibitors and the purine analogue 8-azaguanine. The latter also significantly decreased HDV replication (by 40%) in differentiated HepaRG cells six days post infection. Conclusion Using a novel cell culture model, we identified four small molecules active against the antigenomic HDV ribozyme. These results may provide insights into the structural requirements of molecules designed for the potent and specific inhibition of HDV replication. Impact and implications Chronic hepatitis delta is the most severe form of chronic viral hepatitis and is associated with faster progression towards cirrhosis, liver decompensation, and the development of hepatocellular carcinoma. Despite the current development of several new compounds, there is still a need for efficient antiviral treatments specifically targeting hepatitis delta virus (HDV). This work describes a novel cell culture model that allows for the high-throughput screening of compounds able to inhibit HDV ribozymes. We identified four small molecules active against the antigenomic HDV ribozyme (the ribozyme involved in the early step of HDV replication), with the strongest activity shown by 8-azaguanine, a purine analogue. Our data may provide insights into the structural requirements of molecules designed to inhibit HDV.
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Affiliation(s)
- Eirini D. Tseligka
- Department of Pathology and Immunology, University of Geneva, Switzerland
| | | | - Yves Cambet
- Department of Pathology and Immunology, University of Geneva, Switzerland,READS Unit, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Tifany Schaer
- Department of Pathology and Immunology, University of Geneva, Switzerland
| | - Francesco Negro
- Clinical Pathology, Geneva University Hospital, Geneva, Switzerland,Gastroenterology and Hepatology, Geneva University Hospital, Geneva, Switzerland,Corresponding author. Address: Clinical Pathology, and Gastroenterology and Hepatology, Geneva University Hospital, Geneva, Switzerland.
| | - Sophie Clément
- Department of Pathology and Immunology, University of Geneva, Switzerland
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20
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Khan FS, Goher F, Zhang D, Shi P, Li Z, Htwe YM, Wang Y. Is CRISPR/Cas9 a way forward to fast-track genetic improvement in commercial palms? Prospects and limits. FRONTIERS IN PLANT SCIENCE 2022; 13:1042828. [PMID: 36578341 PMCID: PMC9791139 DOI: 10.3389/fpls.2022.1042828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
Commercially important palms (oil palm, coconut, and date palm) are widely grown perennial trees with tremendous commercial significance due to food, edible oil, and industrial applications. The mounting pressure on the human population further reinforces palms' importance, as they are essential crops to meet vegetable oil needs around the globe. Various conventional breeding methods are used for the genetic improvement of palms. However, adopting new technologies is crucial to accelerate breeding and satisfy the expanding population's demands. CRISPR/Cas9 is an efficient genome editing tool that can incorporate desired traits into the existing DNA of the plant without losing common traits. Recent progress in genome editing in oil palm, coconut and date palm are preliminarily introduced to potential readers. Furthermore, detailed information on available CRISPR-based genome editing and genetic transformation methods are summarized for researchers. We shed light on the possibilities of genome editing in palm crops, especially on the modification of fatty acid biosynthesis in oil palm. Moreover, the limitations in genome editing, including inadequate target gene screening due to genome complexities and low efficiency of genetic transformation, are also highlighted. The prospects of CRISPR/Cas9-based gene editing in commercial palms to improve sustainable production are also addressed in this review paper.
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Affiliation(s)
- Faiza Shafique Khan
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions/Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, China
- Hainan Key Laboratory of Tropical Oil Crops Biology, Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, China
| | - Farhan Goher
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Dapeng Zhang
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions/Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
- Hainan Key Laboratory of Tropical Oil Crops Biology, Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, China
| | - Peng Shi
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions/Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
- Hainan Key Laboratory of Tropical Oil Crops Biology, Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, China
| | - Zhiying Li
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions/Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
- Hainan Key Laboratory of Tropical Oil Crops Biology, Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, China
| | - Yin Min Htwe
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions/Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, China
- Hainan Key Laboratory of Tropical Oil Crops Biology, Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, China
| | - Yong Wang
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions/Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
- Hainan Key Laboratory of Tropical Oil Crops Biology, Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, China
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21
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tRNA Fusion to Streamline RNA Structure Determination: Case Studies in Probing Aminoacyl-tRNA Sensing Mechanisms by the T-Box Riboswitch. CRYSTALS 2022. [DOI: 10.3390/cryst12050694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
RNAs are prone to misfolding and are often more challenging to crystallize and phase than proteins. Here, we demonstrate that tRNA fusion can streamline the crystallization and structure determination of target RNA molecules. This strategy was applied to the T-box riboswitch system to capture a dynamic interaction between the tRNA 3′-UCCA tail and the T-box antiterminator, which senses aminoacylation. We fused the T-box antiterminator domain to the tRNA anticodon arm to capture the intended interaction through crystal packing. This approach drastically improved the probability of crystallization and successful phasing. Multiple structure snapshots captured the antiterminator loop in an open conformation with some resemblance to that observed in the recent co-crystal structures of the full-length T box riboswitch–tRNA complex, which contrasts the resting, closed conformation antiterminator observed in an earlier NMR study. The anticipated tRNA acceptor–antiterminator interaction was captured in a low-resolution crystal structure. These structures combined with our previous success using prohead RNA–tRNA fusions demonstrates tRNA fusion is a powerful method in RNA structure determination.
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22
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Structure of active human telomerase with telomere shelterin protein TPP1. Nature 2022; 604:578-583. [PMID: 35418675 PMCID: PMC9912816 DOI: 10.1038/s41586-022-04582-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 02/23/2022] [Indexed: 12/13/2022]
Abstract
Human telomerase is a RNA-protein complex that extends the 3' end of linear chromosomes by synthesizing multiple copies of the telomeric repeat TTAGGG1. Its activity is a determinant of cancer progression, stem cell renewal and cellular aging2-5. Telomerase is recruited to telomeres and activated for telomere repeat synthesis by the telomere shelterin protein TPP16,7. Human telomerase has a bilobal structure with a catalytic core ribonuclear protein and a H and ACA box ribonuclear protein8,9. Here we report cryo-electron microscopy structures of human telomerase catalytic core of telomerase reverse transcriptase (TERT) and telomerase RNA (TER (also known as hTR)), and of telomerase with the shelterin protein TPP1. TPP1 forms a structured interface with the TERT-unique telomerase essential N-terminal domain (TEN) and the telomerase RAP motif (TRAP) that are unique to TERT, and conformational dynamics of TEN-TRAP are damped upon TPP1 binding, defining the requirements for recruitment and activation. The structures further reveal that the elements of TERT and TER that are involved in template and telomeric DNA handling-including the TEN domain and the TRAP-thumb helix channel-are largely structurally homologous to those in Tetrahymena telomerase10, and provide unique insights into the mechanism of telomerase activity. The binding site of the telomerase inhibitor BIBR153211,12 overlaps a critical interaction between the TER pseudoknot and the TERT thumb domain. Numerous mutations leading to telomeropathies13,14 are located at the TERT-TER and TEN-TRAP-TPP1 interfaces, highlighting the importance of TER-TERT and TPP1 interactions for telomerase activity, recruitment and as drug targets.
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23
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Schaffter SW, Strychalski EA. Cotranscriptionally encoded RNA strand displacement circuits. SCIENCE ADVANCES 2022; 8:eabl4354. [PMID: 35319994 PMCID: PMC8942360 DOI: 10.1126/sciadv.abl4354] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 02/01/2022] [Indexed: 05/21/2023]
Abstract
Engineered molecular circuits that process information in biological systems could address emerging human health and biomanufacturing needs. However, such circuits can be difficult to rationally design and scale. DNA-based strand displacement reactions have demonstrated the largest and most computationally powerful molecular circuits to date but are limited in biological systems due to the difficulty in genetically encoding components. Here, we develop scalable cotranscriptionally encoded RNA strand displacement (ctRSD) circuits that are rationally programmed via base pairing interactions. ctRSD circuits address the limitations of DNA-based strand displacement circuits by isothermally producing circuit components via transcription. We demonstrate circuit programmability in vitro by implementing logic and amplification elements, as well as multilayer cascades. Furthermore, we show that circuit kinetics are accurately predicted by a simple model of coupled transcription and strand displacement, enabling model-driven design. We envision ctRSD circuits will enable the rational design of powerful molecular circuits that operate in biological systems, including living cells.
