1
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Haila GJ, Plante JA, Widen SG, Beasley DWC. Complete genome sequence of Koutango virus strain DakAnD5443 isolated from Tatera kempi in 1968. Microbiol Resour Announc 2023; 12:e0042323. [PMID: 37846978 PMCID: PMC10653001 DOI: 10.1128/mra.00423-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 09/13/2023] [Indexed: 10/18/2023] Open
Abstract
Koutango virus (KOUV), a close relative of West Nile virus, is highly neuroinvasive in animal models and has been associated with human disease. The complete genome of the KOUV prototype strain DakAnD5443 is reported here and may facilitate development of infectious clones for further characterization of this novel flavivirus.
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Affiliation(s)
- Gabriel J. Haila
- Microbiology and Immunology Graduate Program, University of Texas Medical Branch, Galveston, Texas, USA
| | - Jessica A. Plante
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, Texas, USA
| | - Steven G. Widen
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA
- Molecular Genomics Core Facility, University of Texas Medical Branch, Galveston, Texas, USA
| | - David W. C. Beasley
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
- Institutional Office of Regulated Nonclinical Studies, University of Texas Medical Branch, Galveston, Texas, USA
- Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, Texas, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, Texas, USA
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2
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Ramos-Lorente S, Romero-López C, Berzal-Herranz A. Information Encoded by the Flavivirus Genomes beyond the Nucleotide Sequence. Int J Mol Sci 2021; 22:3738. [PMID: 33916729 PMCID: PMC8038387 DOI: 10.3390/ijms22073738] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 03/30/2021] [Accepted: 03/31/2021] [Indexed: 02/05/2023] Open
Abstract
The genus Flavivirus comprises numerous, small, single positive-stranded RNA viruses, many of which are important human pathogens. To store all the information required for their successful propagation, flaviviruses use discrete structural genomic RNA elements to code for functional information by the establishment of dynamic networks of long-range RNA-RNA interactions that promote specific folding. These structural elements behave as true cis-acting, non-coding RNAs (ncRNAs) and have essential regulatory roles in the viral cycle. These include the control of the formation of subgenomic RNAs, known as sfRNAs, via the prevention of the complete degradation of the RNA genome. These sfRNAs are important in ensuring viral fitness. This work summarizes our current knowledge of the functions performed by the genome conformations and the role of RNA-RNA interactions in these functions. It also reviews the role of RNA structure in the production of sfRNAs across the genus Flavivirus, and their existence in related viruses.
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Affiliation(s)
| | - Cristina Romero-López
- Instituto de Parasitología y Biomedicina López-Neyra (IPBLN-CSIC), Av. Conocimiento 17, Armilla, 18016 Granada, Spain;
| | - Alfredo Berzal-Herranz
- Instituto de Parasitología y Biomedicina López-Neyra (IPBLN-CSIC), Av. Conocimiento 17, Armilla, 18016 Granada, Spain;
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3
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The Pseudo-Circular Genomes of Flaviviruses: Structures, Mechanisms, and Functions of Circularization. Cells 2021; 10:cells10030642. [PMID: 33805761 PMCID: PMC7999817 DOI: 10.3390/cells10030642] [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: 01/14/2021] [Revised: 02/19/2021] [Accepted: 03/02/2021] [Indexed: 11/23/2022] Open
Abstract
The circularization of viral genomes fulfills various functions, from evading host defense mechanisms to promoting specific replication and translation patterns supporting viral proliferation. Here, we describe the genomic structures and associated host factors important for flaviviruses genome circularization and summarize their functional roles. Flaviviruses are relatively small, single-stranded, positive-sense RNA viruses with genomes of approximately 11 kb in length. These genomes contain motifs at their 5′ and 3′ ends, as well as in other regions, that are involved in circularization. These motifs are highly conserved throughout the Flavivirus genus and occur both in mature virions and within infected cells. We provide an overview of these sequence motifs and RNA structures involved in circularization, describe their linear and circularized structures, and discuss the proteins that interact with these circular structures and that promote and regulate their formation, aiming to clarify the key features of genome circularization and understand how these affect the flaviviruses life cycle.
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4
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Liu Y, Zhang Y, Wang M, Cheng A, Yang Q, Wu Y, Jia R, Liu M, Zhu D, Chen S, Zhang S, Zhao X, Huang J, Mao S, Ou X, Gao Q, Wang Y, Xu Z, Chen Z, Zhu L, Luo Q, Liu Y, Yu Y, Zhang L, Tian B, Pan L, Chen X. Structures and Functions of the 3' Untranslated Regions of Positive-Sense Single-Stranded RNA Viruses Infecting Humans and Animals. Front Cell Infect Microbiol 2020; 10:453. [PMID: 32974223 PMCID: PMC7481400 DOI: 10.3389/fcimb.2020.00453] [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: 05/20/2020] [Accepted: 07/23/2020] [Indexed: 12/20/2022] Open
Abstract
The 3′ untranslated region (3′ UTR) of positive-sense single-stranded RNA [ssRNA(+)] viruses is highly structured. Multiple elements in the region interact with other nucleotides and proteins of viral and cellular origin to regulate various aspects of the virus life cycle such as replication, translation, and the host-cell response. This review attempts to summarize the primary and higher order structures identified in the 3′UTR of ssRNA(+) viruses and their functional roles.
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Affiliation(s)
- Yuanzhi Liu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yu Zhang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Mingshu Wang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Anchun Cheng
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Qiao Yang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Ying Wu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Renyong Jia
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Mafeng Liu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Dekang Zhu
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Shun Chen
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Shaqiu Zhang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - XinXin Zhao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Juan Huang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Sai Mao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xumin Ou
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Qun Gao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yin Wang
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Zhiwen Xu
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Zhengli Chen
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Ling Zhu
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Qihui Luo
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Yunya Liu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yanling Yu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Ling Zhang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Bin Tian
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Leichang Pan
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xiaoyue Chen
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
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5
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Zeng M, Duan Y, Zhang W, Wang M, Jia R, Zhu D, Liu M, Zhao X, Yang Q, Wu Y, Zhang S, Liu Y, Zhang L, Yu Y, Chen S, Cheng A. Universal RNA Secondary Structure Insight Into Mosquito-Borne Flavivirus (MBFV) cis-Acting RNA Biology. Front Microbiol 2020; 11:473. [PMID: 32292394 PMCID: PMC7118588 DOI: 10.3389/fmicb.2020.00473] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 03/04/2020] [Indexed: 12/22/2022] Open
Abstract
Mosquito-borne flaviviruses (MBFVs) spread between vertebrate (mammals and birds) and invertebrate (mosquitoes) hosts. The cis-acting RNAs of MBFV share common evolutionary origins and contain frequent alterations, which control the balance of linear and circular genome conformations and allow effective replication. Importantly, multiple cis-acting RNAs interact with trans-acting regulatory RNA-binding proteins (RBPs) and affect the MBFV lifecycle process, including viral replicase binding, viral RNA translation-cyclisation-synthesis and nucleocapsid assembly. Considering that extensive structural probing analyses have been performed on MBFV cis-acting RNAs, herein the homologous RNA structures are online folded and consensus structures are constructed by sort. The specific traits and underlying biology of MBFV cis-acting RNA are illuminated accordingly in a review of RNA structure. These findings deepen our understanding of MBFV cis-acting RNA biology and serve as a resource for designing therapeutics in targeting protein-viral RNA interaction or viral RNA secondary structures.
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Affiliation(s)
- Miao Zeng
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yanping Duan
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Wei Zhang
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Mingshu Wang
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Institute of Preventive Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Renyong Jia
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Institute of Preventive Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Dekang Zhu
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Institute of Preventive Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Mafeng Liu
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Institute of Preventive Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Xinxin Zhao
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Institute of Preventive Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Qiao Yang
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Institute of Preventive Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Ying Wu
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Institute of Preventive Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Shaqiu Zhang
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Institute of Preventive Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Yunya Liu
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Ling Zhang
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yangling Yu
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Shun Chen
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Institute of Preventive Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Anchun Cheng
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Institute of Preventive Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
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6
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Different Degrees of 5'-to-3' DAR Interactions Modulate Zika Virus Genome Cyclization and Host-Specific Replication. J Virol 2020; 94:JVI.01602-19. [PMID: 31826997 PMCID: PMC7022364 DOI: 10.1128/jvi.01602-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 12/06/2019] [Indexed: 01/06/2023] Open
Abstract
Mosquito-borne flaviviruses, which include many important human pathogens, such as West Nile virus (WNV), dengue virus (DENV), and Zika virus (ZIKV), have caused numerous emerging epidemics in recent years. Details of the viral genome functions necessary for effective viral replication in mosquito and vertebrate hosts remain obscure. Here, using ZIKV as a model, we found that the conserved "downstream of AUG region" (DAR), which is known to be an essential element for genome cyclization, is involved in viral replication in a host-specific manner. Mutational analysis of the DAR element showed that a single-nucleotide mismatch between the 5' DAR and the 3' DAR had little effect on ZIKV replication in mammalian cells but dramatically impaired viral propagation in mosquito cells. The revertant viruses passaged in mosquito cells generated compensatory mutations restoring the base pairing of the DAR, further confirming the importance of the complementarity of the DAR in mosquito cells. We demonstrate that a single-nucleotide mutation in the DAR is sufficient to destroy long-range RNA interaction of the ZIKV genome and affects de novo RNA synthesis at 28°C instead of 37°C, resulting in the different replication efficiencies of the mutant viruses in mosquito and mammalian cells. Our results reveal a novel function of the circular form of the flavivirus genome in host-specific viral replication, providing new ideas to further explore the functions of the viral genome during host adaptation.IMPORTANCE Flaviviruses naturally cycle between the mosquito vector and vertebrate hosts. The disparate hosts provide selective pressures that drive virus genome evolution to maintain efficient replication during host alteration. Host adaptation may occur at different stages of the viral life cycle, since host-specific viral protein processing and virion conformations have been reported in the individual hosts. However, the viral determinants and the underlying mechanisms associated with host-specific functions remain obscure. In this study, using Zika virus, we found that the DAR-mediated genome cyclization regulates viral replication differently and is under different selection pressures in mammalian and mosquito cells. A more constrained complementarity of the DAR is required in mosquito cells than in mammalian cells. Since the DAR element is stably maintained among mosquito-borne flaviviruses, our findings could provide new information for understanding the role of flavivirus genome cyclization in viral adaptation and RNA evolution in the two hosts.
