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Das NK, Vogt J, Patel A, Banna HA, Koirala D. Structural basis for a highly conserved RNA-mediated enteroviral genome replication. Nucleic Acids Res 2024:gkae627. [PMID: 39036953 DOI: 10.1093/nar/gkae627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 06/28/2024] [Accepted: 07/05/2024] [Indexed: 07/23/2024] Open
Abstract
Enteroviruses contain conserved RNA structures at the extreme 5' end of their genomes that recruit essential proteins 3CD and PCBP2 to promote genome replication. However, the high-resolution structures and mechanisms of these replication-linked RNAs (REPLRs) are limited. Here, we determined the crystal structures of the coxsackievirus B3 and rhinoviruses B14 and C15 REPLRs at 1.54, 2.2 and 2.54 Å resolution, revealing a highly conserved H-type four-way junction fold with co-axially stacked sA-sD and sB-sC helices that are stabilized by a long-range A•C•U base-triple. Such conserved features observed in the crystal structures also allowed us to predict the models of several other enteroviral REPLRs using homology modeling, which generated models almost identical to the experimentally determined structures. Moreover, our structure-guided binding studies with recombinantly purified full-length human PCBP2 showed that two previously proposed binding sites, the sB-loop and 3' spacer, reside proximally and bind a single PCBP2. Additionally, the DNA oligos complementary to the 3' spacer, the high-affinity PCBP2 binding site, abrogated its interactions with enteroviral REPLRs, suggesting the critical roles of this single-stranded region in recruiting PCBP2 for enteroviral genome replication and illuminating the promising prospects of developing therapeutics against enteroviral infections targeting this replication platform.
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Affiliation(s)
- Naba Krishna Das
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, MD 21250, USA
| | - Jeff Vogt
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, MD 21250, USA
| | - Alisha Patel
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, MD 21250, USA
| | - Hasan Al Banna
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, MD 21250, USA
| | - Deepak Koirala
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, MD 21250, USA
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2
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Gottipati K, McNeme SC, Tipo J, White MA, Choi K. Structural basis for cloverleaf RNA-initiated viral genome replication. Nucleic Acids Res 2023; 51:8850-8863. [PMID: 37486760 PMCID: PMC10484678 DOI: 10.1093/nar/gkad618] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 07/07/2023] [Accepted: 07/18/2023] [Indexed: 07/25/2023] Open
Abstract
The genomes of positive-strand RNA viruses serve as a template for both protein translation and genome replication. In enteroviruses, a cloverleaf RNA structure at the 5' end of the genome functions as a switch to transition from viral translation to replication by interacting with host poly(C)-binding protein 2 (PCBP2) and the viral 3CDpro protein. We determined the structures of cloverleaf RNA from coxsackievirus and poliovirus. Cloverleaf RNA folds into an H-type four-way junction and is stabilized by a unique adenosine-cytidine-uridine (A•C-U) base triple involving the conserved pyrimidine mismatch region. The two PCBP2 binding sites are spatially proximal and are located on the opposite end from the 3CDpro binding site on cloverleaf. We determined that the A•C-U base triple restricts the flexibility of the cloverleaf stem-loops resulting in partial occlusion of the PCBP2 binding site, and elimination of the A•C-U base triple increases the binding affinity of PCBP2 to the cloverleaf RNA. Based on the cloverleaf structures and biophysical assays, we propose a new mechanistic model by which enteroviruses use the cloverleaf structure as a molecular switch to transition from viral protein translation to genome replication.
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Affiliation(s)
- Keerthi Gottipati
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA
- Department of Molecular and Cellular Biochemistry, Indiana University, 212 S. Hawthorne Drive, Bloomington, IN 47405, USA
| | - Sean C McNeme
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA
| | - Jerricho Tipo
- Department of Pharmacology and Toxicology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA
| | - Mark A White
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA
| | - Kyung H Choi
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA
- Department of Molecular and Cellular Biochemistry, Indiana University, 212 S. Hawthorne Drive, Bloomington, IN 47405, USA
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3
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Das NK, Hollmann NM, Vogt J, Sevdalis SE, Banna HA, Ojha M, Koirala D. Crystal structure of a highly conserved enteroviral 5' cloverleaf RNA replication element. Nat Commun 2023; 14:1955. [PMID: 37029118 PMCID: PMC10082201 DOI: 10.1038/s41467-023-37658-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 03/23/2023] [Indexed: 04/09/2023] Open
Abstract
The extreme 5'-end of the enterovirus RNA genome contains a conserved cloverleaf-like domain that recruits 3CD and PCBP proteins required for initiating genome replication. Here, we report the crystal structure at 1.9 Å resolution of this domain from the CVB3 genome in complex with an antibody chaperone. The RNA folds into an antiparallel H-type four-way junction comprising four subdomains with co-axially stacked sA-sD and sB-sC helices. Long-range interactions between a conserved A40 in the sC-loop and Py-Py helix within the sD subdomain organize near-parallel orientations of the sA-sB and sC-sD helices. Our NMR studies confirm that these long-range interactions occur in solution and without the chaperone. The phylogenetic analyses indicate that our crystal structure represents a conserved architecture of enteroviral cloverleaf-like domains, including the A40 and Py-Py interactions. The protein binding studies further suggest that the H-shape architecture provides a ready-made platform to recruit 3CD and PCBP2 for viral replication.