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24
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Li JW, Zeng T, Xu ZZ, Li JJ, Hu H, Yu Q, Zhou L, Zheng RR, Luo J, Wang CY. Ribozyme-mediated CRISPR/Cas9 gene editing in pyrethrum (Tanacetum cinerariifolium) hairy roots using a RNA polymerase II-dependent promoter. PLANT METHODS 2022; 18:32. [PMID: 35292048 PMCID: PMC8925089 DOI: 10.1186/s13007-022-00863-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 02/24/2022] [Indexed: 05/14/2023]
Abstract
BACKGROUND Traditional CRISPR/Cas9 systems that rely on U6 or U3 snRNA promoters (RNA polymerase III-dependent promoters) can only achieve constitutive gene editing in plants, hampering the functional analysis of specifically expressed genes. Ribozyme-mediated CRISPR/Cas9 systems increase the types of promoters which can be used to transcribe sgRNA. Therefore, such systems allow specific gene editing; for example, transcription of the artificial gene Ribozyme-sgRNA-Ribozyme (RGR) is initiated by an RNA polymerase II-dependent promoter. Genetic transformation is indispensable for editing plant genes. In certain plant species, including pyrethrum, genetic transformation remains challenging to do, limiting the functional verification of novel CRISPR/Cas9 systems. Thus, this study's aim was to develop a simple Agrobacterium rhizogenes-mediated hairy root transformation system to analyze the function of a ribozyme-mediated CRISPR/Cas9 system in pyrethrum. RESULTS A hairy root transformation system for pyrethrum is described, with a mean transformation frequency of 7%. Transgenic hairy roots transformed with the pBI121 vector exhibited significantly increased beta-glucuronidase staining as a visual marker of transgene expression. Further, a ribozyme-based CRISPR/Cas9 vector was constructed to edit the TcEbFS gene, which catalyzes synthesis of the defense-related compound (E)-β-farnesene in pyrethrum. The vector was transferred into the hairy roots of pyrethrum and two stably transformed hairy root transgenic lines obtained. Editing of the TcEbFS gene in the hairy roots was evaluated by gene sequencing, demonstrating that both hairy root transgenic lines had DNA base loss at the editing target site. Gas chromatography-mass spectrometry showed that the (E)-β-farnesene content was significantly decreased in both hairy root transgenic lines compared with the empty vector control group. Altogether, these results show that RGR can be driven by the CaMV35S promoter to realize TcEbFS gene editing in pyrethrum hairy roots. CONCLUSION An A. rhizogenes-mediated hairy root transformation and ribozyme-mediated CRISPR/Cas9 gene editing system in pyrethrum was established, thereby facilitating gene editing in specific organs or at a particular developmental stage in future pyrethrum research.
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Affiliation(s)
- Jia-Wen Li
- Key Laboratory for Biology of Horticultural Plants, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Tuo Zeng
- Key Laboratory for Biology of Horticultural Plants, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, China
| | - Zhi-Zhuo Xu
- Key Laboratory for Biology of Horticultural Plants, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jin-Jin Li
- Key Laboratory for Biology of Horticultural Plants, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hao Hu
- Key Laboratory for Biology of Horticultural Plants, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qin Yu
- Key Laboratory for Biology of Horticultural Plants, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Li Zhou
- Key Laboratory for Biology of Horticultural Plants, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ri-Ru Zheng
- Key Laboratory for Biology of Horticultural Plants, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jing Luo
- Key Laboratory for Biology of Horticultural Plants, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Cai-Yun Wang
- Key Laboratory for Biology of Horticultural Plants, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China.
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Rivas M, Fox GE. Nonstandard RNA/RNA interactions likely enhance folding and stability of segmented ribosomes. RNA (NEW YORK, N.Y.) 2022; 28:340-352. [PMID: 34876487 PMCID: PMC8848935 DOI: 10.1261/rna.079006.121] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 11/26/2021] [Indexed: 05/21/2023]
Abstract
The ribosome is the molecular factory that catalyzes all coded protein synthesis in extant organisms. Eukaryotic ribosomes are typically assembled out of four rRNAs; namely, 5S, 5.8S, 18S, and 28S. However, the 28S rRNA of some trypanosomatid organisms has been found to be segmented into six independent rRNAs of different sizes. The two largest segments have multiple sites where they jointly form stems comprised of standard base pairs that can hold them together. However, such regions of interaction are not observed among the four smaller RNAs. Early reports suggested that trypanosomatid segmented ribosome assembly was essentially achieved thanks to their association with rProteins. However, examination of cryo-EM ribosomal structures from Trypanosoma brucei, Leishmania donovani, and Trypanosoma cruzi reveals several long-range nonstandard RNA/RNA interactions. Most of these interactions are clusters of individual hydrogen bonds and so are not readily predictable. However, taken as a whole, they represent significant stabilizing energy that likely facilitates rRNA assembly and the overall stability of the segmented ribosomes. In the context of origin of life studies, the current results provide a better understanding of the true nature of RNA sequence space and what might be possible without an RNA replicase.
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Affiliation(s)
- Mario Rivas
- Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204, USA
| | - George E Fox
- Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204, USA
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26
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Abstract
In recent years, it has become clear that RNA molecules are involved in almost all vital cellular processes and pathogenesis of human disorders. The functional diversity of RNA comes from its structural richness. Although composed of only four nucleotides, RNA molecules present a plethora of secondary and tertiary structures critical for intra and intermolecular contacts with other RNAs and ligands (proteins, small metabolites, etc.). In order to fully understand RNA function it is necessary to define its spatial structure. Crystallography, nuclear magnetic resonance and cryogenic electron microscopy have demonstrated considerable success in determining the structures of biologically important RNA molecules. However, these powerful methods require large amounts of sample. Despite their limitations, chemical synthesis and in vitro transcription are usually employed to obtain milligram quantities of RNA for structural studies, delivering simple and effective methods for large-scale production of homogenous samples. The aim of this paper is to provide an overview of methods for large-scale RNA synthesis with emphasis on chemical synthesis and in vitro transcription. We also present our own results of testing the efficiency of these approaches in order to adapt the material acquisition strategy depending on the desired RNA construct.
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27
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Pacin-Ruiz B, Cortese MF, Tabernero D, Sopena S, Gregori J, García-García S, Casillas R, Najarro A, Aldama U, Palom A, Rando-Segura A, Galán A, Vila M, Riveiro-Barciela M, Quer J, González-Aseguinolaza G, Buti M, Rodríguez-Frías F. Inspecting the Ribozyme Region of Hepatitis Delta Virus Genotype 1: Conservation and Variability. Viruses 2022; 14:v14020215. [PMID: 35215809 PMCID: PMC8877431 DOI: 10.3390/v14020215] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/18/2022] [Accepted: 01/19/2022] [Indexed: 02/07/2023] Open
Abstract
The hepatitis delta virus (HDV) genome has an autocatalytic region called the ribozyme, which is essential for viral replication. The aim of this study was to use next-generation sequencing (NGS) to analyze the ribozyme quasispecies (QS) in order to study its evolution and identify highly conserved regions potentially suitable for a gene-silencing strategy. HDV RNA was extracted from 2 longitudinal samples of chronic HDV patients and the ribozyme (nucleotide, nt 688-771) was analyzed using NGS. QS conservation, variability and genetic distance were analyzed. Mutations were identified by aligning sequences with their specific genotype consensus. The main relevant mutations were tested in vitro. The ribozyme was conserved overall, with a hyper-conserved region between nt 715-745. No difference in QS was observed over time. The most variable region was between nt 739-769. Thirteen mutations were observed, with three showing a higher frequency: T23C, T69C and C64 deletion. This last strongly reduced HDV replication by more than 1 log in vitro. HDV Ribozyme QS was generally highly conserved and was maintained during follow-up. The most conserved portion may be a valuable target for a gene-silencing strategy. The presence of the C64 deletion may strongly impair viral replication, as it is a potential mechanism of viral persistence.