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7
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Andrews RJ, Roche J, Moss WN. ScanFold: an approach for genome-wide discovery of local RNA structural elements-applications to Zika virus and HIV. PeerJ 2018; 6:e6136. [PMID: 30627482 PMCID: PMC6317755 DOI: 10.7717/peerj.6136] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 11/15/2018] [Indexed: 12/24/2022] Open
Abstract
In addition to encoding RNA primary structures, genomes also encode RNA secondary and tertiary structures that play roles in gene regulation and, in the case of RNA viruses, genome replication. Methods for the identification of functional RNA structures in genomes typically rely on scanning analysis windows, where multiple partially-overlapping windows are used to predict RNA structures and folding metrics to deduce regions likely to form functional structure. Separate structural models are produced for each window, where the step size can greatly affect the returned model. This makes deducing unique local structures challenging, as the same nucleotides in each window can be alternatively base paired. We are presenting here a new approach where all base pairs from analysis windows are considered and weighted by favorable folding. This results in unique base pairing throughout the genome and the generation of local regions/structures that can be ranked by their propensity to form unusually thermodynamically stable folds. We applied this approach to the Zika virus (ZIKV) and HIV-1 genomes. ZIKV is linked to a variety of neurological ailments including microcephaly and Guillain-Barré syndrome and its (+)-sense RNA genome encodes two, previously described, functionally essential structured RNA regions. HIV, the cause of AIDS, contains multiple functional RNA motifs in its genome, which have been extensively studied. Our approach is able to successfully identify and model the structures of known functional motifs in both viruses, while also finding additional regions likely to form functional structures. All data have been archived at the RNAStructuromeDB (www.structurome.bb.iastate.edu), a repository of RNA folding data for humans and their pathogens.
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Affiliation(s)
- Ryan J. Andrews
- Roy J. Carver Department of Biophysics, Biochemistry and Molecular Biology, Iowa State University, Ames, IA, USA
| | - Julien Roche
- Roy J. Carver Department of Biophysics, Biochemistry and Molecular Biology, Iowa State University, Ames, IA, USA
| | - Walter N. Moss
- Roy J. Carver Department of Biophysics, Biochemistry and Molecular Biology, Iowa State University, Ames, IA, USA
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8
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A Massively Parallel Selection of Small Molecule-RNA Motif Binding Partners Informs Design of an Antiviral from Sequence. Chem 2018; 4:2384-2404. [PMID: 30719503 DOI: 10.1016/j.chempr.2018.08.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Many RNAs cause disease; however, RNA is rarely exploited as a small-molecule drug target. Our programmatic focus is to define privileged RNA motif small-molecule interactions to enable the rational design of compounds that modulate RNA biology starting from only sequence. We completed a massive, library-versus-library screen that probed over 50 million binding events between RNA motifs and small molecules. The resulting data provide a rich encyclopedia of small-molecule RNA recognition patterns, defining chemotypes and RNA motifs that confer selective, avid binding. The resulting interaction maps were mined against the entire viral genome of hepatitis C virus (HCV). A small molecule was identified that avidly bound RNA motifs present in the HCV 30 UTR and inhibited viral replication while having no effect on host cells. Collectively, this study represents the first whole-genome pattern recognition between small molecules and RNA folds.
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9
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The 5' and 3' Untranslated Regions of the Flaviviral Genome. Viruses 2017; 9:v9060137. [PMID: 28587300 PMCID: PMC5490814 DOI: 10.3390/v9060137] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 05/16/2017] [Accepted: 05/29/2017] [Indexed: 01/30/2023] Open
Abstract
Flaviviruses are enveloped arthropod-borne viruses with a single-stranded, positive-sense RNA genome that can cause serious illness in humans and animals. The 11 kb 5′ capped RNA genome consists of a single open reading frame (ORF), and is flanked by 5′ and 3′ untranslated regions (UTR). The ORF is a polyprotein that is processed into three structural and seven non-structural proteins. The UTRs have been shown to be important for viral replication and immune modulation. Both of these regions consist of elements that are essential for genome cyclization, resulting in initiation of RNA synthesis. Genome mutation studies have been employed to investigate each component of the essential elements to show the necessity of each component and its role in viral RNA replication and growth. Furthermore, the highly structured 3′UTR is responsible for the generation of subgenomic flavivirus RNA (sfRNA) that helps the virus evade host immune response, thereby affecting viral pathogenesis. In addition, changes within the 3′UTR have been shown to affect transmissibility between vector and host, which can influence the development of vaccines.
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10
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Fernández-Sanlés A, Ríos-Marco P, Romero-López C, Berzal-Herranz A. Functional Information Stored in the Conserved Structural RNA Domains of Flavivirus Genomes. Front Microbiol 2017; 8:546. [PMID: 28421048 PMCID: PMC5376627 DOI: 10.3389/fmicb.2017.00546] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 03/15/2017] [Indexed: 02/05/2023] Open
Abstract
The genus Flavivirus comprises a large number of small, positive-sense single-stranded, RNA viruses able to replicate in the cytoplasm of certain arthropod and/or vertebrate host cells. The genus, which has some 70 member species, includes a number of emerging and re-emerging pathogens responsible for outbreaks of human disease around the world, such as the West Nile, dengue, Zika, yellow fever, Japanese encephalitis, St. Louis encephalitis, and tick-borne encephalitis viruses. Like other RNA viruses, flaviviruses have a compact RNA genome that efficiently stores all the information required for the completion of the infectious cycle. The efficiency of this storage system is attributable to supracoding elements, i.e., discrete, structural units with essential functions. This information storage system overlaps and complements the protein coding sequence and is highly conserved across the genus. It therefore offers interesting potential targets for novel therapeutic strategies. This review summarizes our knowledge of the features of flavivirus genome functional RNA domains. It also provides a brief overview of the main achievements reported in the design of antiviral nucleic acid-based drugs targeting functional genomic RNA elements.
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Affiliation(s)
- Alba Fernández-Sanlés
- Department of Molecular Biology, Instituto de Parasitología y Biomedicina "López-Neyra," Consejo Superior de Investigaciones Científicas (IPBLN-CSIC)Granada, Spain
| | - Pablo Ríos-Marco
- Department of Molecular Biology, Instituto de Parasitología y Biomedicina "López-Neyra," Consejo Superior de Investigaciones Científicas (IPBLN-CSIC)Granada, Spain
| | - Cristina Romero-López
- Department of Molecular Biology, Instituto de Parasitología y Biomedicina "López-Neyra," Consejo Superior de Investigaciones Científicas (IPBLN-CSIC)Granada, Spain
| | - Alfredo Berzal-Herranz
- Department of Molecular Biology, Instituto de Parasitología y Biomedicina "López-Neyra," Consejo Superior de Investigaciones Científicas (IPBLN-CSIC)Granada, Spain
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11
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Yun SI, Lee YM. Zika virus: An emerging flavivirus. J Microbiol 2017; 55:204-219. [PMID: 28243937 DOI: 10.1007/s12275-017-7063-6] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 02/15/2017] [Indexed: 01/18/2023]
Abstract
Zika virus (ZIKV) is a previously little-known flavivirus closely related to Japanese encephalitis, West Nile, dengue, and yellow fever viruses, all of which are primarily transmitted by blood-sucking mosquitoes. Since its discovery in Uganda in 1947, ZIKV has continued to expand its geographic range, from equatorial Africa and Asia to the Pacific Islands, then further afield to South and Central America and the Caribbean. Currently, ZIKV is actively circulating not only in much of Latin America and its neighbors but also in parts of the Pacific Islands and Southeast Asia. Although ZIKV infection generally causes only mild symptoms in some infected individuals, it is associated with a range of neuroimmunological disorders, including Guillain-Barré syndrome, meningoencephalitis, and myelitis. Recently, maternal ZIKV infection during pregnancy has been linked to neonatal malformations, resulting in various degrees of congenital abnormalities, microcephaly, and even abortion. Despite its emergence as an important public health problem, however, little is known about ZIKV biology, and neither vaccine nor drug is available to control ZIKV infection. This article provides a brief introduction to ZIKV with a major emphasis on its molecular virology, in order to help facilitate the development of diagnostics, therapeutics, and vaccines.