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Affiliation(s)
- Naba K Das
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD, 21250, USA
| | - Nele M Hollmann
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD, 21250, USA
- Howard Hughes Medical Institute, University of Maryland Baltimore County, Baltimore, MD, 21250, USA
| | - Jeff Vogt
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD, 21250, USA
| | - Spiridon E Sevdalis
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Hasan A Banna
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD, 21250, USA
| | - Manju Ojha
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD, 21250, USA
| | - Deepak Koirala
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD, 21250, USA.
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Bhattarai K, Holcik M. Diverse roles of heterogeneous nuclear ribonucleoproteins in viral life cycle. FRONTIERS IN VIROLOGY 2022. [DOI: 10.3389/fviro.2022.1044652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Understanding the host-virus interactions helps to decipher the viral replication strategies and pathogenesis. Viruses have limited genetic content and rely significantly on their host cell to establish a successful infection. Viruses depend on the host for a broad spectrum of cellular RNA-binding proteins (RBPs) throughout their life cycle. One of the major RBP families is the heterogeneous nuclear ribonucleoproteins (hnRNPs) family. hnRNPs are typically localized in the nucleus, where they are forming complexes with pre-mRNAs and contribute to many aspects of nucleic acid metabolism. hnRNPs contain RNA binding motifs and frequently function as RNA chaperones involved in pre-mRNA processing, RNA splicing, and export. Many hnRNPs shuttle between the nucleus and the cytoplasm and influence cytoplasmic processes such as mRNA stability, localization, and translation. The interactions between the hnRNPs and viral components are well-known. They are critical for processing viral nucleic acids and proteins and, therefore, impact the success of the viral infection. This review discusses the molecular mechanisms by which hnRNPs interact with and regulate each stage of the viral life cycle, such as replication, splicing, translation, and assembly of virus progeny. In addition, we expand on the role of hnRNPs in the antiviral response and as potential targets for antiviral drug research and development.
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5
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Wang J, Sun D, Wang M, Cheng A, Zhu Y, Mao S, Ou X, Zhao X, Huang J, Gao Q, Zhang S, Yang Q, Wu Y, Zhu D, Jia R, Chen S, Liu M. Multiple functions of heterogeneous nuclear ribonucleoproteins in the positive single-stranded RNA virus life cycle. Front Immunol 2022; 13:989298. [PMID: 36119073 PMCID: PMC9478383 DOI: 10.3389/fimmu.2022.989298] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 08/12/2022] [Indexed: 11/13/2022] Open
Abstract
The heterogeneous nuclear ribonucleoproteins (hnRNPs) are a diverse family of RNA binding proteins that are implicated in RNA metabolism, such as alternative splicing, mRNA stabilization and translational regulation. According to their different cellular localization, hnRNPs display multiple functions. Most hnRNPs were predominantly located in the nucleus, but some of them could redistribute to the cytoplasm during virus infection. HnRNPs consist of different domains and motifs that enable these proteins to recognize predetermined nucleotide sequences. In the virus-host interactions, hnRNPs specifically bind to viral RNA or proteins. And some of the viral protein-hnRNP interactions require the viral RNA or other host factors as the intermediate. Through various mechanisms, hnRNPs could regulate viral translation, viral genome replication, the switch of translation to replication and virion release. This review highlights the common features and the distinguish roles of hnRNPs in the life cycle of positive single-stranded RNA viruses.
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Affiliation(s)
- Jingming Wang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Di Sun
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Mingshu Wang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Anchun Cheng
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
- *Correspondence: Anchun Cheng,
| | - Yukun Zhu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Sai Mao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Xuming Ou
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Xinxin Zhao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Juan Huang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Qun Gao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Shaqiu Zhang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Qiao Yang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Ying Wu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Dekang Zhu
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Renyong Jia
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Shun Chen
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Mafeng Liu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
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Persistent Enterovirus Infection: Little Deletions, Long Infections. Vaccines (Basel) 2022; 10:vaccines10050770. [PMID: 35632526 PMCID: PMC9143164 DOI: 10.3390/vaccines10050770] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 05/04/2022] [Accepted: 05/10/2022] [Indexed: 01/27/2023] Open
Abstract
Enteroviruses have now been shown to persist in cell cultures and in vivo by a novel mechanism involving the deletion of varying amounts of the 5′ terminal genomic region termed domain I (also known as the cloverleaf). Molecular clones of coxsackievirus B3 (CVB3) genomes with 5′ terminal deletions (TD) of varying length allow the study of these mutant populations, which are able to replicate in the complete absence of wildtype virus genomes. The study of TD enteroviruses has revealed numerous significant differences from canonical enteroviral biology. The deletions appear and become the dominant population when an enterovirus replicates in quiescent cell populations, but can also occur if one of the cis-acting replication elements of the genome (CRE-2C) is artificially mutated in the element’s stem and loop structures. This review discusses how the TD genomes arise, how they interact with the host, and their effects on host biology.