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Affiliation(s)
- Beatriz Pacin-Ruiz
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Vall d’Hebron University Hospital, 08035 Barcelona, Spain; (B.P.-R.); (S.S.); (S.G.-G.); (R.C.); (A.N.); (U.A.); (A.G.); (M.V.); (F.R.-F.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Instituto de Salud Carlos III, 28029 Madrid, Spain; (M.R.-B.); (M.B.)
| | - María Francesca Cortese
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Vall d’Hebron University Hospital, 08035 Barcelona, Spain; (B.P.-R.); (S.S.); (S.G.-G.); (R.C.); (A.N.); (U.A.); (A.G.); (M.V.); (F.R.-F.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Instituto de Salud Carlos III, 28029 Madrid, Spain; (M.R.-B.); (M.B.)
- Correspondence: (M.F.C.); (D.T.)
| | - David Tabernero
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Vall d’Hebron University Hospital, 08035 Barcelona, Spain; (B.P.-R.); (S.S.); (S.G.-G.); (R.C.); (A.N.); (U.A.); (A.G.); (M.V.); (F.R.-F.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Instituto de Salud Carlos III, 28029 Madrid, Spain; (M.R.-B.); (M.B.)
- Correspondence: (M.F.C.); (D.T.)
| | - Sara Sopena
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Vall d’Hebron University Hospital, 08035 Barcelona, Spain; (B.P.-R.); (S.S.); (S.G.-G.); (R.C.); (A.N.); (U.A.); (A.G.); (M.V.); (F.R.-F.)
| | - Josep Gregori
- Liver Unit, Liver Disease, Laboratory-Viral Hepatitis, Vall d’Hebron Institut Recerca-Vall d’Hebron University Hospital, 08035 Barcelona, Spain; (J.G.); (J.Q.)
| | - Selene García-García
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Vall d’Hebron University Hospital, 08035 Barcelona, Spain; (B.P.-R.); (S.S.); (S.G.-G.); (R.C.); (A.N.); (U.A.); (A.G.); (M.V.); (F.R.-F.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Instituto de Salud Carlos III, 28029 Madrid, Spain; (M.R.-B.); (M.B.)
| | - Rosario Casillas
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Vall d’Hebron University Hospital, 08035 Barcelona, Spain; (B.P.-R.); (S.S.); (S.G.-G.); (R.C.); (A.N.); (U.A.); (A.G.); (M.V.); (F.R.-F.)
| | - Adrián Najarro
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Vall d’Hebron University Hospital, 08035 Barcelona, Spain; (B.P.-R.); (S.S.); (S.G.-G.); (R.C.); (A.N.); (U.A.); (A.G.); (M.V.); (F.R.-F.)
| | - Unai Aldama
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Vall d’Hebron University Hospital, 08035 Barcelona, Spain; (B.P.-R.); (S.S.); (S.G.-G.); (R.C.); (A.N.); (U.A.); (A.G.); (M.V.); (F.R.-F.)
| | - Adriana Palom
- Liver Unit, Department of Internal Medicine, Vall d’Hebron University Hospital, 08035 Barcelona, Spain;
| | - Ariadna Rando-Segura
- Department of Microbiology, Vall d’Hebron University Hospital, 08035 Barcelona, Spain;
| | - Anna Galán
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Vall d’Hebron University Hospital, 08035 Barcelona, Spain; (B.P.-R.); (S.S.); (S.G.-G.); (R.C.); (A.N.); (U.A.); (A.G.); (M.V.); (F.R.-F.)
| | - Marta Vila
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Vall d’Hebron University Hospital, 08035 Barcelona, Spain; (B.P.-R.); (S.S.); (S.G.-G.); (R.C.); (A.N.); (U.A.); (A.G.); (M.V.); (F.R.-F.)
| | - Mar Riveiro-Barciela
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Instituto de Salud Carlos III, 28029 Madrid, Spain; (M.R.-B.); (M.B.)
- Liver Unit, Department of Internal Medicine, Vall d’Hebron University Hospital, 08035 Barcelona, Spain;
| | - Josep Quer
- Liver Unit, Liver Disease, Laboratory-Viral Hepatitis, Vall d’Hebron Institut Recerca-Vall d’Hebron University Hospital, 08035 Barcelona, Spain; (J.G.); (J.Q.)
| | | | - María Buti
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Instituto de Salud Carlos III, 28029 Madrid, Spain; (M.R.-B.); (M.B.)
- Liver Unit, Department of Internal Medicine, Vall d’Hebron University Hospital, 08035 Barcelona, Spain;
| | - Francisco Rodríguez-Frías
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Vall d’Hebron University Hospital, 08035 Barcelona, Spain; (B.P.-R.); (S.S.); (S.G.-G.); (R.C.); (A.N.); (U.A.); (A.G.); (M.V.); (F.R.-F.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Instituto de Salud Carlos III, 28029 Madrid, Spain; (M.R.-B.); (M.B.)
- Biochemistry and Molecular Biology Department, Universitat Autònoma de Barcelona (UAB), Plaça Cívica, 08193 Bellaterra, Spain
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28
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Flores R, Navarro B, Serra P, Di Serio F. A Scenario for the Emergence of Protoviroids in the RNA World and for Their Further Evolution into Viroids and Viroid-Like RNAs by Modular Recombinations and Mutations. Virus Evol 2022; 8:veab107. [PMID: 35223083 PMCID: PMC8865084 DOI: 10.1093/ve/veab107] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 12/10/2021] [Accepted: 01/14/2022] [Indexed: 11/14/2022] Open
Abstract
Abstract
Viroids are tiny, circular and non-coding RNAs that are able to replicate and systemically infect plants. The smallest known pathogens, they have been proposed to represent survivors from the RNA world that likely preceded the cellular world currently dominating life on the earth. Although the small, circular and compact nature of viroid genomes, some of which are also endowed with catalytic activity mediated by hammerhead ribozymes, support this proposal, the lack of feasible evolutionary routes and the identification of hammerhead ribozymes in a large number of DNA genomes of organisms along the tree of life has led some to question such a proposal. Here, we reassess the origin and subsequent evolution of viroids by complementing phylogenetic reconstructions with molecular data, including the primary and higher-order structure of the genomic RNAs, their replication and recombination mechanisms and selected biological information. Features of some viroid-like RNAs found in plants, animal, and possibly fungi are also considered. The resulting evolutionary scenario supports the emergence of protoviroids in the RNA world, mainly as replicative modules, followed by further increase in genome complexity based on module/domain shuffling and combination, and mutation. Such a modular evolutionary scenario would have facilitated the inclusion in the protoviroid genomes of complex RNA structures (or coding sequences, as in the case of hepatitis ∂ virus and delta-like agents), likely needed for their adaptation from the RNA world to a life based on cells, thus generating the ancestors of current infectious viroids and viroid-like RNAs. Other non-infectious viroid-like RNAs, such as retroviroid-like RNA elements and retrozymes, could also be derived from protoviroids if their reverse transcription and integration into viral or eukaryotic DNA, respectively, are considered as a possible key step in their evolution. Comparison of evidence supporting a general and modular evolutionary model for viroids and viroid-like RNAs with that favoring alternative scenarios provides reasonable reasons to keep alive the hypothesis that these small RNA pathogens may be relics of a precellular world.
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Affiliation(s)
| | - Beatriz Navarro
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Via Amendola 122/D, Bari 70126, Italy
| | - Pedro Serra
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas–Universidad Politécnica de Valencia, Ingeniero Fausto Elio s/n, Valencia 46022, Spain
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Olzog VJ, Freist LI, Goldmann R, Fallmann J, Weinberg CE. Application of RtcB ligase to monitor self-cleaving ribozyme activity by RNA-seq. Biol Chem 2022; 403:705-715. [PMID: 35025187 DOI: 10.1515/hsz-2021-0408] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 12/24/2021] [Indexed: 11/15/2022]
Abstract
Self-cleaving ribozymes are catalytic RNAs and can be found in all domains of life. They catalyze a site-specific cleavage that results in a 5' fragment with a 2',3' cyclic phosphate (2',3' cP) and a 3' fragment with a 5' hydroxyl (5' OH) end. Recently, several strategies to enrich self-cleaving ribozymes by targeted biochemical methods have been introduced by us and others. Here, we develop an alternative strategy in which 5' OH RNAs are specifically ligated by RtcB ligase, which first guanylates the 3' phosphate of the adapter and then ligates it directly to RNAs with 5' OH ends. Our results demonstrate that adapter ligation to highly structured ribozyme fragments is much more efficient using the thermostable RtcB ligase from Pyrococcus horikoshii than the broadly applied Escherichia coli enzyme. Moreover, we investigated DNA, RNA and modified RNA adapters for their suitability in RtcB ligation reactions. We used the optimized RtcB-mediated ligation to produce RNA-seq libraries and captured a spiked 3' twister ribozyme fragment from E. coli total RNA. This RNA-seq-based method is applicable to detect ribozyme fragments as well as other cellular RNAs with 5' OH termini from total RNA.