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Affiliation(s)
- Sang-Im Yun
- Department of Animal, Dairy, and Veterinary Sciences, Utah State University, Logan, UT, 84322-4815, USA
| | - Young-Min Lee
- Department of Animal, Dairy, and Veterinary Sciences, Utah State University, Logan, UT, 84322-4815, USA. .,Utah Science Technology and Research, College of Agriculture and Applied Sciences, Utah State University, Logan, UT, 84322-4815, USA.
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Hodge K, Tunghirun C, Kamkaew M, Limjindaporn T, Yenchitsomanus PT, Chimnaronk S. Identification of a Conserved RNA-dependent RNA Polymerase (RdRp)-RNA Interface Required for Flaviviral Replication. J Biol Chem 2016; 291:17437-49. [PMID: 27334920 DOI: 10.1074/jbc.m116.724013] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Indexed: 02/01/2023] Open
Abstract
Dengue virus, an ∼10.7-kb positive-sense RNA virus, is the most common arthropod-communicated pathogen in the world. Despite dengue's clear epidemiological importance, mechanisms for its replication remain elusive. Here, we probed the entire dengue genome for interactions with viral RNA-dependent RNA polymerase (RdRp), and we identified the dominant interaction as a loop-forming ACAG motif in the 3' positive-stranded terminus, complicating the prevailing model of replication. A subset of interactions coincides with known flaviviral recombination sites inside the viral protein-coding region. Specific recognition of the RNA element occurs via an arginine patch in the C-terminal thumb domain of RdRp. We also show that the highly conserved nature of the consensus RNA motif may relate to its tolerance to various mutations in the interacting region of RdRp. Disruption of the interaction resulted in loss of viral replication ability in cells. This unique RdRp-RNA interface is found throughout flaviviruses, implying possibilities for broad disease interventions.
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Affiliation(s)
- Kenneth Hodge
- From the Laboratory of RNA Biology, Institute of Molecular Biosciences, Mahidol University, Salaya Campus, Nakhon Pathom 73170 and
| | - Chairat Tunghirun
- From the Laboratory of RNA Biology, Institute of Molecular Biosciences, Mahidol University, Salaya Campus, Nakhon Pathom 73170 and
| | - Maliwan Kamkaew
- From the Laboratory of RNA Biology, Institute of Molecular Biosciences, Mahidol University, Salaya Campus, Nakhon Pathom 73170 and
| | | | - Pa-Thai Yenchitsomanus
- Division of Molecular Medicine, Department of Research and Development, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Sarin Chimnaronk
- From the Laboratory of RNA Biology, Institute of Molecular Biosciences, Mahidol University, Salaya Campus, Nakhon Pathom 73170 and
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Ye Q, Liu ZY, Han JF, Jiang T, Li XF, Qin CF. Genomic characterization and phylogenetic analysis of Zika virus circulating in the Americas. INFECTION GENETICS AND EVOLUTION 2016; 43:43-9. [PMID: 27156653 DOI: 10.1016/j.meegid.2016.05.004] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Revised: 05/02/2016] [Accepted: 05/03/2016] [Indexed: 02/04/2023]
Abstract
The rapid spread and potential link with birth defects have made Zika virus (ZIKV) a global public health problem. The virus was discovered 70years ago, yet the knowledge about its genomic structure and the genetic variations associated with current ZIKV explosive epidemics remains not fully understood. In this review, the genome organization, especially conserved terminal structures of ZIKV genome were characterized and compared with other mosquito-borne flaviviruses. It is suggested that major viral proteins of ZIKV share high structural and functional similarity with other known flaviviruses as shown by sequence comparison and prediction of functional motifs in viral proteins. Phylogenetic analysis demonstrated that all ZIKV strains circulating in the America form a unique clade within the Asian lineage. Furthermore, we identified a series of conserved amino acid residues that differentiate the Asian strains including the current circulating American strains from the ancient African strains. Overall, our findings provide an overview of ZIKV genome characterization and evolutionary dynamics in the Americas and point out critical clues for future virological and epidemiological studies.
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Affiliation(s)
- Qing Ye
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Zhong-Yu Liu
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Jian-Feng Han
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Tao Jiang
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China; State Key Laboratory of Pathogen and Biosecurity, Beijing 100071, China
| | - Xiao-Feng Li
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China; State Key Laboratory of Pathogen and Biosecurity, Beijing 100071, China
| | - Cheng-Feng Qin
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China; State Key Laboratory of Pathogen and Biosecurity, Beijing 100071, China.
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Ecuador Paraiso Escondido Virus, a New Flavivirus Isolated from New World Sand Flies in Ecuador, Is the First Representative of a Novel Clade in the Genus Flavivirus. J Virol 2015; 89:11773-85. [PMID: 26355096 PMCID: PMC4645344 DOI: 10.1128/jvi.01543-15] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 09/04/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED A new flavivirus, Ecuador Paraiso Escondido virus (EPEV), named after the village where it was discovered, was isolated from sand flies (Psathyromyia abonnenci, formerly Lutzomyia abonnenci) that are unique to the New World. This represents the first sand fly-borne flavivirus identified in the New World. EPEV exhibited a typical flavivirus genome organization. Nevertheless, the maximum pairwise amino acid sequence identity with currently recognized flaviviruses was 52.8%. Phylogenetic analysis of the complete coding sequence showed that EPEV represents a distinct clade which diverged from a lineage that was ancestral to the nonvectored flaviviruses Entebbe bat virus, Yokose virus, and Sokoluk virus and also the Aedes-associated mosquito-borne flaviviruses, which include yellow fever virus, Sepik virus, Saboya virus, and others. EPEV replicated in C6/36 mosquito cells, yielding high infectious titers, but failed to reproduce either in vertebrate cell lines (Vero, BHK, SW13, and XTC cells) or in suckling mouse brains. This surprising result, which appears to eliminate an association with vertebrate hosts in the life cycle of EPEV, is discussed in the context of the evolutionary origins of EPEV in the New World. IMPORTANCE The flaviviruses are rarely (if ever) vectored by sand fly species, at least in the Old World. We have identified the first representative of a sand fly-associated flavivirus, Ecuador Paraiso Escondido virus (EPEV), in the New World. EPEV constitutes a novel clade according to current knowledge of the flaviviruses. Phylogenetic analysis of the virus genome showed that EPEV roots the Aedes-associated mosquito-borne flaviviruses, including yellow fever virus. In light of this new discovery, the New World origin of EPEV is discussed together with that of the other flaviviruses.
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Raheel U, Jamal M, Zaidi NUSS. A Molecular Approach Designed to Limit the Replication of Mature DENV2 in Host Cells. Viral Immunol 2015; 28:378-84. [PMID: 26154890 DOI: 10.1089/vim.2015.0034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Dengue virus (DENV) is an arthropod-borne virus, which belongs to the Flaviviridae family, and completes its life cycle in two hosts: humans and mosquitoes. For DENV maturation, the surface pre-membrane (prM) protein is cleaved to form a mature membrane protein (M) by furin, which is a cellular enzyme subsequently releasing the mature virus from the host dendritic cell. The objective of the current study was to inhibit mature DENV isotype 2 (DENV2) by RNA-interference in a Vero-81 cell line. Mature DENV2 was propagated in and isolated from U937 cells expressing dendritic cell-specific intracellular adhesion molecule-3-grabbing non-integrin. Maturation of DENV2 was confirmed by Western blot analysis, where virus stock lacking prM was considered mature. Inhibition studies were carried out by transfection of Vero-81 cells with six synthetic siRNAs along with a control siRNA. Reduction in cellular DENV2 was observed also by focus-reduction assay, immunofluorescence assay (IFA), and real-time quantitative polymerase chain reaction (RT-qPCR). Cells transfected with DENV2SsiRNA2, which was targeting the structural region M of mature DENV2, was able to reduce DENV2 titer by up to 85% in focus reduction assays. A significant reduction in mature DENV2 RNA load was observed by RT-qPCR, confirming the previous findings. IFA also revealed reduced levels of cellular DENV2. These results demonstrated that mature DENV2 can be effectively inhibited by synthetic siRNA targeting the structural region of the genome. Mature DENV2 can be successfully inhibited by siRNAs, and specifically high knock-down efficiency is observed by siRNAs against M region of mature DENV2. This study shows that M represents a potential target for RNAi based inhibitory approaches.
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Affiliation(s)
- Ummar Raheel
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST) , Islamabad, Pakistan
| | - Muhsin Jamal
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST) , Islamabad, Pakistan
| | - Najam Us Sahar Sadaf Zaidi
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST) , Islamabad, Pakistan
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Dridi M, Rosseel T, Orton R, Johnson P, Lecollinet S, Muylkens B, Lambrecht B, Van Borm S. Next-generation sequencing shows West Nile virus quasispecies diversification after a single passage in a carrion crow (Corvus corone) in vivo infection model. J Gen Virol 2015; 96:2999-3009. [PMID: 26297666 DOI: 10.1099/jgv.0.000231] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
West Nile virus (WNV) occurs as a population of genetic variants (quasispecies) infecting a single animal. Previous low-resolution viral genetic diversity estimates in sampled wild birds and mosquitoes, and in multiple-passage adaptation studies in vivo or in cell culture, suggest that WNV genetic diversification is mostly limited to the mosquito vector. This study investigated genetic diversification of WNV in avian hosts during a single passage using next-generation sequencing. Wild-captured carrion crows were subcutaneously infected using a clonal Middle-East WNV. Blood samples were collected 2 and 4 days post-infection. A reverse-transcription (RT)-PCR approach was used to amplify the WNV genome directly from serum samples prior to next-generation sequencing resulting in an average depth of at least 700 × in each sample. Appropriate controls were sequenced to discriminate biologically relevant low-frequency variants from experimentally introduced errors. The WNV populations in the wild crows showed significant diversification away from the inoculum virus quasispecies structure. By contrast, WNV populations in intracerebrally infected day-old chickens did not diversify from that of the inoculum. Where previous studies concluded that WNV genetic diversification is only experimentally demonstrated in its permissive insect vector species, we have experimentally shown significant diversification of WNV populations in a wild bird reservoir species.