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7
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Abstract
Type 1 diabetes (T1D) is a chronic autoimmune disease characterized by insulin deficiency and resultant hyperglycemia. Complex interactions of genetic and environmental factors trigger the onset of autoimmune mechanisms responsible for development of autoimmunity to β cell antigens and subsequent development of T1D. A potential role of virus infections has long been hypothesized, and growing evidence continues to implicate enteroviruses as the most probable triggering viruses. Recent studies have strengthened the association between enteroviruses and development of autoimmunity in T1D patients, potentially through persistent infections. Enterovirus infections may contribute to different stages of disease development. We review data from both human cohort studies and experimental research exploring the potential roles and molecular mechanisms by which enterovirus infections can impact disease outcome.
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Affiliation(s)
- Richard E. Lloyd
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Manasi Tamhankar
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Åke Lernmark
- Department of Clinical Sciences, Lund University/CRC, Skane University Hospital, Malmö 214 28, Sweden
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Host restriction factor A3G inhibits the replication of Enterovirus D68 through competitively binding 5' UTR with PCBP1. J Virol 2021; 96:e0170821. [PMID: 34730395 DOI: 10.1128/jvi.01708-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The host restriction factor APOBEC3G (A3G) presents extensively inhibition on a variety of viruses, including retroviruses, DNA and RNA viruses. Our recent study showed that A3G inhibits enterovirus 71 (EV71) and coxsackievirus A16 (CA16) via competitively binding 5'UTR with the host protein poly(C)-binding protein 1 (PCBP1) that is required for multiple EVs replication. However, in addition to EV71 and CA16, whether A3G inhibits other EVs has not been investigated. Here, we demonstrate that A3G could inhibit EVD68 replication, which needs PCBP1 for its replication, but not CA6 that PCBP1 is dispensable for CA6 replication. Further investigation revealed that nucleic acid binding activity of A3G is required for EVD68 restriction, which is similar to the mechanism presented in EV71 restriction. Mechanistically, A3G competitively binds to the cloverleaf (1-123) and the stem-loop IV (234-446) domains of EVD68 5'UTR with PCBP1, thereby inhibiting the 5'UTR activity of EVD68, whereas A3G doesn't interact with CA6 5'UTR results in no effect on CA6 replication. Moreover, non-structural protein 2C encoded by EVD68 overcomes A3G suppression through inducing A3G degradation via the autophagy-lysosome pathway. Our finding revealed that A3G might have broad spectrum antiviral activity against multiple EVs through the general mechanism, which might provide important information for the development of anti-EVs strategy. Importance As the two major pathogens causing hand, food, and mouth disease (HFMD), EV71 and CA16 attract more attention for the discovery of pathogenesis, the involvement of cellular proteins and so on. However, other EVs such as CA6 or EVD68 constantly occurred sporadic or might spread widely in recent years worldwide. Therefore, more information related to these EVs needs to be further investigated so as to develop broad-spectrum anti-EVs inhibitor. In this study, we first reveal that PCBP1 involved in PV and EV71 virus replication, also is required for the replication of EVD68 but not CA6. Then we found that the host restriction factor A3G specifically inhibits the replication of EVD68 but not CA6 via competitively binding to the 5'UTR of EVD68 with PCBP1. Our findings broaden the knowledge related to EVs replication and the interplay between EVs and host factors.
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Cellular Protein HuR Regulates the Switching of Genomic RNA Templates for Differential Functions during the Coxsackievirus B3 Life Cycle. J Virol 2021; 95:e0091521. [PMID: 34406862 DOI: 10.1128/jvi.00915-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Coxsackievirus B3 (CVB3) is an enterovirus belonging to the family Picornaviridae. Its 5' untranslated region (UTR) contains a cloverleaf structure followed by an internal ribosome entry site (IRES). The cloverleaf forms an RNA-protein complex known to regulate virus replication, translation, and stability of the genome, and the IRES regulates virus RNA translation. For positive-strand RNA-containing viruses, such as members of the flaviviruses or enteroviruses, the genomic RNA is used for translation, replication, and encapsidation. Only a few regulatory mechanisms which govern the accessibility of genomic RNA templates for translation or replication have been reported. Here, we report the role of human antigen R (HuR) in regulating the fate of CVB3 positive-strand RNA into the replication cycle or translation cycle. We have observed that synthesis of HuR is induced during CVB3 infection, and it suppresses viral replication by displacing PCBP-2 (a positive regulator of virus replication) at the cloverleaf RNA. Silencing of HuR increases viral RNA replication and consequently reduces viral RNA translation in a replication-dependent manner. Furthermore, we have shown that HuR level is upregulated upon CVB3 infection. Moreover, HuR limits virus replication and can coordinate the availability of genomic RNA templates for translation, replication, or encapsidation. Our study highlights the fact that the relative abundance of translation factors and replication factors in the cell decides the outcome of viral infection. IMPORTANCE A positive-strand RNA virus must balance the availability of its genomic template for different viral processes at different stages of its life cycle. A few host proteins are shown to be important to help the virus in switching the usage of a template between these processes. These proteins inhibit translation either by displacing a stimulator of translation or by binding to an alternative site. Both mechanisms lead to ribosome clearance and availability of the genomic strand for replication. We have shown that HuR also helps in maintaining this balance by inhibiting replication and subsequently promoting translation and packaging.