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Affiliation(s)
- V Janett Olzog
- Faculty of Life Sciences, Institute for Biochemistry, Leipzig University, Brüderstraße 34, D-04103 Leipzig, Germany
| | - Lena I Freist
- Faculty of Life Sciences, Institute for Biochemistry, Leipzig University, Brüderstraße 34, D-04103 Leipzig, Germany
| | - Robin Goldmann
- Department of Computer Science, Bioinformatics Group, and Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstraße 16-18, D-04107 Leipzig, Germany
| | - Jörg Fallmann
- Department of Computer Science, Bioinformatics Group, and Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstraße 16-18, D-04107 Leipzig, Germany
| | - Christina E Weinberg
- Faculty of Life Sciences, Institute for Biochemistry, Leipzig University, Brüderstraße 34, D-04103 Leipzig, Germany
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30
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Rosenbach H, Span I. Obtaining Crystals of Nucleic Acids in Complex with the Protein U1A Using the Soaking Method. Methods Mol Biol 2022; 2439:105-115. [PMID: 35226318 DOI: 10.1007/978-1-0716-2047-2_8] [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] [Indexed: 06/14/2023]
Abstract
X-ray crystallography is one of the most prominent techniques for determining high-resolution structures of nucleic acids. The major challenges are to obtain well-diffracting single crystals and to solve the phase problem. The absence of structural information impedes the elucidation of the molecular details of biological processes. A particularly intriguing example is the RNA-cleavage catalyzed by the 10-23 deoxyribozyme (DNAzyme). This DNAzyme consists of a catalytic core that is flanked by two substrate binding arms, which can be designed to bind any RNA of interest. Structure elucidation of the 10-23 DNAzyme in a biologically relevant conformation faces three major challenges: (1) stabilization of the RNA substrate to capture the DNA:RNA complex in the pre-catalytic conformation, (2) prevention of the formation of an artificial duplex conformation due to a self-complementary sequence in the catalytic core of the DNAzyme, and (3) the crystallization of nucleic acids with their uniform surfaces. Here, we provide a protocol for an innovative strategy facilitating the crystallization of protein:nucleic acid complexes using a soaking approach and discuss on how to apply this protocol for the structure elucidation of the 10-23 DNAzyme. For this purpose, we describe the purification procedure of an optimized variant of the RNA-binding protein U1A, the crystallization of this specific U1A variant, the soaking process with its specific RNA hairpin loop, and finally suggest a strategy for applying this procedure on the 10-23 DNAzyme in complex with its specific RNA target.
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Affiliation(s)
- Hannah Rosenbach
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Ingrid Span
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany.
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31
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Nagata S, Kiyohara R, Toh H. Constraint of Base Pairing on HDV Genome Evolution. Viruses 2021; 13:v13122350. [PMID: 34960619 PMCID: PMC8708965 DOI: 10.3390/v13122350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 10/11/2021] [Accepted: 11/02/2021] [Indexed: 11/17/2022] Open
Abstract
The hepatitis delta virus is a single-stranded circular RNA virus, which is characterized by high self-complementarity. About 70% of the genome sequences can form base-pairs with internal nucleotides. There are many studies on the evolution of the hepatitis delta virus. However, the secondary structure has not been taken into account in these studies. In this study, we developed a method to examine the effect of base pairing as a constraint on the nucleotide substitutions during the evolution of the hepatitis delta virus. The method revealed that the base pairing can reduce the evolutionary rate in the non-coding region of the virus. In addition, it is suggested that the non-coding nucleotides without base pairing may be under some constraint, and that the intensity of the constraint is weaker than that by the base pairing but stronger than that on the synonymous site.
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32
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[Delta hepatitis: Epidemiology, diagnostic, natural history and treatment]. Rev Med Interne 2021; 43:160-169. [PMID: 34799189 DOI: 10.1016/j.revmed.2021.10.329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 09/17/2021] [Accepted: 10/17/2021] [Indexed: 11/20/2022]
Abstract
Hepatitis B virus is a small enveloped RNA virus, which replicates independently but requires the hepatitis B virus (HBV) to provide the envelope proteins necessary for the assembly of its own viral particles. Approximately 5% of chronic hepatitis B virus carriers are infected with HDV. HBV vaccination remains the best preventive treatment for HDV. All HBV patients should be screened for HDV (anti-HDV serology). In case of positive HDV serology, HDV replication (HDV RNA) should be investigated using a sensitive and specific technique. Hepatitis Delta is often complicated by cirrhosis and hepatocellular carcinoma (HCC). For this reason, every patient with Delta cirrhosis should be screened for HCC by abdominal ultrasound every 6 months. The historical treatment was based on PEG-IFN with many side effects. A new treatment has been approved, Bulevirtide (Hepcludex®) an HDV/HBV entry inhibitor, for any patient with chronic hepatitis Delta infection (CHD) with active replication (except in decompensated cirrhosis), at a dose of 2mg/day by subcutaneous injection. The exact duration on-treatment is unknown, thus treatment should be continued if clinical benefit is observed.
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33
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Chen LY, Pang XY, Goyal H, Yang RX, Xu HG. Hepatitis D: challenges in the estimation of true prevalence and laboratory diagnosis. Gut Pathog 2021; 13:66. [PMID: 34717740 PMCID: PMC8557527 DOI: 10.1186/s13099-021-00462-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 10/19/2021] [Indexed: 02/07/2023] Open
Abstract
Hepatitis delta virus (HDV) is a defective single negative chain RNA virus, as its envelope protein synthesis is dependent on hepatitis B virus (HBV). Studies have consistently shown that coinfection of HBV and HDV is the most serious form of viral hepatitis, with accelerated progression to liver cirrhosis and hepatocellular carcinoma. About 74 million of HBV surface antigen (HBsAg) positive patients worldwide are also co-infected with HDV. Besides, patients with intravenous drug use and high-risk sexual behavior are at higher risk of HDV infection. Therapeutic schedules for HDV are limited, and relapse of HDV has been observed after treatment with pegylated interferon alpha. To reduce the transmission of HDV, all people infected with HBV should be screened for HDV. At present, several serological and molecular detection methods are widely used in the diagnosis of HDV. However, due to the lack of international standards diagnostic results from different laboratories are often not comparable. Therefore, the true prevalence of HDV is still unclear. In this manuscript, we have analyzed various factors influencing the estimation of HDV prevalence. We have also discussed about the advantages and disadvantages of currently available HDV laboratory diagnostic methods, in order to provide some ideas for improving the detection of HDV.
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Affiliation(s)
- Lin-Yuan Chen
- Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xiao-Yu Pang
- Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Hemant Goyal
- Department of Internal Medicine Macon, Mercer University School of Medicine, Georgia, USA
| | - Rui-Xia Yang
- Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China.
| | - Hua-Guo Xu
- Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China.