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Affiliation(s)
- M Dridi
- Operational Direction of Viral Diseases, Veterinary and Agrochemical Research Center (CODA-CERVA-VAR), 99 Groeselenberg, 1180 Brussels, Belgium
| | - T Rosseel
- Operational Direction of Viral Diseases, Veterinary and Agrochemical Research Center (CODA-CERVA-VAR), 99 Groeselenberg, 1180 Brussels, Belgium
| | - R Orton
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G61 1QH, UK
| | - P Johnson
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - S Lecollinet
- UMR1161 Virologie INRA, ANSES, ENVA, French Agency for Food, Environmental and Occupational Health & Safety (Anses), 23 avenue du Général De Gaulle, 94706 Maisons-Alfort, France
| | - B Muylkens
- Integrated Veterinary Research Unit, University of Namur, 61 rue de Bruxelles, 5000 Namur, Belgium
| | - B Lambrecht
- Operational Direction of Viral Diseases, Veterinary and Agrochemical Research Center (CODA-CERVA-VAR), 99 Groeselenberg, 1180 Brussels, Belgium
| | - S Van Borm
- Operational Direction of Viral Diseases, Veterinary and Agrochemical Research Center (CODA-CERVA-VAR), 99 Groeselenberg, 1180 Brussels, Belgium
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Brinton MA, Basu M. Functions of the 3' and 5' genome RNA regions of members of the genus Flavivirus. Virus Res 2015; 206:108-19. [PMID: 25683510 DOI: 10.1016/j.virusres.2015.02.006] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 02/04/2015] [Indexed: 11/26/2022]
Abstract
The positive sense genomes of members of the genus Flavivirus in the family Flaviviridae are ∼ 11 kb in length and have a 5' type I cap but no 3' poly-A. The 3' and 5' terminal regions contain short conserved sequences that are proposed to be repeated remnants of an ancient sequence. However, the functions of most of these conserved sequences have not yet been determined. The terminal regions of the genome also contain multiple conserved RNA structures. Functional data for many of these structures have been obtained. Three sets of complementary 3' and 5' terminal region sequences, some of which are located in conserved RNA structures, interact to form a panhandle structure that is required for initiation of minus strand RNA synthesis with the 5' terminal structure functioning as the promoter. How the switch from the terminal RNA structure base pairing to the long distance RNA-RNA interaction is triggered and regulated is not well understood but evidence suggests involvement of a cell protein binding to three sites on the 3' terminal RNA structures and a cis-acting metastable 3' RNA element in the 3' terminal RNA structure. Cell proteins may also be involved in facilitating exponential replication of nascent genomic RNA within replication vesicles at later times of the infection cycle. Other conserved RNA structures and/or sequences in the 3' and 5' terminal regions have been proposed to regulate genome translation. Additional functions of the 3' and 5' terminal sequences have also been reported.
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Affiliation(s)
- Margo A Brinton
- Department of Biology, Georgia State University, Atlanta, GA, USA.
| | - Mausumi Basu
- Department of Biology, Georgia State University, Atlanta, GA, USA
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Kasprzak WK, Shapiro BA. MPGAfold in dengue secondary structure prediction. Methods Mol Biol 2014; 1138:199-224. [PMID: 24696339 PMCID: PMC6354254 DOI: 10.1007/978-1-4939-0348-1_13] [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] [Indexed: 06/16/2024]
Abstract
This chapter presents the computational prediction of the secondary structures within the 5' and 3' untranslated regions of the dengue virus serotype 2 (DENV2), with the focus on the conformational prediction of the two dumbbell-like structures, 5' DB and 3' DB, found in the core region of the 3' untranslated region of DENV2. For secondary structure prediction purposes we used a 719 nt-long subgenomic RNA construct from DENV2, which we refer to as the minigenome. The construct combines the 5'-most 226 nt from the 5' UTR and a fragment of the capsid coding region with the last 42 nt from the non-structural protein NS5 coding region and the 451 nt of the 3' UTR. This minigenome has been shown to contain the elements needed for translation, as well as negative strand RNA synthesis. We present the Massively Parallel Genetic Algorithm MPGAfold, a non-deterministic algorithm, that was used to predict the secondary structures of the DENV2 719 nt long minigenome construct, as well as our computational workbench called StructureLab that was used to interactively explore the solution spaces produced by MPGAfold. The MPGAfold algorithm is first introduced at the conceptual level. Then specific parameters guiding its performance are discussed and illustrated with a representative selection of the results from the study. Plots of the solution spaces generated by MPGAfold illustrate the algorithm, while selected secondary structures focus on variable formation of the dumbbell structures and other identified structural motifs. They also serve as illustrations of some of the capabilities of the StructureLab workbench. Results of the computational structure determination calculations are discussed and compared to the experimental data.
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19
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Replication cycle and molecular biology of the West Nile virus. Viruses 2013; 6:13-53. [PMID: 24378320 PMCID: PMC3917430 DOI: 10.3390/v6010013] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Revised: 12/12/2013] [Accepted: 12/12/2013] [Indexed: 12/27/2022] Open
Abstract
West Nile virus (WNV) is a member of the genus Flavivirus in the family Flaviviridae. Flaviviruses replicate in the cytoplasm of infected cells and modify the host cell environment. Although much has been learned about virion structure and virion-endosomal membrane fusion, the cell receptor(s) used have not been definitively identified and little is known about the early stages of the virus replication cycle. Members of the genus Flavivirus differ from members of the two other genera of the family by the lack of a genomic internal ribosomal entry sequence and the creation of invaginations in the ER membrane rather than double-membrane vesicles that are used as the sites of exponential genome synthesis. The WNV genome 3' and 5' sequences that form the long distance RNA-RNA interaction required for minus strand initiation have been identified and contact sites on the 5' RNA stem loop for NS5 have been mapped. Structures obtained for many of the viral proteins have provided information relevant to their functions. Viral nonstructural protein interactions are complex and some may occur only in infected cells. Although interactions between many cellular proteins and virus components have been identified, the functions of most of these interactions have not been delineated.
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Identification of cis-acting nucleotides and a structural feature in West Nile virus 3'-terminus RNA that facilitate viral minus strand RNA synthesis. J Virol 2013; 87:7622-36. [PMID: 23637406 DOI: 10.1128/jvi.00212-13] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The 3'-terminal nucleotides (nt) of West Nile virus (WNV) genomic RNA form a penultimate 16-nt small stem-loop (SSL) and an 80-nt terminal stem-loop (SL). These RNA structures are conserved in divergent flavivirus genomes. A previous in vitro study using truncated WNV 3' RNA structures predicted a putative tertiary interaction between the 5' side of the 3'-terminal SL and the loop of the SSL. Although substitution or deletion of the 3' G (nt 87) within the SSL loop, which forms the only G-C pair in the predicted tertiary interaction, in a WNV infectious clone was lethal, a finding consistent with the involvement in a functionally relevant pseudoknot interaction, extensive mutagenesis of nucleotides in the terminal SL did not identify a cis-acting pairing partner for this SSL 3' G. However, both the sequence and the structural context of two adjacent base pairs flanked by symmetrical internal loops in the 3'-terminal SL were shown to be required for efficient viral RNA replication. Nuclear magnetic resonance analysis confirmed the predicted SSL and SL structures but not the tertiary interaction. The SSL was previously reported to contain one of three eEF1A binding sites, and G87 in the SSL loop was shown to be involved in eEF1A binding. The nucleotides at the bottom part of the 3'-terminal SL switch between 3' RNA-RNA and 3'-5' RNA-RNA interactions. The data suggest that interaction of the 3' SL RNA with eEF1A at three sites and a unique metastable structural feature may participate in regulating structural changes in the 3'-terminal SL.
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Novel cis-acting element within the capsid-coding region enhances flavivirus viral-RNA replication by regulating genome cyclization. J Virol 2013; 87:6804-18. [PMID: 23576500 DOI: 10.1128/jvi.00243-13] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
cis-Acting elements in the viral genome RNA (vRNA) are essential for the translation, replication, and/or encapsidation of RNA viruses. In this study, a novel conserved cis-acting element was identified in the capsid-coding region of mosquito-borne flavivirus. The downstream of 5' cyclization sequence (5'CS) pseudoknot (DCS-PK) element has a three-stem pseudoknot structure, as demonstrated by structure prediction and biochemical analysis. Using dengue virus as a model, we show that DCS-PK enhances vRNA replication and that its function depends on its secondary structure and specific primary sequence. Mutagenesis revealed that the highly conserved stem 1 and loop 2, which are involved in potential loop-helix interactions, are crucial for DCS-PK function. A predicted loop 1-stem 3 base triple interaction is important for the structural stability and function of DCS-PK. Moreover, the function of DCS-PK depends on its position relative to the 5'CS, and the presence of DCS-PK facilitates the formation of 5'-3' RNA complexes. Taken together, our results reveal that the cis-acting element DCS-PK enhances vRNA replication by regulating genome cyclization, and DCS-PK might interplay with other cis-acting elements to form a functional vRNA cyclization domain, thus playing critical roles during the flavivirus life cycle and evolution.