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Honkimaa A, Kimura B, Sioofy-Khojine AB, Lin J, Laiho J, Oikarinen S, Hyöty H. Genetic Adaptation of Coxsackievirus B1 during Persistent Infection in Pancreatic Cells. Microorganisms 2020; 8:microorganisms8111790. [PMID: 33203081 PMCID: PMC7697981 DOI: 10.3390/microorganisms8111790] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/10/2020] [Accepted: 11/11/2020] [Indexed: 12/16/2022] Open
Abstract
Coxsackie B (CVB) viruses have been associated with type 1 diabetes. We have recently observed that CVB1 was linked to the initiation of the autoimmune process leading to type 1 diabetes in Finnish children. Viral persistency in the pancreas is currently considered as one possible mechanism. In the current study persistent infection was established in pancreatic ductal and beta cell lines (PANC-1 and 1.1B4) using four different CVB1 strains, including the prototype strain and three clinical isolates. We sequenced 5′ untranslated region (UTR) and regions coding for structural and non-structural proteins and the second single open reading frame (ORF) protein of all persisting CVB1 strains using next generation sequencing to identify mutations that are common for all of these strains. One mutation, K257R in VP1, was found from all persisting CVB1 strains. The mutations were mainly accumulated in viral structural proteins, especially at BC, DE, EF loops and C-terminus of viral capsid protein 1 (VP1), the puff region of VP2, the knob region of VP3 and infection-enhancing epitope of VP4. This showed that the capsid region of the viruses sustains various changes during persistency some of which could be hallmark(s) of persistency.
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Affiliation(s)
- Anni Honkimaa
- Faculty of Medicine and Health Technology, Tampere University, 33520 Tampere, Finland; (B.K.); (A.B.S.-K.); (J.L.); (S.O.); (H.H.)
- Correspondence:
| | - Bryn Kimura
- Faculty of Medicine and Health Technology, Tampere University, 33520 Tampere, Finland; (B.K.); (A.B.S.-K.); (J.L.); (S.O.); (H.H.)
| | - Amir-Babak Sioofy-Khojine
- Faculty of Medicine and Health Technology, Tampere University, 33520 Tampere, Finland; (B.K.); (A.B.S.-K.); (J.L.); (S.O.); (H.H.)
| | - Jake Lin
- Finnish Institute of Molecular Medicine (FIMM), University of Helsinki, 00290 Helsinki, Finland;
| | - Jutta Laiho
- Faculty of Medicine and Health Technology, Tampere University, 33520 Tampere, Finland; (B.K.); (A.B.S.-K.); (J.L.); (S.O.); (H.H.)
| | - Sami Oikarinen
- Faculty of Medicine and Health Technology, Tampere University, 33520 Tampere, Finland; (B.K.); (A.B.S.-K.); (J.L.); (S.O.); (H.H.)
| | - Heikki Hyöty
- Faculty of Medicine and Health Technology, Tampere University, 33520 Tampere, Finland; (B.K.); (A.B.S.-K.); (J.L.); (S.O.); (H.H.)
- Fimlab Laboratories, Pirkanmaa Hospital District, 33520 Tampere, Finland
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Structures and Functions of Viral 5' Non-Coding Genomic RNA Domain-I in Group-B Enterovirus Infections. Viruses 2020; 12:v12090919. [PMID: 32839386 PMCID: PMC7552046 DOI: 10.3390/v12090919] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/17/2020] [Accepted: 08/19/2020] [Indexed: 12/22/2022] Open
Abstract
Group-B enteroviruses (EV-B) are ubiquitous naked single-stranded positive RNA viral pathogens that are responsible for common acute or persistent human infections. Their genome is composed in the 5′ end by a non-coding region, which is crucial for the initiation of the viral replication and translation processes. RNA domain-I secondary structures can interact with viral or cellular proteins to form viral ribonucleoprotein (RNP) complexes regulating viral genomic replication, whereas RNA domains-II to -VII (internal ribosome entry site, IRES) are known to interact with cellular ribosomal subunits to initiate the viral translation process. Natural 5′ terminally deleted viral forms lacking some genomic RNA domain-I secondary structures have been described in EV-B induced murine or human infections. Recent in vitro studies have evidenced that the loss of some viral RNP complexes in the RNA domain-I can modulate the viral replication and infectivity levels in EV-B infections. Moreover, the disruption of secondary structures of RNA domain-I could impair viral RNA sensing by RIG-I (Retinoic acid inducible gene I) or MDA5 (melanoma differentiation-associated protein 5) receptors, a way to overcome antiviral innate immune response. Overall, natural 5′ terminally deleted viral genomes resulting in the loss of various structures in the RNA domain-I could be major key players of host–cell interactions driving the development of acute or persistent EV-B infections.