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Liu G, Jiang H, Sun W, Zhang J, Chen D, Murchie AIH. The function of twister ribozyme variants in non-LTR retrotransposition in Schistosoma mansoni. Nucleic Acids Res 2021; 49:10573-10588. [PMID: 34551436 PMCID: PMC8501958 DOI: 10.1093/nar/gkab818] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 08/23/2021] [Accepted: 09/08/2021] [Indexed: 12/13/2022] Open
Abstract
The twister ribozyme is widely distributed over numerous organisms and is especially abundant in Schistosoma mansoni, but has no confirmed biological function. Of the 17 non-LTR retrotransposons known in S. mansoni, none have thus far been associated with ribozymes. Here we report the identification of novel twister variant (T-variant) ribozymes and their function in S. mansoni non-LTR retrotransposition. We show that T-variant ribozymes are located at the 5′ end of Perere-3 non-LTR retrotransposons in the S. mansoni genome. T-variant ribozymes were demonstrated to be catalytically active in vitro. In reporter constructs, T-variants were shown to cleave in vivo, and cleavage of T-variants was sufficient for the translation of downstream reporter genes. Our analysis shows that the T-variants and Perere-3 are transcribed together. Target site duplications (TSDs); markers of target-primed reverse transcription (TPRT) and footmarks of retrotransposition, are located adjacent to the T-variant cleavage site and suggest that T-variant cleavage has taken place inS. mansoni. Sequence heterogeneity in the TSDs indicates that Perere-3 retrotransposition is not site-specific. The TSD sequences contribute to the 5′ end of the terminal ribozyme helix (P1 stem). Based on these results we conclude that T-variants have a functional role in Perere-3 retrotransposition.
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Affiliation(s)
- Getong Liu
- Fudan University Pudong Medical Center, and Institutes of Biomedical Sciences, Shanghai Medical College, Key Laboratory of Medical Epigenetics and Metabolism, Fudan University, Shanghai 200032, China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Hengyi Jiang
- Fudan University Pudong Medical Center, and Institutes of Biomedical Sciences, Shanghai Medical College, Key Laboratory of Medical Epigenetics and Metabolism, Fudan University, Shanghai 200032, China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Wenxia Sun
- Fudan University Pudong Medical Center, and Institutes of Biomedical Sciences, Shanghai Medical College, Key Laboratory of Medical Epigenetics and Metabolism, Fudan University, Shanghai 200032, China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Jun Zhang
- Fudan University Pudong Medical Center, and Institutes of Biomedical Sciences, Shanghai Medical College, Key Laboratory of Medical Epigenetics and Metabolism, Fudan University, Shanghai 200032, China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Dongrong Chen
- Fudan University Pudong Medical Center, and Institutes of Biomedical Sciences, Shanghai Medical College, Key Laboratory of Medical Epigenetics and Metabolism, Fudan University, Shanghai 200032, China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Alastair I H Murchie
- Fudan University Pudong Medical Center, and Institutes of Biomedical Sciences, Shanghai Medical College, Key Laboratory of Medical Epigenetics and Metabolism, Fudan University, Shanghai 200032, China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
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35
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Peng H, Latifi B, Müller S, Lupták A, Chen IA. Self-cleaving ribozymes: substrate specificity and synthetic biology applications. RSC Chem Biol 2021; 2:1370-1383. [PMID: 34704043 PMCID: PMC8495972 DOI: 10.1039/d0cb00207k] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 06/14/2021] [Indexed: 12/22/2022] Open
Abstract
Various self-cleaving ribozymes appearing in nature catalyze the sequence-specific intramolecular cleavage of RNA and can be engineered to catalyze cleavage of appropriate substrates in an intermolecular fashion, thus acting as true catalysts. The mechanisms of the small, self-cleaving ribozymes have been extensively studied and reviewed previously. Self-cleaving ribozymes can possess high catalytic activity and high substrate specificity; however, substrate specificity is also engineerable within the constraints of the ribozyme structure. While these ribozymes share a common fundamental catalytic mechanism, each ribozyme family has a unique overall architecture and active site organization, indicating that several distinct structures yield this chemical activity. The multitude of catalytic structures, combined with some flexibility in substrate specificity within each family, suggests that such catalytic RNAs, taken together, could access a wide variety of substrates. Here, we give an overview of 10 classes of self-cleaving ribozymes and capture what is understood about their substrate specificity and synthetic applications. Evolution of these ribozymes in an RNA world might be characterized by the emergence of a new ribozyme family followed by rapid adaptation or diversification for specific substrates. Self-cleaving ribozymes have become important tools of synthetic biology. Here we summarize the substrate specificity and applications of the main classes of these ribozymes.![]()
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Affiliation(s)
- Huan Peng
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles CA 90095 USA
| | - Brandon Latifi
- Department of Pharmaceutical Sciences, University of California Irvine CA 92697 USA
| | - Sabine Müller
- Institute for Biochemistry, University Greifswald 17487 Greifswald Germany
| | - Andrej Lupták
- Department of Pharmaceutical Sciences, University of California Irvine CA 92697 USA
| | - Irene A Chen
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles CA 90095 USA
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36
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Pujari N, Saundh SL, Acquah FA, Mooers BHM, Ferré-D’Amaré AR, Leung AKW. Engineering Crystal Packing in RNA Structures I: Past and Future Strategies for Engineering RNA Packing in Crystals. CRYSTALS 2021; 11:952. [PMID: 34745656 PMCID: PMC8570644 DOI: 10.3390/cryst11080952] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
X-ray crystallography remains a powerful method to gain atomistic insights into the catalytic and regulatory functions of RNA molecules. However, the technique requires the preparation of diffraction-quality crystals. This is often a resource- and time-consuming venture because RNA crystallization is hindered by the conformational heterogeneity of RNA, as well as the limited opportunities for stereospecific intermolecular interactions between RNA molecules. The limited success at crystallization explains in part the smaller number of RNA-only structures in the Protein Data Bank. Several approaches have been developed to aid the formation of well-ordered RNA crystals. The majority of these are construct-engineering techniques that aim to introduce crystal contacts to favor the formation of well-diffracting crystals. A typical example is the insertion of tetraloop-tetraloop receptor pairs into non-essential RNA segments to promote intermolecular association. Other methods of promoting crystallization involve chaperones and crystallization-friendly molecules that increase RNA stability and improve crystal packing. In this review, we discuss the various techniques that have been successfully used to facilitate crystal packing of RNA molecules, recent advances in construct engineering, and directions for future research in this vital aspect of RNA crystallography.
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Affiliation(s)
- Narsimha Pujari
- Department of Veterinary Biomedical Sciences, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
| | - Stephanie L. Saundh
- Department of Veterinary Biomedical Sciences, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
| | - Francis A. Acquah
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Blaine H. M. Mooers
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
- Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Adrian R. Ferré-D’Amaré
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, MD 20892, USA
| | - Adelaine Kwun-Wai Leung
- Department of Veterinary Biomedical Sciences, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
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37
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Zhang W, Qiu Y, Zhou L, Yin J, Wang L, Zhi H, Xu K. Development of a Viral RdRp-Assisted Gene Silencing System and Its Application in the Identification of Host Factors of Plant (+)RNA Virus. Front Microbiol 2021; 12:682921. [PMID: 34394029 PMCID: PMC8358433 DOI: 10.3389/fmicb.2021.682921] [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: 03/19/2021] [Accepted: 06/24/2021] [Indexed: 11/13/2022] Open
Abstract
Gene silencing induced by hairpin RNA or virus infection expression is one of the major tools in genetics studies in plants. However, when dealing with essential genes, virus-induced gene silencing (VIGS) and transgenic expression of hairpin RNA could lead to plant death, while transient expression of hairpin RNA in leaves is often less competent in downregulating target gene mRNA levels. Here, we developed a transient double-stranded RNA (dsRNA) expression system assisted by a modified viral RNA-dependent RNA polymerase (RdRp) in plant leaves. We show that this system is more effective in inducing gene silencing than the intron-spliced hairpin RNA expression. Furthermore, by using this system, we tested the role of the early secretory pathway during infection of Soybean mosaic potyvirus (SMV). We found that key components of the coat protein complex II vesicles are required for the multiplication of SMV. Overall, this dsRNA-based gene silencing system is effective in downregulating plant gene expression and can be used to identify host genes involved in plant-virus interactions.