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Tumban E, Maes NE, Schirtzinger EE, Young KI, Hanson CT, Whitehead SS, Hanley KA. Replacement of conserved or variable sequences of the mosquito-borne dengue virus 3' UTR with homologous sequences from Modoc virus does not change infectivity for mosquitoes. J Gen Virol 2012; 94:783-788. [PMID: 23255623 DOI: 10.1099/vir.0.046664-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The genus Flavivirus includes both vector-borne and no known vector (NKV) species, but the molecular determinants of transmission mode are not known. Conserved sequence differences between the two groups occur in 5' and 3' UTRs. To investigate the impact of these differences on transmission, chimeric genomes were generated, in which UTRs, UTRs+capsid, or the upper 3' UTR stem-loop of mosquito-borne dengue virus (DENV) were replaced with homologous regions from NKV Modoc virus (MODV); the conserved pentanucleotide sequence (CPS) was also deleted from the DENV genome. Virus was not recovered following transfection of these genomes in three different cell types. However, DENV genomes in which the CPS or variable region (VR) of the 3' UTR were replaced with MODV sequences were recovered and infected Aedes aegypti mosquitoes with similar efficiencies to DENV. These results demonstrate that neither vector-borne CPS nor VR is required for vector-borne transmission.
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Affiliation(s)
- Ebenezer Tumban
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, Albuquerque, NM 87131, USA.,Molecular Biology Program, New Mexico State University, Las Cruces, NM 88003, USA
| | - Nyree E Maes
- Molecular Biology Program, New Mexico State University, Las Cruces, NM 88003, USA
| | - Erin E Schirtzinger
- Department of Biology, New Mexico State University, Las Cruces, NM 88003, USA
| | - Katherine I Young
- Department of Biology, New Mexico State University, Las Cruces, NM 88003, USA
| | - Christopher T Hanson
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD 20892, USA
| | - Stephen S Whitehead
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kathryn A Hanley
- Department of Biology, New Mexico State University, Las Cruces, NM 88003, USA.,Molecular Biology Program, New Mexico State University, Las Cruces, NM 88003, USA
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Bahuon C, Desprès P, Pardigon N, Panthier JJ, Cordonnier N, Lowenski S, Richardson J, Zientara S, Lecollinet S. IS-98-ST1 West Nile virus derived from an infectious cDNA clone retains neuroinvasiveness and neurovirulence properties of the original virus. PLoS One 2012; 7:e47666. [PMID: 23110088 PMCID: PMC3479121 DOI: 10.1371/journal.pone.0047666] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Accepted: 09/14/2012] [Indexed: 01/25/2023] Open
Abstract
Infectious clones of West Nile virus (WNV) have previously been generated and used to decipher the role of viral proteins in WNV virulence. The majority of molecular clones obtained to date have been derived from North American, Australian, or African isolates. Here, we describe the construction of an infectious cDNA clone of a Mediterranean WNV strain, IS-98-ST1. We characterized the biological properties of the recovered recombinant virus in cell culture and in mice. The growth kinetics of recombinant and parental WNV were similar in Vero cells. Moreover, the phenotype of recombinant and parental WNV was indistinguishable as regards viremia, viral load in the brain, and mortality in susceptible and resistant mice. Finally, the pathobiology of the infectious clone was examined in embryonated chicken eggs. The capacity of different WNV strains to replicate in embryonated chicken eggs closely paralleled their ability to replicate in mice, suggesting that inoculation of embryonated chicken eggs could provide a practical in vivo model for the study of WNV pathogenesis. In conclusion, the IS-98-ST1 infectious clone will allow assessment of the impact of selected mutations and novel genomic changes appearing in emerging European strains pathogenicity and endemic or epidemic potential. This will be invaluable in the context of an increasing number of outbreaks and enhanced severity of infections in the Mediterranean basin and Eastern Europe.
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Affiliation(s)
- Céline Bahuon
- UMR 1161 VIROLOGIE ANSES-INRA-ENVA, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Maisons-Alfort, France.
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24
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Zaidi NUSS, Kanwal N, Ghazal A, Fatima K, Javed F, Qadri I. Phylogenetic and structural analysis of HCV nonstructural protein 4A from Pakistani patients. Virus Genes 2011; 44:1-7. [PMID: 21948004 DOI: 10.1007/s11262-011-0672-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Accepted: 09/08/2011] [Indexed: 11/28/2022]
Abstract
Hepatitis C virus nonstructural protein, NS4A, is a small protein comprising of about 54 amino acids. Despite its small size, it plays key role in many viral and cellular functions. The most important of which is its role as the co-factor of viral serine protease and helicase (NS3). Our study examines the phylogenetic and structural analysis of this coding region after isolation from Pakistani HCV patient samples. Phylogenetic analysis of the gene revealed that Pakistani 3a HCV strains do not show significant divergence from those reported from the rest of the world. The findings of this study also depict that NS4A sequence is conserved within genotypes, whereas it shows variations among different genotypes. While predicting the tertiary structure of the protein two important mutations (H28Y & E32G) were observed when comparing the Pakistani sequences with that of a reference HCV (genotype 3a) strain NZL (D17763). These mutations were observed in the central domain of NS4A which is responsible for interaction with NS3. Taken together, these mutations within the NS4A coding region can play an important role in the binding capacity of NS4A with HCV serine protease NS3.
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Affiliation(s)
- Najam us Sahar Sadaf Zaidi
- NUST Center of Virology & Immunology, National University of Sciences & Technology, Islamabad, Pakistan.
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25
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Manzano M, Reichert ED, Polo S, Falgout B, Kasprzak W, Shapiro BA, Padmanabhan R. Identification of cis-acting elements in the 3'-untranslated region of the dengue virus type 2 RNA that modulate translation and replication. J Biol Chem 2011; 286:22521-34. [PMID: 21515677 PMCID: PMC3121397 DOI: 10.1074/jbc.m111.234302] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2011] [Revised: 04/21/2011] [Indexed: 12/30/2022] Open
Abstract
Using the massively parallel genetic algorithm for RNA folding, we show that the core region of the 3'-untranslated region of the dengue virus (DENV) RNA can form two dumbbell structures (5'- and 3'-DBs) of unequal frequencies of occurrence. These structures have the propensity to form two potential pseudoknots between identical five-nucleotide terminal loops 1 and 2 (TL1 and TL2) and their complementary pseudoknot motifs, PK2 and PK1. Mutagenesis using a DENV2 replicon RNA encoding the Renilla luciferase reporter indicated that all four motifs and the conserved sequence 2 (CS2) element within the 3'-DB are important for replication. However, for translation, mutation of TL1 alone does not have any effect; TL2 mutation has only a modest effect in translation, but translation is reduced by ∼60% in the TL1/TL2 double mutant, indicating that TL1 exhibits a cooperative synergy with TL2 in translation. Despite the variable contributions of individual TL and PK motifs in translation, WT levels are achieved when the complementarity between TL1/PK2 and TL2/PK1 is maintained even under conditions of inhibition of the translation initiation factor 4E function mediated by LY294002 via a noncanonical pathway. Taken together, our results indicate that the cis-acting RNA elements in the core region of DENV2 RNA that include two DB structures are required not only for RNA replication but also for optimal translation.
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Affiliation(s)
- Mark Manzano
- From the Department of Microbiology and Immunology, Georgetown University School of Medicine, Washington, D. C. 20057
| | - Erin D. Reichert
- From the Department of Microbiology and Immunology, Georgetown University School of Medicine, Washington, D. C. 20057
| | - Stephanie Polo
- the Center for Biologics Evaluation and Review, Food and Drug Administration, Bethesda, Maryland 20892
| | - Barry Falgout
- the Center for Biologics Evaluation and Review, Food and Drug Administration, Bethesda, Maryland 20892
| | | | - Bruce A. Shapiro
- the Center for Cancer Research Nanobiology Program, NCI-Frederick, National Institutes of Health, Frederick, Maryland 21702
| | - Radhakrishnan Padmanabhan
- From the Department of Microbiology and Immunology, Georgetown University School of Medicine, Washington, D. C. 20057
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26
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NF90 binds the dengue virus RNA 3' terminus and is a positive regulator of dengue virus replication. PLoS One 2011; 6:e16687. [PMID: 21386893 PMCID: PMC3046124 DOI: 10.1371/journal.pone.0016687] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2010] [Accepted: 12/22/2010] [Indexed: 12/03/2022] Open
Abstract
Background Viral RNA translation and replication are regulated by sequence and structural elements in the 5′ and 3′ untranslated regions (UTR) and by host cell and/or viral proteins that bind them. Dengue virus has a single-stranded RNA genome with positive polarity, a 5′ m7GpppG cap, and a conserved 3′-terminal stem loop (SL) that is linked to proposed functions in viral RNA transcription and translation. Mechanisms explaining the contributions of host proteins to viral RNA translation and replication are poorly defined, yet understanding host protein-viral RNA interactions may identify new targets for therapeutic intervention. This study was directed at identifying functionally significant host proteins that bind the conserved dengue virus RNA 3′ terminus. Methodology/Principal Findings Proteins eluted from a dengue 3′ SL RNA affinity column at increasing ionic strength included two with double-strand RNA binding motifs (NF90/DRBP76 and DEAH box polypeptide 9/RNA helicase A (RHA)), in addition to NF45, which forms a heterodimer with NF90. Although detectable NF90 and RHA proteins localized to the nucleus of uninfected cells, immunofluorescence revealed cytoplasmic NF90 in dengue virus-infected cells, leading us to hypothesize that NF90 has a functional role(s) in dengue infections. Cells depleted of NF90 were used to quantify viral RNA transcript levels and production of infectious dengue virus. NF90 depletion was accompanied by a 50%-70% decrease in dengue RNA levels and in production of infectious viral progeny. Conclusions/Significance The results indicate that NF90 interacts with the 3′ SL structure of the dengue RNA and is a positive regulator of dengue virus replication. NF90 depletion diminished the production of infectious dengue virus by more than 50%, which may have important significance for identifying therapeutic targets to limit a virus that threatens more than a billion people worldwide.