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Bouin A, Gretteau PA, Wehbe M, Renois F, N'Guyen Y, Lévêque N, Vu MN, Tracy S, Chapman NM, Bruneval P, Fornes P, Semler BL, Andreoletti L. Enterovirus Persistence in Cardiac Cells of Patients With Idiopathic Dilated Cardiomyopathy Is Linked to 5' Terminal Genomic RNA-Deleted Viral Populations With Viral-Encoded Proteinase Activities. Circulation 2020; 139:2326-2338. [PMID: 30755025 DOI: 10.1161/circulationaha.118.035966] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND Group B enteroviruses are common causes of acute myocarditis, which can be a precursor of chronic myocarditis and dilated cardiomyopathy, leading causes of heart transplantation. To date, the specific viral functions involved in the development of dilated cardiomyopathy remain unclear. METHODS Total RNA from cardiac tissue of patients with dilated cardiomyopathy was extracted, and sequences corresponding to the 5' termini of enterovirus RNAs were identified. After next-generation RNA sequencing, viral cDNA clones mimicking the enterovirus RNA sequences found in patient tissues were generated in vitro, and their replication and impact on host cell functions were assessed on primary human cardiac cells in culture. RESULTS Major enterovirus B populations characterized by 5' terminal genomic RNA deletions ranging from 17 to 50 nucleotides were identified either alone or associated with low proportions of intact 5' genomic termini. In situ hybridization and immunohistological assays detected these persistent genomes in clusters of cardiomyocytes. Transfection of viral RNA into primary human cardiomyocytes demonstrated that deleted forms of genomic RNAs displayed early replication activities in the absence of detectable viral plaque formation, whereas mixed deleted and complete forms generated particles capable of inducing cytopathic effects at levels distinct from those observed with full-length forms alone. Moreover, deleted or full-length and mixed forms of viral RNA were capable of directing translation and production of proteolytically active viral proteinase 2A in human cardiomyocytes. CONCLUSIONS We demonstrate that persistent viral forms are composed of B-type enteroviruses harboring a 5' terminal deletion in their genomic RNAs and that these viruses alone or associated with full-length populations of helper RNAs could impair cardiomyocyte functions by the proteolytic activity of viral proteinase 2A in cases of unexplained dilated cardiomyopathy. These results provide a better understanding of the molecular mechanisms that underlie the persistence of EV forms in human cardiac tissues and should stimulate the development of new therapeutic strategies based on specific inhibitors of the coxsackievirus B proteinase 2A activity for acute and chronic cardiac infections.
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Affiliation(s)
- Alexis Bouin
- EA-4684 Cardiovir, Faculty of Medicine, University of Reims Champagne-Ardenne, Reims, France (A.B., P.-A.G., M.W., F.R., Y.N., A.R., P.F., L.A.).,Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine (A.B., M.N.V., B.L.S.)
| | - Paul-Antoine Gretteau
- EA-4684 Cardiovir, Faculty of Medicine, University of Reims Champagne-Ardenne, Reims, France (A.B., P.-A.G., M.W., F.R., Y.N., A.R., P.F., L.A.)
| | - Michel Wehbe
- EA-4684 Cardiovir, Faculty of Medicine, University of Reims Champagne-Ardenne, Reims, France (A.B., P.-A.G., M.W., F.R., Y.N., A.R., P.F., L.A.).,Centre AZM pour la recherche en biotechnologie et ses applications, Université Libanaise, Tripoli, Lebanon (M.W.)
| | - Fanny Renois
- EA-4684 Cardiovir, Faculty of Medicine, University of Reims Champagne-Ardenne, Reims, France (A.B., P.-A.G., M.W., F.R., Y.N., A.R., P.F., L.A.).,LUNAM University, Oniris, LABERCA, UMR INRA 1329, Nantes, France (F.R.).,CHU Robert Debré, Laboratoire de Virologie Médicale et Moléculaire, Reims, France (F.R., Y.N., N.L., P.F., L.A.)
| | - Yohan N'Guyen
- EA-4684 Cardiovir, Faculty of Medicine, University of Reims Champagne-Ardenne, Reims, France (A.B., P.-A.G., M.W., F.R., Y.N., A.R., P.F., L.A.).,CHU Robert Debré, Laboratoire de Virologie Médicale et Moléculaire, Reims, France (F.R., Y.N., N.L., P.F., L.A.)
| | - Nicolas Lévêque
- CHU Robert Debré, Laboratoire de Virologie Médicale et Moléculaire, Reims, France (F.R., Y.N., N.L., P.F., L.A.).,EA-4331 LITEC, Faculty of Medicine and Pharmacy, University Hospital of Poitiers, France (N.L.)