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Affiliation(s)
- Wang Zhang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Yanglin Qiu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Lingyun Zhou
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Jinlong Yin
- National Center for Soybean Improvement, National Key Laboratory for Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Soybean-Ministry of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Liqun Wang
- National Center for Soybean Improvement, National Key Laboratory for Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Soybean-Ministry of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Haijian Zhi
- National Center for Soybean Improvement, National Key Laboratory for Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Soybean-Ministry of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Kai Xu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, China
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38
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Netter HJ, Barrios MH, Littlejohn M, Yuen LKW. Hepatitis Delta Virus (HDV) and Delta-Like Agents: Insights Into Their Origin. Front Microbiol 2021; 12:652962. [PMID: 34234753 PMCID: PMC8256844 DOI: 10.3389/fmicb.2021.652962] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 05/12/2021] [Indexed: 01/05/2023] Open
Abstract
Hepatitis delta virus (HDV) is a human pathogen, and the only known species in the genus Deltavirus. HDV is a satellite virus and depends on the hepatitis B virus (HBV) for packaging, release, and transmission. Extracellular HDV virions contain the genomic HDV RNA, a single-stranded negative-sense and covalently closed circular RNA molecule, which is associated with the HDV-encoded delta antigen forming a ribonucleoprotein complex, and enveloped by the HBV surface antigens. Replication occurs in the nucleus and is mediated by host enzymes and assisted by cis-acting ribozymes allowing the formation of monomer length molecules which are ligated by host ligases to form unbranched rod-like circles. Recently, meta-transcriptomic studies investigating various vertebrate and invertebrate samples identified RNA species with similarities to HDV RNA. The delta-like agents may be representatives of novel subviral agents or satellite viruses which share with HDV, the self-complementarity of the circular RNA genome, the ability to encode a protein, and the presence of ribozyme sequences. The widespread distribution of delta-like agents across different taxa with considerable phylogenetic distances may be instrumental in comprehending their evolutionary history by elucidating the transition from transcriptome to cellular circular RNAs to infectious subviral agents.
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Affiliation(s)
- Hans J Netter
- Victorian Infectious Diseases Reference Laboratory (VIDRL), Melbourne Health, The Peter Doherty Institute, Melbourne, VIC, Australia.,School of Science, Royal Melbourne Institute of Technology (RMIT) University, Melbourne, VIC, Australia
| | - Marilou H Barrios
- Victorian Infectious Diseases Reference Laboratory (VIDRL), Melbourne Health, The Peter Doherty Institute, Melbourne, VIC, Australia.,The Peter Doherty Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Margaret Littlejohn
- Victorian Infectious Diseases Reference Laboratory (VIDRL), Melbourne Health, The Peter Doherty Institute, Melbourne, VIC, Australia
| | - Lilly K W Yuen
- Victorian Infectious Diseases Reference Laboratory (VIDRL), Melbourne Health, The Peter Doherty Institute, Melbourne, VIC, Australia
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39
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Hovlinc is a recently evolved class of ribozyme found in human lncRNA. Nat Chem Biol 2021; 17:601-607. [PMID: 33753927 DOI: 10.1038/s41589-021-00763-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 01/06/2021] [Accepted: 02/02/2021] [Indexed: 01/31/2023]
Abstract
Although naturally occurring catalytic RNA molecules-ribozymes-have attracted a great deal of research interest, very few have been identified in humans. Here, we developed a genome-wide approach to discovering self-cleaving ribozymes and identified a naturally occurring ribozyme in humans. The secondary structure and biochemical properties of this ribozyme indicate that it belongs to an unidentified class of small, self-cleaving ribozymes. The sequence of the ribozyme exhibits a clear evolutionary path, from its appearance between ~130 and ~65 million years ago (Ma), to acquiring self-cleavage activity very recently, ~13-10 Ma, in the common ancestors of humans, chimpanzees and gorillas. The ribozyme appears to be functional in vivo and is embedded within a long noncoding RNA belonging to a class of very long intergenic noncoding RNAs. The presence of a catalytic RNA enzyme in lncRNA creates the possibility that these transcripts could function by carrying catalytic RNA domains.
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40
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Mizutani Y, Uesaka K, Ota A, Calassanzio M, Ratti C, Suzuki T, Fujimori F, Chiba S. De novo Sequencing of Novel Mycoviruses From Fusarium sambucinum: An Attempt on Direct RNA Sequencing of Viral dsRNAs. Front Microbiol 2021; 12:641484. [PMID: 33927702 PMCID: PMC8076516 DOI: 10.3389/fmicb.2021.641484] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 03/16/2021] [Indexed: 11/17/2022] Open
Abstract
An increasing number of viruses are continuously being found in a wide range of organisms, including fungi. Recent studies have revealed a wide viral diversity in microbes and a potential importance of these viruses in the natural environment. Although virus exploration has been accelerated by short-read, high-throughput sequencing (HTS), and viral de novo sequencing is still challenging because of several biological/molecular features such as micro-diversity and secondary structure of RNA genomes. This study conducted de novo sequencing of multiple double-stranded (ds) RNA (dsRNA) elements that were obtained from fungal viruses infecting two Fusarium sambucinum strains, FA1837 and FA2242, using conventional HTS and long-read direct RNA sequencing (DRS). De novo assembly of the read data from both technologies generated near-entire genomic sequence of the viruses, and the sequence homology search and phylogenetic analysis suggested that these represented novel species of the Hypoviridae, Totiviridae, and Mitoviridae families. However, the DRS-based consensus sequences contained numerous indel errors that differed from the HTS consensus sequences, and these errors hampered accurate open reading frame (ORF) prediction. Although with its present performance, the use of DRS is premature to determine viral genome sequences, the DRS-mediated sequencing shows great potential as a user-friendly platform for a one-shot, whole-genome sequencing of RNA viruses due to its long-reading ability and relative structure-tolerant nature.
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Affiliation(s)
- Yukiyoshi Mizutani
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Kazuma Uesaka
- Center for Gene Research, Nagoya University, Nagoya, Japan
| | - Ayane Ota
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Matteo Calassanzio
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Claudio Ratti
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Takamasa Suzuki
- College of Bioscience and Biotechnology, Chubu University, Kasugai, Japan
| | - Fumihiro Fujimori
- Graduate School of Humanities and Life Sciences, Tokyo Kasei University, Itabashi, Japan
| | - Sotaro Chiba
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
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41
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Affinity and Structural Analysis of the U1A RNA Recognition Motif with Engineered Methionines to Improve Experimental Phasing. CRYSTALS 2021; 11. [PMID: 33777416 PMCID: PMC7996396 DOI: 10.3390/cryst11030273] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
RNA plays a central role in all organisms and can fold into complex structures to orchestrate function. Visualization of such structures often requires crystallization, which can be a bottleneck in the structure-determination process. To promote crystallization, an RNA-recognition motif (RRM) of the U1A spliceosomal protein has been co-opted as a crystallization module. Specifically, the U1-snRNA hairpin II (hpII) single-stranded loop recognized by U1A can be transplanted into an RNA target to promote crystal contacts and to attain phase information via molecular replacement or anomalous diffraction methods using selenomethionine. Herein, we produced the F37M/F77M mutant of U1A to augment the phasing capability of this powerful crystallization module. Selenomethionine-substituted U1A(F37M/F77M) retains high affinity for hpII (K D of 59.7 ± 11.4 nM). The 2.20 Å resolution crystal structure reveals that the mutated sidechains make new S-π interactions in the hydrophobic core and are useful for single-wavelength anomalous diffraction. Crystals were also attained of U1A(F37M/F77M) in complex with a bacterial preQ1-II riboswitch. The F34M/F37M/F77M mutant was introduced similarly into a lab-evolved U1A variant (TBP6.9) that recognizes the internal bulged loop of HIV-1 TAR RNA. We envision that this short RNA sequence can be placed into non-essential duplex regions to promote crystallization and phasing of target RNAs. We show that selenomethionine-substituted TBP6.9(F34M/F37M/F77M) binds a TAR variant wherein the apical loop was replaced with a GNRA tetraloop (K D of 69.8 ± 2.9 nM), laying the groundwork for use of TBP6.9(F34M/F37M/F77M) as a crystallization module. These new tools are available to the research community.