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27
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Basu M, Brinton MA. West Nile virus (WNV) genome RNAs with up to three adjacent mutations that disrupt long distance 5'-3' cyclization sequence basepairs are viable. Virology 2011; 412:220-32. [PMID: 21292293 DOI: 10.1016/j.virol.2011.01.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2010] [Revised: 11/19/2010] [Accepted: 01/06/2011] [Indexed: 12/30/2022]
Abstract
Mosquito-borne flavivirus genomes contain conserved 5' and 3' cyclization sequences (CYC) that facilitate long distance RNA-RNA interactions. In previous studies, flavivirus replicon RNA replication was completely inhibited by single or multiple mismatching CYC nt substitutions. In the present study, full-length WNV genomes with one, two or three mismatching CYC substitutions showed reduced replication efficiencies but were viable and generated revertants with increased replication efficiency. Several different three adjacent mismatching CYC substitution mutant RNAs were rescued by a second site mutation that created an additional basepair (nts 147-10913) on the internal genomic side of the 5'-3' CYC. The finding that full-length genomes with up to three mismatching CYC mutations are viable and can be rescued by a single nt spontaneous mutation indicates that more than three adjacent CYC basepair substitutions would be required to increase the safety of vaccine genomes by creating mismatches in inter-genomic recombinants.
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Affiliation(s)
- Mausumi Basu
- Department of Biology, Georgia State University, Atlanta, GA 30302, USA
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28
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Tumban E, Mitzel DN, Maes NE, Hanson CT, Whitehead SS, Hanley KA. Replacement of the 3' untranslated variable region of mosquito-borne dengue virus with that of tick-borne Langat virus does not alter vector specificity. J Gen Virol 2011; 92:841-8. [PMID: 21216984 DOI: 10.1099/vir.0.026997-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The four major flavivirus clades are transmitted by mosquitoes, ticks, directly between vertebrates or directly between arthropods, respectively, but the molecular determinants of mode of transmission in flaviviruses are unknown. To assess the role of the UTRs in transmission, we generated chimeric genomes in which the 5' UTR, capsid and/or 3' UTR of mosquito-borne dengue virus serotype 4 (rDENV-4) were replaced, separately or in combination, with those of tick-borne Langat virus (rLGTV). None of the chimeric genomes yielded detectable virus following transfection. Replacement of the variable region (VR) in the rDENV-4 3' UTR with that of rLGTV generated virus rDENV-4-rLGTswapVR, which showed lower replication than its wild-type parents in mammalian but not mosquito cells in culture and was able to infect mosquitoes in vivo. Neither rDENV-4 nor rDENV-4-rLGTswapVR could infect larval Ixodes scapularis ticks immersed in virus, while rLGTV was highly infectious via this route.
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Affiliation(s)
- Ebenezer Tumban
- Molecular Biology Program, New Mexico State University, Las Cruces, NM 88003, USA
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29
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Zhang B, Dong H, Ye H, Tilgner M, Shi PY. Genetic analysis of West Nile virus containing a complete 3'CSI RNA deletion. Virology 2010; 408:138-45. [PMID: 20965539 DOI: 10.1016/j.virol.2010.09.033] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2010] [Revised: 09/27/2010] [Accepted: 09/29/2010] [Indexed: 10/18/2022]
Abstract
We report a genetic interplay among three pairs of long-distance RNA interactions that are involved in West Nile virus (WNV) genome cyclization and replication: 5'CS/3'CSI (conserved sequence), 5'UAR/3'UAR (upstream AUG region), and 5'DAR/3'DAR (downstream AUG region). Deletion of the complete 3'CSI element is lethal for WNV replication, but the replication of the 3'CSI deletion virus could be rescued by second site mutations. Functional analysis, using a genome-length RNA and replicon, mapped the compensatory mutations to the 5'UAR/3'UAR and 5'DAR/3'DAR regions. Biochemical analysis showed that the 3'CSI deletion abolished the 5' and 3' RNA interaction of the genome; the compensatory mutations could partially restore the 5' and 3' genome cyclization. These results demonstrate, for the first time, that a flavivirus without 3'CSI could restore genome cyclization and viral replication through enhancement of the 5'UAR/3'UAR and 5'DAR/3'DAR interactions.
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Affiliation(s)
- Bo Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
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30
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3' cis-acting elements that contribute to the competence and efficiency of Japanese encephalitis virus genome replication: functional importance of sequence duplications, deletions, and substitutions. J Virol 2009; 83:7909-30. [PMID: 19494005 DOI: 10.1128/jvi.02541-08] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The positive-strand RNA genome of Japanese encephalitis virus (JEV) terminates in a highly conserved 3'-noncoding region (3'NCR) of six domains (V, X, I, II-1, II-2, and III in the 5'-to-3' direction). By manipulating the JEV genomic RNA, we have identified important roles for RNA elements present within the 574-nucleotide 3'NCR in viral replication. The two 3'-proximal domains (II-2 and III) were sufficient for RNA replication and virus production, whereas the remaining four (V, X, I, and II-1) were dispensable for RNA replication competence but required for maximal replication efficiency. Surprisingly, a lethal mutant lacking all of the 3'NCR except domain III regained viability through pseudoreversion by duplicating an 83-nucleotide sequence from the 3'-terminal region of the viral open reading frame. Also, two viable mutants displayed severe genetic instability; these two mutants rapidly developed 12 point mutations in domain II-2 in the mutant lacking domains V, X, I, and II-1 and showed the duplication of seven upstream sequences of various sizes at the junction between domains II-1 and II-2 in the mutant lacking domains V, X, and I. In all cases, the introduction of these spontaneous mutations led to an increase in RNA production that paralleled the level of protein accumulation and virus yield. Interestingly, the mutant lacking domains V, X, I, and II-1 was able to replicate in hamster BHK-21 and human neuroblastoma SH-SY5Y cells but not in mosquito C6/36 cells, indicating a cell type-specific restriction of its viral replication. Thus, our findings provide the basis for a detailed map of the 3' cis-acting elements in JEV genomic RNA, which play an essential role in viral replication. They also provide experimental evidence for the function of 3' direct repeat sequences and suggest possible mechanisms for the emergence of these sequences in the 3'NCR of JEV and perhaps in other flaviviruses.
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31
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Grinev A, Daniel S, Stramer S, Rossmann S, Caglioti S, Rios M. Genetic variability of West Nile virus in US blood donors, 2002-2005. Emerg Infect Dis 2008; 14:436-44. [PMID: 18325259 PMCID: PMC2570840 DOI: 10.3201/eid1403.070463] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
This virus is diverging from precursor isolates as its geographic distribution expands. West Nile virus (WNV) was detected in the United States in 1999, has reoccurred every summer since, and has become endemic. Transfusion transmission was documented in 2002, and screening of blood donations for WNV began in 2003. We investigated genetic variation of WNV in human isolates obtained from specimens collected from 30 infected blood donors who tested positive for WNV RNA during 2002–2005. Complete genomic sequences of 8 isolates and structural gene sequences from 22 additional isolates were analyzed. We found some genetic diversity in isolates from different geographic regions and genetic divergence from reported sequences from epidemics in 1999–2001. Nucleotide divergence of structural genes showed a small increase from 2002 (0.18%) to 2005 (0.37%), suggesting absence of strong selective pressure and limited genetic evolution of WNV during that period. Nevertheless, WNV has continued to diverge from precursor isolates as geographic distribution of the virus has expanded.
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32
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Dong H, Zhang B, Shi PY. Terminal structures of West Nile virus genomic RNA and their interactions with viral NS5 protein. Virology 2008; 381:123-35. [PMID: 18799181 DOI: 10.1016/j.virol.2008.07.040] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2008] [Revised: 07/23/2008] [Accepted: 07/30/2008] [Indexed: 12/11/2022]
Abstract
Genome cyclization is essential for flavivirus replication. We used RNases to probe the structures formed by the 5'-terminal 190 nucleotides and the 3'-terminal 111 nucleotides of the West Nile virus (WNV) genomic RNA. When analyzed individually, the two RNAs adopt stem-loop structures as predicted by the thermodynamic-folding program. However, when mixed together, the two RNAs form a duplex that is mediated through base-pairings of two sets of RNA elements (5'CS/3'CSI and 5'UAR/3'UAR). Formation of the RNA duplex facilitates a conformational change that leaves the 3'-terminal nucleotides of the genome (position -8 to -16) to be single-stranded. Viral NS5 binds specifically to the 5'-terminal stem-loop (SL1) of the genomic RNA. The 5'SL1 RNA structure is essential for WNV replication. The study has provided further evidence to suggest that flavivirus genome cyclization and NS5/5'SL1 RNA interaction facilitate NS5 binding to the 3' end of the genome for the initiation of viral minus-strand RNA synthesis.