| | - Michelle N Vu
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine (A.B., M.N.V., B.L.S.)
| | - Steven Tracy
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (S.T., N.M.C.)
| | - Nora M Chapman
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (S.T., N.M.C.)
| | - Patrick Bruneval
- Service d'Anatomie Pathologique, Hôpital Européen Georges Pompidou, Paris, France (P.B.)
| | - Paul Fornes
- EA-4684 Cardiovir, Faculty of Medicine, University of Reims Champagne-Ardenne, Reims, France (A.B., P.-A.G., M.W., F.R., Y.N., A.R., P.F., L.A.)
| | - Bert L Semler
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine (A.B., M.N.V., B.L.S.)
| | - Laurent Andreoletti
- EA-4684 Cardiovir, Faculty of Medicine, University of Reims Champagne-Ardenne, Reims, France (A.B., P.-A.G., M.W., F.R., Y.N., A.R., P.F., L.A.)
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13
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Holmes AC, Zagnoli-Vieira G, Caldecott KW, Semler BL. Effects of TDP2/VPg Unlinkase Activity on Picornavirus Infections Downstream of Virus Translation. Viruses 2020; 12:E166. [PMID: 32023921 PMCID: PMC7077319 DOI: 10.3390/v12020166] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 01/20/2020] [Accepted: 01/22/2020] [Indexed: 12/12/2022] Open
Abstract
In this study, we characterized the role of host cell protein tyrosyl-DNA phosphodiesterase 2 (TDP2) activity, also known as VPg unlinkase, in picornavirus infections in a human cell model of infection. TDP2/VPg unlinkase is used by picornaviruses to remove the small polypeptide, VPg (Virus Protein genome-linked, the primer for viral RNA synthesis), from virus genomic RNA. We utilized a CRISPR/Cas-9-generated TDP2 knock out (KO) human retinal pigment epithelial-1 (hRPE-1) cell line, in addition to the wild type (WT) counterpart for our studies. We determined that in the absence of TDP2, virus growth kinetics for two enteroviruses (poliovirus and coxsackievirus B3) were delayed by about 2 h. Virus titers were reduced by ~2 log10 units for poliovirus and 0.5 log10 units for coxsackievirus at 4 hours post-infection (hpi), and by ~1 log10 unit at 6 hpi for poliovirus. However, virus titers were nearly indistinguishable from those of control cells by the end of the infectious cycle. We determined that this was not the result of an alternative source of VPg unlinkase activity being activated in the absence of TPD2 at late times of infection. Viral protein production in TDP2 KO cells was also substantially reduced at 4 hpi for poliovirus infection, consistent with the observed growth kinetics delay, but reached normal levels by 6 hpi. Interestingly, this result differs somewhat from what has been reported previously for the TDP2 KO mouse cell model, suggesting that either cell type or species-specific differences might be playing a role in the observed phenotype. We also determined that catalytically inactive TDP2 does not rescue the growth defect, confirming that TDP2 5' phosphodiesterase activity is required for efficient virus replication. Importantly, we show for the first time that polysomes can assemble efficiently on VPg-linked RNA after the initial round of translation in a cell culture model, but both positive and negative strand RNA production is impaired in the absence of TDP2 at mid-times of infection, indicating that the presence of VPg on the viral RNA affects a step in the replication cycle downstream of translation (e.g., RNA synthesis). In agreement with this conclusion, we found that double-stranded RNA production (a marker of viral RNA synthesis) is delayed in TDP2 KO RPE-1 cells. Moreover, we show that premature encapsidation of nascent, VPg-linked RNA is not responsible for the observed virus growth defect. Our studies provide the first lines of evidence to suggest that either negative- or positive-strand RNA synthesis (or both) is a likely candidate for the step that requires the removal of VPg from the RNA for an enterovirus infection to proceed efficiently.
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Affiliation(s)
- Autumn C. Holmes
- Department of Microbiology & Molecular Genetics and Center for Virus Research, University of California, Irvine, CA 92697, USA;
| | - Guido Zagnoli-Vieira
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton BN1 9RQ, UK; (G.Z.-V.); (K.W.C.)
| | - Keith W. Caldecott
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton BN1 9RQ, UK; (G.Z.-V.); (K.W.C.)