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42
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An RNA-centric historical narrative around the Protein Data Bank. J Biol Chem 2021; 296:100555. [PMID: 33744291 PMCID: PMC8080527 DOI: 10.1016/j.jbc.2021.100555] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 02/17/2021] [Accepted: 03/16/2021] [Indexed: 01/06/2023] Open
Abstract
Some of the amazing contributions brought to the scientific community by the Protein Data Bank (PDB) are described. The focus is on nucleic acid structures with a bias toward RNA. The evolution and key roles in science of the PDB and other structural databases for nucleic acids illustrate how small initial ideas can become huge and indispensable resources with the unflinching willingness of scientists to cooperate globally. The progress in the understanding of the molecular interactions driving RNA architectures followed the rapid increase in RNA structures in the PDB. That increase was consecutive to improvements in chemical synthesis and purification of RNA molecules, as well as in biophysical methods for structure determination and computer technology. The RNA modeling efforts from the early beginnings are also described together with their links to the state of structural knowledge and technological development. Structures of RNA and of its assemblies are physical objects, which, together with genomic data, allow us to integrate present-day biological functions and the historical evolution in all living species on earth.
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43
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Aptamers, Riboswitches, and Ribozymes in S. cerevisiae Synthetic Biology. Life (Basel) 2021; 11:life11030248. [PMID: 33802772 PMCID: PMC8002509 DOI: 10.3390/life11030248] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/12/2021] [Accepted: 03/15/2021] [Indexed: 01/09/2023] Open
Abstract
Among noncoding RNA sequences, riboswitches and ribozymes have attracted the attention of the synthetic biology community as circuit components for translation regulation. When fused to aptamer sequences, ribozymes and riboswitches are enabled to interact with chemicals. Therefore, protein synthesis can be controlled at the mRNA level without the need for transcription factors. Potentially, the use of chemical-responsive ribozymes/riboswitches would drastically simplify the design of genetic circuits. In this review, we describe synthetic RNA structures that have been used so far in the yeast Saccharomyces cerevisiae. We present their interaction mode with different chemicals (e.g., theophylline and antibiotics) or proteins (such as the RNase III) and their recent employment into clustered regularly interspaced short palindromic repeats–CRISPR-associated protein 9 (CRISPR-Cas) systems. Particular attention is paid, throughout the whole paper, to their usage and performance into synthetic gene circuits.
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44
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Hopfinger MC, Kirkpatrick CC, Znosko BM. Predictions and analyses of RNA nearest neighbor parameters for modified nucleotides. Nucleic Acids Res 2020; 48:8901-8913. [PMID: 32810273 PMCID: PMC7498315 DOI: 10.1093/nar/gkaa654] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/02/2020] [Accepted: 07/27/2020] [Indexed: 12/21/2022] Open
Abstract
The most popular RNA secondary structure prediction programs utilize free energy (ΔG°37) minimization and rely upon thermodynamic parameters from the nearest neighbor (NN) model. Experimental parameters are derived from a series of optical melting experiments; however, acquiring enough melt data to derive accurate NN parameters with modified base pairs is expensive and time consuming. Given the multitude of known natural modifications and the continuing use and development of unnatural nucleotides, experimentally characterizing all modified NNs is impractical. This dilemma necessitates a computational model that can predict NN thermodynamics where experimental data is scarce or absent. Here, we present a combined molecular dynamics/quantum mechanics protocol that accurately predicts experimental NN ΔG°37 parameters for modified nucleotides with neighboring Watson–Crick base pairs. NN predictions for Watson-Crick and modified base pairs yielded an overall RMSD of 0.32 kcal/mol when compared with experimentally derived parameters. NN predictions involving modified bases without experimental parameters (N6-methyladenosine, 2-aminopurineriboside, and 5-methylcytidine) demonstrated promising agreement with available experimental melt data. This procedure not only yields accurate NN ΔG°37 predictions but also quantifies stacking and hydrogen bonding differences between modified NNs and their canonical counterparts, allowing investigators to identify energetic differences and providing insight into sources of (de)stabilization from nucleotide modifications.
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Affiliation(s)
| | | | - Brent M Znosko
- Department of Chemistry, Saint Louis University, Saint Louis, MO 63103, USA
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45
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The evolution and clinical impact of hepatitis B virus genome diversity. Nat Rev Gastroenterol Hepatol 2020; 17:618-634. [PMID: 32467580 DOI: 10.1038/s41575-020-0296-6] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/20/2020] [Indexed: 02/06/2023]
Abstract
The global burden of hepatitis B virus (HBV) is enormous, with 257 million persons chronically infected, resulting in more than 880,000 deaths per year worldwide. HBV exists as nine different genotypes, which differ in disease progression, natural history and response to therapy. HBV is an ancient virus, with the latest reports greatly expanding the host range of the Hepadnaviridae (to include fish and reptiles) and casting new light on the origins and evolution of this viral family. Although there is an effective preventive vaccine, there is no cure for chronic hepatitis B, largely owing to the persistence of a viral minichromosome that is not targeted by current therapies. HBV persistence is also facilitated through aberrant host immune responses, possibly due to the diverse intra-host viral populations that can respond to host-mounted and therapeutic selection pressures. This Review summarizes current knowledge on the influence of HBV diversity on disease progression and treatment response and the potential effect on new HBV therapies in the pipeline. The mechanisms by which HBV diversity can occur both within the individual host and at a population level are also discussed.
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46
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Binas O, de Jesus V, Landgraf T, Völklein AE, Martins J, Hymon D, Kaur Bains J, Berg H, Biedenbänder T, Fürtig B, Lakshmi Gande S, Niesteruk A, Oxenfarth A, Shahin Qureshi N, Schamber T, Schnieders R, Tröster A, Wacker A, Wirmer-Bartoschek J, Wirtz Martin MA, Stirnal E, Azzaoui K, Richter C, Sreeramulu S, José Blommers MJ, Schwalbe H. 19 F NMR-Based Fragment Screening for 14 Different Biologically Active RNAs and 10 DNA and Protein Counter-Screens. Chembiochem 2020; 22:423-433. [PMID: 32794266 PMCID: PMC7436455 DOI: 10.1002/cbic.202000476] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 08/11/2020] [Indexed: 11/17/2022]
Abstract
We report here the nuclear magnetic resonance 19F screening of 14 RNA targets with different secondary and tertiary structure to systematically assess the druggability of RNAs. Our RNA targets include representative bacterial riboswitches that naturally bind with nanomolar affinity and high specificity to cellular metabolites of low molecular weight. Based on counter‐screens against five DNAs and five proteins, we can show that RNA can be specifically targeted. To demonstrate the quality of the initial fragment library that has been designed for easy follow‐up chemistry, we further show how to increase binding affinity from an initial fragment hit by chemistry that links the identified fragment to the intercalator acridine. Thus, we achieve low‐micromolar binding affinity without losing binding specificity between two different terminator structures.
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Affiliation(s)
- Oliver Binas
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Vanessa de Jesus
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Tom Landgraf
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Albrecht Eduard Völklein
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Jason Martins
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Daniel Hymon
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Jasleen Kaur Bains
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Hannes Berg
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Thomas Biedenbänder
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Boris Fürtig
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Santosh Lakshmi Gande
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Anna Niesteruk
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Andreas Oxenfarth
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Nusrat Shahin Qureshi
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Tatjana Schamber
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Robbin Schnieders
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Alix Tröster
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Anna Wacker
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Julia Wirmer-Bartoschek
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Maria Alexandra Wirtz Martin
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Elke Stirnal
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Kamal Azzaoui
- Saverna Therapeutics, Gewerbestrasse 24, 4123, Allschwil, Switzerland
| | - Christian Richter
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Sridhar Sreeramulu
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | | | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
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47
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Micura R, Höbartner C. Fundamental studies of functional nucleic acids: aptamers, riboswitches, ribozymes and DNAzymes. Chem Soc Rev 2020; 49:7331-7353. [PMID: 32944725 DOI: 10.1039/d0cs00617c] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
This review aims at juxtaposing common versus distinct structural and functional strategies that are applied by aptamers, riboswitches, and ribozymes/DNAzymes. Focusing on recently discovered systems, we begin our analysis with small-molecule binding aptamers, with emphasis on in vitro-selected fluorogenic RNA aptamers and their different modes of ligand binding and fluorescence activation. Fundamental insights are much needed to advance RNA imaging probes for detection of exo- and endogenous RNA and for RNA process tracking. Secondly, we discuss the latest gene expression-regulating mRNA riboswitches that respond to the alarmone ppGpp, to PRPP, to NAD+, to adenosine and cytidine diphosphates, and to precursors of thiamine biosynthesis (HMP-PP), and we outline new subclasses of SAM and tetrahydrofolate-binding RNA regulators. Many riboswitches bind protein enzyme cofactors that, in principle, can catalyse a chemical reaction. For RNA, however, only one system (glmS ribozyme) has been identified in Nature thus far that utilizes a small molecule - glucosamine-6-phosphate - to participate directly in reaction catalysis (phosphodiester cleavage). We wonder why that is the case and what is to be done to reveal such likely existing cellular activities that could be more diverse than currently imagined. Thirdly, this brings us to the four latest small nucleolytic ribozymes termed twister, twister-sister, pistol, and hatchet as well as to in vitro selected DNA and RNA enzymes that promote new chemistry, mainly by exploiting their ability for RNA labelling and nucleoside modification recognition. Enormous progress in understanding the strategies of nucleic acids catalysts has been made by providing thorough structural fundaments (e.g. first structure of a DNAzyme, structures of ribozyme transition state mimics) in combination with functional assays and atomic mutagenesis.