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Affiliation(s)
- Hongping Dong
- Wadsworth Center, New York State Department of Health, Albany, New York 12201, USA
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33
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Mutation of mapped TIA-1/TIAR binding sites in the 3' terminal stem-loop of West Nile virus minus-strand RNA in an infectious clone negatively affects genomic RNA amplification. J Virol 2008; 82:10657-70. [PMID: 18768985 DOI: 10.1128/jvi.00991-08] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Previous data showed that the cellular proteins TIA-1 and TIAR bound specifically to the West Nile virus 3' minus-strand stem-loop [WNV3'(-)SL] RNA (37) and colocalized with flavivirus replication complexes in WNV- and dengue virus-infected cells (21). In the present study, the sites on the WNV3'(-)SL RNA required for efficient in vitro T-cell intracellular antigen-related (TIAR) and T-cell intracellular antigen-1 (TIA-1) protein binding were mapped to short AU sequences (UAAUU) located in two internal loops of the WNV3'(-)SL RNA structure. Infectious clone RNAs with all or most of the binding site nucleotides in one of the 3' (-)SL loops deleted or substituted did not produce detectable virus after transfection or subsequent passage. With one exception, deletion/mutation of a single terminal nucleotide in one of the binding sequences had little effect on the efficiency of protein binding or virus production, but mutation of a nucleotide in the middle of a binding sequence reduced both the in vitro protein binding efficiency and virus production. Plaque size, intracellular genomic RNA levels, and virus production progressively decreased with decreasing in vitro TIAR/TIA-1 binding activity, but the translation efficiency of the various mutant RNAs was similar to that of the parental RNA. Several of the mutant RNAs that inefficiently interacted with TIAR/TIA-1 in vitro rapidly reverted in vivo, indicating that they could replicate at a low level and suggesting that an interaction between TIAR/TIA-1 and the viral 3'(-)SL RNA is not required for initial low-level symmetric RNA replication but instead facilitates the subsequent asymmetric amplification of genome RNA from the minus-strand template.
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34
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Groenenboom MAC, Hogeweg P. The dynamics and efficacy of antiviral RNA silencing: A model study. BMC SYSTEMS BIOLOGY 2008; 2:28. [PMID: 18366769 PMCID: PMC2373878 DOI: 10.1186/1752-0509-2-28] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2007] [Accepted: 03/26/2008] [Indexed: 11/10/2022]
Abstract
Background Mathematical modeling is important to provide insight in the complicated pathway of RNA silencing. RNA silencing is an RNA based mechanism that is widely used by eukaryotes to fight viruses, and to control gene expression. Results We here present the first mathematical model that combines viral growth with RNA silencing. The model involves a plus-strand RNA virus that replicates through a double-strand RNA intermediate. The model of the RNA silencing pathway consists of cleavage of viral RNA into siRNA by Dicer, target cleavage of viral RNA via the RISC complex, and a secondary response. We found that, depending on the strength of the silencing response, different viral growth patterns can occur. Silencing can decrease viral growth, cause oscillations, or clear the virus completely. Our model can explain various observed phenomena, even when they seem contradictory at first: the diverse responses to the removal of RNA dependent RNA polymerase; different viral growth curves; and the great diversity in observed siRNA ratios. Conclusion The model presented here is an important step in the understanding of the natural functioning of RNA silencing in viral infections.
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Affiliation(s)
- Marian A C Groenenboom
- Theoretical Biology and Bioinformatics, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands.
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35
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Alvarez DE, Filomatori CV, Gamarnik AV. Functional analysis of dengue virus cyclization sequences located at the 5' and 3'UTRs. Virology 2008; 375:223-35. [PMID: 18289628 DOI: 10.1016/j.virol.2008.01.014] [Citation(s) in RCA: 113] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2007] [Revised: 12/30/2007] [Accepted: 01/12/2008] [Indexed: 11/25/2022]
Abstract
Flavivirus RNA replication involves cyclization of the viral genome. A model for this process includes a promoter element at the 5' end of the genome and long-range RNA-RNA interactions. Two pairs of complementary sequences present at the ends of the viral RNA, known as 5'-3'CS and 5'-3'UAR, have been proposed to be involved in dengue virus genome cyclization. The requirement of 5'-3'CS complementarity for viral replication has been experimentally demonstrated for dengue and other mosquito borne flaviviruses. Here, we performed a functional analysis to study the role of 5'-3'UAR sequences using genomic and subgenomic dengue virus RNAs. We found that single mutations disrupting 5'-3' complementarity greatly compromised viral RNA synthesis. Although in most of the cases incorporation of compensatory mutations re-established viral RNA replication, certain nucleotides were found to be involved in alternative secondary structures also important for viral replication. In addition, mutations within 5' or 3'UAR in the context of an infectious dengue virus RNA resulted in spontaneous mutations that restored UAR base pairings. Together, we propose that specific UAR nucleotides as well as 5'-3'UAR complementarity constitute cis-acting signals involved in amplification of the dengue virus genome.
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Affiliation(s)
- Diego E Alvarez
- Fundación Instituto Leloir, Avenida Patricias Argentinas 435, Buenos Aires 1405, Argentina
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36
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Davis WG, Blackwell JL, Shi PY, Brinton MA. Interaction between the cellular protein eEF1A and the 3'-terminal stem-loop of West Nile virus genomic RNA facilitates viral minus-strand RNA synthesis. J Virol 2007; 81:10172-87. [PMID: 17626087 PMCID: PMC2045417 DOI: 10.1128/jvi.00531-07] [Citation(s) in RCA: 127] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
RNase footprinting and nitrocellulose filter binding assays were previously used to map one major and two minor binding sites for the cell protein eEF1A on the 3'(+) stem-loop (SL) RNA of West Nile virus (WNV) (3). Base substitutions in the major eEF1A binding site or adjacent areas of the 3'(+) SL were engineered into a WNV infectious clone. Mutations that decreased, as well as ones that increased, eEF1A binding in in vitro assays had a negative effect on viral growth. None of these mutations affected the efficiency of translation of the viral polyprotein from the genomic RNA, but all of the mutations that decreased in vitro eEF1A binding to the 3' SL RNA also decreased viral minus-strand RNA synthesis in transfected cells. Also, a mutation that increased the efficiency of eEF1A binding to the 3' SL RNA increased minus-strand RNA synthesis in transfected cells, which resulted in decreased synthesis of genomic RNA. These results strongly suggest that the interaction between eEF1A and the WNV 3' SL facilitates viral minus-strand synthesis. eEF1A colocalized with viral replication complexes (RC) in infected cells and antibody to eEF1A coimmunoprecipitated viral RC proteins, suggesting that eEF1A facilitates an interaction between the 3' end of the genome and the RC. eEF1A bound with similar efficiencies to the 3'-terminal SL RNAs of four divergent flaviviruses, including a tick-borne flavivirus, and colocalized with dengue virus RC in infected cells. These results suggest that eEF1A plays a similar role in RNA replication for all flaviviruses.
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Affiliation(s)
- William G Davis
- Department of Biology, Georgia State University, Atlanta, GA 30302-4010, USA
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37
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Silva PAGC, Molenkamp R, Dalebout TJ, Charlier N, Neyts JH, Spaan WJM, Bredenbeek PJ. Conservation of the pentanucleotide motif at the top of the yellow fever virus 17D 3' stem-loop structure is not required for replication. J Gen Virol 2007; 88:1738-1747. [PMID: 17485534 DOI: 10.1099/vir.0.82811-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The pentanucleotide (PN) sequence 5'-CACAG-3' at the top of the 3' stem-loop structure of the flavivirus genome is well conserved in the arthropod-borne viruses but is more variable in flaviviruses with no known vector. In this study, the sequence requirements of the PN motif for yellow fever virus 17D (YFV) replication were determined. In general, individual mutations at either the second, third or fourth positions were tolerated and resulted in replication-competent virus. Mutations at the fifth position were lethal. Base pairing of the nucleotide at the first position of the PN motif and a nucleotide four positions downstream of the PN (ninth position) was a major determinant for replication. Despite the fact that the majority of the PN mutants were able to replicate efficiently, they were outcompeted by parental YFV-17D virus following repeated passages in double-infected cell cultures. Surprisingly, some of the virus mutants at the first and/or the ninth position that maintained the possibility of forming a base pair were found to have a similar fitness to YFV-17D under these conditions. Overall, these experiments suggest that YFV is less dependent on sequence conservation of the PN motif for replication in animal cells than West Nile virus. However, in animal cell culture, YFV has a preference for the wt CACAG PN sequence. The molecular mechanisms behind this preference remain to be elucidated.