| | - Bert L. Semler
- Department of Microbiology & Molecular Genetics and Center for Virus Research, University of California, Irvine, CA 92697, USA;
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14
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Mahmud B, Horn CM, Tapprich WE. Structure of the 5' Untranslated Region of Enteroviral Genomic RNA. J Virol 2019; 93:e01288-19. [PMID: 31534036 PMCID: PMC6854513 DOI: 10.1128/jvi.01288-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 09/11/2019] [Indexed: 12/14/2022] Open
Abstract
Enteroviral RNA genomes share a long, highly structured 5' untranslated region (5' UTR) containing a type I internal ribosome entry site (IRES). The 5' UTR is composed of stably folded RNA domains connected by unstructured RNA regions. Proper folding and functioning of the 5' UTR underlies the efficiency of viral replication and also determines viral virulence. We have characterized the structure of 5' UTR genomic RNA from coxsackievirus B3 using selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) and base-specific chemical probes in solution. Our results revealed novel structural features, including realignment of major domains, newly identified long-range interactions, and an intrinsically disordered connecting region. Together, these newly identified features contribute to a model for enteroviral 5' UTRs with type I IRES elements that links structure to function during the hierarchical processes directed by genomic RNA during viral infection.IMPORTANCE Enterovirus infections are responsible for human diseases, including myocarditis, pancreatitis, acute flaccid paralysis, and poliomyelitis. The virulence of these viruses depends on efficient recognition of the RNA genome by a large family of host proteins and protein synthesis factors, which in turn relies on the three-dimensional folding of the first 750 nucleotides of the molecule. Structural information about this region of the genome, called the 5' untranslated region (5' UTR), is needed to assist in the process of vaccine and antiviral development. This work presents a model for the structure of the enteroviral 5' UTR. The model includes an RNA element called an intrinsically disordered RNA region (IDRR). Intrinsically disordered proteins (IDPs) are well known, but correlates in RNA have not been proposed. The proposed IDRR is a 20-nucleotide region, long known for its functional importance, where structural flexibility helps explain recognition by factors controlling multiple functional states.
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Affiliation(s)
- Bejan Mahmud
- Biology Department, University of Nebraska at Omaha, Omaha, Nebraska, USA
| | - Christopher M Horn
- Biology Department, University of Nebraska at Omaha, Omaha, Nebraska, USA
| | - William E Tapprich
- Biology Department, University of Nebraska at Omaha, Omaha, Nebraska, USA
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15
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Bouin A, Nguyen Y, Wehbe M, Renois F, Fornes P, Bani-Sadr F, Metz D, Andreoletti L. Major Persistent 5' Terminally Deleted Coxsackievirus B3 Populations in Human Endomyocardial Tissues. Emerg Infect Dis 2018; 22:1488-90. [PMID: 27434549 PMCID: PMC4982168 DOI: 10.3201/eid2208.160186] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
We performed deep sequencing analysis of the enterovirus 5′ noncoding region in cardiac biopsies from a patient with dilated cardiomyopathy. Results displayed a mix of deleted and full-length coxsackievirus B3, characterized by a low viral RNA load (8.102 copies/μg of nucleic acids) and a low viral RNA positive-sense to RNA negative-sense ratio of 4.8.
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16
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Functional Consequences of RNA 5'-Terminal Deletions on Coxsackievirus B3 RNA Replication and Ribonucleoprotein Complex Formation. J Virol 2017; 91:JVI.00423-17. [PMID: 28539455 DOI: 10.1128/jvi.00423-17] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 05/17/2017] [Indexed: 12/11/2022] Open
Abstract
Group B coxsackieviruses are responsible for chronic cardiac infections. However, the molecular mechanisms by which the virus can persist in the human heart long after the signs of acute myocarditis have abated are still not completely understood. Recently, coxsackievirus B3 strains with 5'-terminal deletions in genomic RNAs were isolated from a patient suffering from idiopathic dilated cardiomyopathy, suggesting that such mutant viruses may be the forms responsible for persistent infection. These deletions lacked portions of 5' stem-loop I, which is an RNA secondary structure required for viral RNA replication. In this study, we assessed the consequences of the genomic deletions observed in vivo for coxsackievirus B3 biology. Using cell extracts from HeLa cells, as well as transfection of luciferase replicons in two types of cardiomyocytes, we demonstrated that coxsackievirus RNAs harboring 5' deletions ranging from 7 to 49 nucleotides in length can be translated nearly as efficiently as those of wild-type virus. However, these 5' deletions greatly reduced the synthesis of viral RNA in vitro, which was detected only for the 7- and 21-nucleotide deletions. Since 5' stem-loop I RNA forms a ribonucleoprotein complex with cellular and viral proteins involved in viral RNA replication, we investigated the binding of the host cell protein PCBP2, as well as viral protein 3CDpro, to deleted positive-strand RNAs corresponding to the 5' end. We found that binding of these proteins was conserved but that ribonucleoprotein complex formation required higher PCBP2 and 3CDpro concentrations, depending on the size of the deletion. Overall, this study confirmed the characteristics of persistent CVB3 infection observed in heart tissues and provided a possible explanation for the low level of RNA replication observed for the 5'-deleted viral genomes-a less stable ribonucleoprotein complex formed with proteins involved in viral RNA replication.IMPORTANCE Dilated cardiomyopathy is the most common indication for heart transplantation worldwide, and coxsackie B viruses are detected in about one-third of idiopathic dilated cardiomyopathies. Terminal deletions at the 5' end of the viral genome involving an RNA secondary structure required for RNA replication have been recently reported as a possible mechanism of virus persistence in the human heart. These mutations are likely to disrupt the correct folding of an RNA secondary structure required for viral RNA replication. In this report, we demonstrate that transfected RNAs harboring 5'-terminal sequence deletions are able to direct the synthesis of viral proteins, but not genomic RNAs, in human and murine cardiomyocytes. Moreover, we show that the binding of cellular and viral replication factors to viral RNA is conserved despite genomic deletions but that the impaired RNA synthesis associated with terminally deleted viruses could be due to destabilization of the ribonucleoprotein complexes formed.