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Affiliation(s)
- Ronald Micura
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck CMBI, Leopold-Franzens University Innsbruck, Innsbruck, Austria.
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48
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Rosenbach H, Victor J, Etzkorn M, Steger G, Riesner D, Span I. Molecular Features and Metal Ions That Influence 10-23 DNAzyme Activity. Molecules 2020; 25:E3100. [PMID: 32646019 PMCID: PMC7412337 DOI: 10.3390/molecules25133100] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 06/25/2020] [Accepted: 07/03/2020] [Indexed: 12/17/2022] Open
Abstract
Deoxyribozymes (DNAzymes) with RNA hydrolysis activity have a tremendous potential as gene suppression agents for therapeutic applications. The most extensively studied representative is the 10-23 DNAzyme consisting of a catalytic loop and two substrate binding arms that can be designed to bind and cleave the RNA sequence of interest. The RNA substrate is cleaved between central purine and pyrimidine nucleotides. The activity of this DNAzyme in vitro is considerably higher than in vivo, which was suggested to be related to its divalent cation dependency. Understanding the mechanism of DNAzyme catalysis is hindered by the absence of structural information. Numerous biological studies, however, provide comprehensive insights into the role of particular deoxynucleotides and functional groups in DNAzymes. Here we provide an overview of the thermodynamic properties, the impact of nucleobase modifications within the catalytic loop, and the role of different metal ions in catalysis. We point out features that will be helpful in developing novel strategies for structure determination and to understand the mechanism of the 10-23 DNAzyme. Consideration of these features will enable to develop improved strategies for structure determination and to understand the mechanism of the 10-23 DNAzyme. These insights provide the basis for improving activity in cells and pave the way for developing DNAzyme applications.
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Affiliation(s)
- Hannah Rosenbach
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225 Duesseldorf, Germany; (H.R.); (J.V.); (M.E.); (G.S.); (D.R.)
| | - Julian Victor
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225 Duesseldorf, Germany; (H.R.); (J.V.); (M.E.); (G.S.); (D.R.)
| | - Manuel Etzkorn
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225 Duesseldorf, Germany; (H.R.); (J.V.); (M.E.); (G.S.); (D.R.)
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Wilhelm-Johnen-Straße, 52428 Jülich, Germany
| | - Gerhard Steger
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225 Duesseldorf, Germany; (H.R.); (J.V.); (M.E.); (G.S.); (D.R.)
| | - Detlev Riesner
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225 Duesseldorf, Germany; (H.R.); (J.V.); (M.E.); (G.S.); (D.R.)
| | - Ingrid Span
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225 Duesseldorf, Germany; (H.R.); (J.V.); (M.E.); (G.S.); (D.R.)
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49
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Wu J, Zhou C, Li J, Li C, Tao X, Leontis NB, Zirbel CL, Bisaro DM, Ding B. Functional analysis reveals G/U pairs critical for replication and trafficking of an infectious non-coding viroid RNA. Nucleic Acids Res 2020; 48:3134-3155. [PMID: 32083649 PMCID: PMC7102988 DOI: 10.1093/nar/gkaa100] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 02/03/2020] [Accepted: 02/18/2020] [Indexed: 01/19/2023] Open
Abstract
While G/U pairs are present in many RNAs, the lack of molecular studies to characterize the roles of multiple G/U pairs within a single RNA limits our understanding of their biological significance. From known RNA 3D structures, we observed that the probability a G/U will form a Watson-Crick (WC) base pair depends on sequence context. We analyzed 17 G/U pairs in the 359-nucleotide genome of Potato spindle tuber viroid (PSTVd), a circular non-coding RNA that replicates and spreads systemically in host plants. Most putative G/U base pairs were experimentally supported by selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE). Deep sequencing PSTVd genomes from plants inoculated with a cloned master sequence revealed naturally occurring variants, and showed that G/U pairs are maintained to the same extent as canonical WC base pairs. Comprehensive mutational analysis demonstrated that nearly all G/U pairs are critical for replication and/or systemic spread. Two selected G/U pairs were found to be required for PSTVd entry into, but not for exit from, the host vascular system. This study identifies critical roles for G/U pairs in the survival of an infectious RNA, and increases understanding of structure-based regulation of replication and trafficking of pathogen and cellular RNAs.
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Affiliation(s)
- Jian Wu
- Department of Molecular Genetics, Center for Applied Plant Sciences, Center for RNA Biology, and Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, USA.,Graduate Program in Molecular, Cellular, and Developmental Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Cuiji Zhou
- Department of Molecular Genetics, Center for Applied Plant Sciences, Center for RNA Biology, and Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, USA
| | - James Li
- Department of Molecular Genetics, Center for Applied Plant Sciences, Center for RNA Biology, and Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Chun Li
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaorong Tao
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Neocles B Leontis
- Department of Chemistry, Bowling Green State University, Bowling Green, OH 43403, USA
| | - Craig L Zirbel
- Department of Mathematics and Statistics, Bowling Green State University, Bowling Green, OH 43403, USA
| | - David M Bisaro
- Department of Molecular Genetics, Center for Applied Plant Sciences, Center for RNA Biology, and Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, USA.,Graduate Program in Molecular, Cellular, and Developmental Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Biao Ding
- Department of Molecular Genetics, Center for Applied Plant Sciences, Center for RNA Biology, and Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, USA.,Graduate Program in Molecular, Cellular, and Developmental Biology, The Ohio State University, Columbus, OH 43210, USA
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50
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Li J, Mohammed-Elsabagh M, Paczkowski F, Li Y. Circular Nucleic Acids: Discovery, Functions and Applications. Chembiochem 2020; 21:1547-1566. [PMID: 32176816 DOI: 10.1002/cbic.202000003] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 02/13/2020] [Indexed: 12/14/2022]
Abstract
Circular nucleic acids (CNAs) are nucleic acid molecules with a closed-loop structure. This feature comes with a number of advantages including complete resistance to exonuclease degradation, much better thermodynamic stability, and the capability of being replicated by a DNA polymerase in a rolling circle manner. Circular functional nucleic acids, CNAs containing at least a ribozyme/DNAzyme or a DNA/RNA aptamer, not only inherit the advantages of CNAs but also offer some unique application opportunities, such as the design of topology-controlled or enabled molecular devices. This article will begin by summarizing the discovery, biogenesis, and applications of naturally occurring CNAs, followed by discussing the methods for constructing artificial CNAs. The exploitation of circular functional nucleic acids for applications in nanodevice engineering, biosensing, and drug delivery will be reviewed next. Finally, the efforts to couple functional nucleic acids with rolling circle amplification for ultra-sensitive biosensing and for synthesizing multivalent molecular scaffolds for unique applications in biosensing and drug delivery will be recapitulated.
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Affiliation(s)
- Jiuxing Li
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
| | - Mostafa Mohammed-Elsabagh
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
| | - Freeman Paczkowski
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
| | - Yingfu Li
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
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