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Affiliation(s)
- Patrícia A G C Silva
- Department of Medical Microbiology, Leiden University Medical Center, PO Box 9600, NL-2300 RC Leiden, The Netherlands
| | - Richard Molenkamp
- Department of Medical Microbiology, Leiden University Medical Center, PO Box 9600, NL-2300 RC Leiden, The Netherlands
| | - Tim J Dalebout
- Department of Medical Microbiology, Leiden University Medical Center, PO Box 9600, NL-2300 RC Leiden, The Netherlands
| | - Nathalie Charlier
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, B-3000 Leuven, Belgium
| | - Johan H Neyts
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, B-3000 Leuven, Belgium
| | - Willy J M Spaan
- Department of Medical Microbiology, Leiden University Medical Center, PO Box 9600, NL-2300 RC Leiden, The Netherlands
| | - Peter J Bredenbeek
- Department of Medical Microbiology, Leiden University Medical Center, PO Box 9600, NL-2300 RC Leiden, The Netherlands
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38
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Davis CT, Galbraith SE, Zhang S, Whiteman MC, Li L, Kinney RM, Barrett ADT. A combination of naturally occurring mutations in North American West Nile virus nonstructural protein genes and in the 3' untranslated region alters virus phenotype. J Virol 2007; 81:6111-6. [PMID: 17376926 PMCID: PMC1900292 DOI: 10.1128/jvi.02387-06] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We previously reported mutations in North American West Nile viruses (WNVs) with a small-plaque (sp), temperature-sensitive (ts), and/or mouse-attenuated (att) phenotype. Using an infectious clone, site-directed mutations and 3' untranslated region (3'UTR) exchanges were introduced into the WNV NY99 genome. Characterization of mutants demonstrated that a combination of mutations involving the NS4B protein (E249G) together with either a mutation in the NS5 protein (A804V) or three mutations in the 3'UTR (A10596G, C10774U, A10799G) produced sp, ts, and/or att variants. These results suggested that the discovery of North American WNV-phenotypic variants is rare because of the apparent requirement of concurrent polygenic mutations.
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Affiliation(s)
- C Todd Davis
- Department of Pathology, University of Texas Medical Branch, 301 University Blvd., Galveston, TX 77555, USA
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39
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Romero TA, Tumban E, Jun J, Lott WB, Hanley KA. Secondary structure of dengue virus type 4 3' untranslated region: impact of deletion and substitution mutations. J Gen Virol 2006; 87:3291-3296. [PMID: 17030863 DOI: 10.1099/vir.0.82182-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Several studies have generated computer-based predictions of secondary structure of the 3' untranslated region (UTR) of Dengue virus (DEN); however, experimental verification of the formation of these structures in vitro is lacking. This study assessed the congruence of Mfold predictions of secondary structure of the core region of the DEN type 4 3' UTR with nuclease maps of this region. Maps and predictions were largely consistent. Maps supported the existence of previously predicted pseudoknots and identified putative regions of dynamic folding. Additionally, this study investigated previously identified conserved elements in the flavivirus 3' UTR that differ among viruses with different modes of transmission. Specific regions of mosquito-borne DEN type 4 were either deleted or replaced with homologous sequences from tick-borne Langat virus. All of these mutations caused substantial distortion of secondary structure, yet viruses carrying these mutations were viable.
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Affiliation(s)
- Tammy A Romero
- Molecular Biology Program, New Mexico State University (NMSU), Las Cruces, NM 88003, USA
| | - Ebenezer Tumban
- Molecular Biology Program, New Mexico State University (NMSU), Las Cruces, NM 88003, USA
| | - Jeongwon Jun
- Molecular Biology Program, New Mexico State University (NMSU), Las Cruces, NM 88003, USA
| | - William B Lott
- School of Life Sciences, Queensland University of Technology, Brisbane, QLD 4001, Australia
| | - Kathryn A Hanley
- Department of Biology, New Mexico State University (NMSU), Las Cruces, NM 88003, USA
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40
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Filomatori CV, Lodeiro MF, Alvarez DE, Samsa MM, Pietrasanta L, Gamarnik AV. A 5' RNA element promotes dengue virus RNA synthesis on a circular genome. Genes Dev 2006; 20:2238-49. [PMID: 16882970 PMCID: PMC1553207 DOI: 10.1101/gad.1444206] [Citation(s) in RCA: 284] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The mechanisms of RNA replication of plus-strand RNA viruses are still unclear. Here, we identified the first promoter element for RNA synthesis described in a flavivirus. Using dengue virus as a model, we found that the viral RdRp discriminates the viral RNA by specific recognition of a 5' element named SLA. We demonstrated that RNA-RNA interactions between 5' and 3' end sequences of the viral genome enhance dengue virus RNA synthesis only in the presence of an intact SLA. We propose a novel mechanism for minus-strand RNA synthesis in which the viral polymerase binds SLA at the 5' end of the genome and reaches the site of initiation at the 3' end via long-range RNA-RNA interactions. These findings provide an explanation for the strict requirement of dengue virus genome cyclization during viral replication.
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Kofler RM, Hoenninger VM, Thurner C, Mandl CW. Functional analysis of the tick-borne encephalitis virus cyclization elements indicates major differences between mosquito-borne and tick-borne flaviviruses. J Virol 2006; 80:4099-113. [PMID: 16571826 PMCID: PMC1440478 DOI: 10.1128/jvi.80.8.4099-4113.2006] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The linear, positive-stranded RNA genome of flaviviruses is thought to adopt a circularized conformation via interactions of short complementary sequence elements located within its terminal regions. This process of RNA cyclization is a crucial precondition for RNA replication. In the case of mosquito-borne flaviviruses, highly conserved cyclization sequences (CS) have been identified, and their functionality has been experimentally confirmed. Here, we provide an experimental identification of CS elements of tick-borne encephalitis virus (TBEV). These elements, termed 5'-CS-A and 3'-CS-A, are conserved among various tick-borne flaviviruses, but they are unrelated to the mosquito-borne CS elements and are located at different genomic positions. The 5'-CS-A element is situated upstream rather than downstream of the AUG start codon and, in contrast to mosquito-borne flaviviruses, it was found that the entire protein C coding region is not essential for TBEV replication. The complementary 3'-CS-A element is located within the bottom stem rather than upstream of the characteristic 3'-terminal stem-loop structure, implying that this part of the proposed structure cannot be formed when the genome is in its circularized conformation. Finally, we demonstrate that the CS-A elements can also mediate their function when the 5'-CS-A element is moved from its natural position to one corresponding to the mosquito-borne CS. The recognition of essential RNA elements and their differences between mosquito-borne and tick-borne flaviviruses has practical implications for the design of replicons in vaccine and vector development.
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Affiliation(s)
- Regina M Kofler
- Clinical Institute of Virology, Medical University of Vienna, Kinderspitalgasse 15, A-1095 Vienna, Austria
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Alvarez DE, De Lella Ezcurra AL, Fucito S, Gamarnik AV. Role of RNA structures present at the 3'UTR of dengue virus on translation, RNA synthesis, and viral replication. Virology 2005; 339:200-12. [PMID: 16002117 DOI: 10.1016/j.virol.2005.06.009] [Citation(s) in RCA: 214] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2005] [Revised: 04/19/2005] [Accepted: 06/02/2005] [Indexed: 11/17/2022]
Abstract
We have developed a dengue virus replicon system that can be used to discriminate between translation and RNA replication. Using this system, we analyzed the functional role of well-defined RNA elements present at the 3'UTR of dengue virus in mammalian and mosquito cells. Our results show that deletion of individual domains of the 3'UTR did not significantly affect translation of the input RNA but seriously compromised or abolished RNA synthesis. We demonstrated that complementarity between sequences present at the 5' and 3' ends of the genome is essential for dengue virus RNA synthesis, while deletion of domains A2 or A3 within the 3'UTR resulted in replicons with decreased RNA amplification. We also characterized the vaccine candidate rDEN2Delta30 in the replicon system and found that viral attenuation is caused by inefficient RNA synthesis. Furthermore, using both the replicon system and recombinant viruses, we identified an RNA region of the 3'UTR that enhances dengue virus replication in BHK cells while is dispensable in mosquito cells.
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Affiliation(s)
- Diego E Alvarez
- Fundación Instituto Leloir, Avenida Patricias Argentinas 435, Buenos Aires 1405, Argentina
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Holden KL, Stein DA, Pierson TC, Ahmed AA, Clyde K, Iversen PL, Harris E. Inhibition of dengue virus translation and RNA synthesis by a morpholino oligomer targeted to the top of the terminal 3' stem-loop structure. Virology 2005; 344:439-52. [PMID: 16214197 DOI: 10.1016/j.virol.2005.08.034] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2005] [Revised: 06/18/2005] [Accepted: 08/24/2005] [Indexed: 11/20/2022]
Abstract
Dengue virus (DEN) is a major public health problem worldwide and causes a spectrum of diseases, for which no antiviral treatments exist. Peptide-conjugated phosphorodiamidate morpholino oligomers (P-PMOs) complementary to the DEN 5' stem-loop (5'SL) and to the DEN 3' cyclization sequence (3'CS) inhibit DEN replication, presumably by blocking critical RNA-RNA or RNA-protein interactions involved in viral translation and/or RNA synthesis. Here, a third P-PMO, complementary to the top of the 3' stem-loop (3'SLT), inhibited DEN replication in BHK cells. Using a novel DEN2 reporter replicon and a DEN2 reporter mRNA, we determined that the 5'SL P-PMO inhibited viral translation, the 3'CS P-PMO blocked viral RNA synthesis but not viral translation, and the 3'SLT P-PMO inhibited both viral translation and RNA synthesis. These results show that the 3'CS and the 3'SL domains regulate DEN translation and RNA synthesis and further demonstrate that P-PMOs are potentially useful as antiviral agents.
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Affiliation(s)
- Katherine Lynn Holden
- Division of Infectious Diseases, School of Public Health, University of California at Berkeley, 140 Warren Hall, Berkeley, CA 94720-7360, USA
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