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17
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Warden MS, Tonelli M, Cornilescu G, Liu D, Hopersberger LJ, Ponniah K, Pascal SM. Structure of RNA Stem Loop B from the Picornavirus Replication Platform. Biochemistry 2017; 56:2549-2557. [PMID: 28459542 DOI: 10.1021/acs.biochem.7b00141] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The presumptive RNA cloverleaf at the start of the 5'-untranslated region of the picornavirus genome is an essential element in replication. Stem loop B (SLB) of the cloverleaf is a recognition site for the host polyC-binding protein, which initiates a switch from translation to replication. Here we present the solution structure of human rhinovirus isotype 14 SLB using nuclear magnetic resonance spectroscopy. SLB adopts a predominantly A-form helical structure. The stem contains five Watson-Crick base pairs and one wobble base pair and is capped by an eight-nucleotide loop. The wobble base pair introduces perturbations into the helical parameters but does not appear to introduce flexibility. However, the helix major groove appears to be accessible. Flexibility is seen throughout the loop and in the terminal nucleotides. The pyrimidine-rich region of the loop, the apparent recognition site for the polyC-binding protein, is the most disordered region of the structure.
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Affiliation(s)
- Meghan S Warden
- Department of Chemistry and Biochemistry, Old Dominion University , Norfolk, Virginia 23529, United States
| | - Marco Tonelli
- National Magnetic Resonance Facility at Madison (NMRFAM), University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Gabriel Cornilescu
- National Magnetic Resonance Facility at Madison (NMRFAM), University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Dong Liu
- Department of Chemistry and Biochemistry, Old Dominion University , Norfolk, Virginia 23529, United States
| | - Lorelei J Hopersberger
- Department of Chemistry and Biochemistry, Old Dominion University , Norfolk, Virginia 23529, United States
| | - Komala Ponniah
- Department of Chemistry and Biochemistry, Old Dominion University , Norfolk, Virginia 23529, United States
| | - Steven M Pascal
- Department of Chemistry and Biochemistry, Old Dominion University , Norfolk, Virginia 23529, United States
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18
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Prostova MA, Gmyl AP, Bakhmutov DV, Shishova AA, Khitrina EV, Kolesnikova MS, Serebryakova MV, Isaeva OV, Agol VI. Mutational robustness and resilience of a replicative cis-element of RNA virus: Promiscuity, limitations, relevance. RNA Biol 2016; 12:1338-54. [PMID: 26488412 DOI: 10.1080/15476286.2015.1100794] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Since replication of RNA-viruses is generally a low-fidelity process, it would be advantageous, if specific interactions of their genomic cis-elements with dedicated ligands are relatively tolerant to mutations. The specificity/promiscuity trade-off of such interactions was addressed here by investigating structural requirements of the oriL (also known as the clover leaf-like element), of poliovirus RNA, a replicative cis-element containing a conserved essential tetraloop functionally interacting with the viral protein 3CD. The sequence of this tetraloop and 2 adjacent base-pairs was randomized in the viral genome, and viable viruses were selected in susceptible cells. Strikingly, each position of this octanucleotide in 62 investigated viable viruses could be occupied by any nucleotide (with the exception of one position, which lacked U), though with certain sequence preferences, confirmed by engineering mutant viral genomes whose phenotypic properties were found to correlate with the strength of the cis-element/ligand interaction. The results were compatible with a hypothesis that functional recognition by 3CD requires that this tetraloop should stably or temporarily adopt a YNMG-like (Y=U/C, N=any nucleotide, M=A/C) fold. The fitness of "weak" viruses could be increased by compensatory mutations "improving" the tetraloops. Otherwise, the recognition of "bad" tetraloops might be facilitated by alterations in the 3CD protein. The virus appeared to tolerate mutations in its cis-element relaying on either robustness (spatial structure degeneracy) or resilience (a combination of dynamic RNA folding, low-fidelity replication modifying the cis-element or its ligand, and negative selection). These mechanisms (especially resilience involving metastable low-fit intermediates) can also contribute to the viral evolvability.
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Affiliation(s)
- Maria A Prostova
- a M P Chumakov Institute of Poliomyelitis and Viral Encephalitides ; Moscow Russia
| | - Anatoly P Gmyl
- a M P Chumakov Institute of Poliomyelitis and Viral Encephalitides ; Moscow Russia.,b M V Lomonosov Moscow State University ; Moscow Russia
| | - Denis V Bakhmutov
- a M P Chumakov Institute of Poliomyelitis and Viral Encephalitides ; Moscow Russia.,c Deceased
| | - Anna A Shishova
- a M P Chumakov Institute of Poliomyelitis and Viral Encephalitides ; Moscow Russia
| | - Elena V Khitrina
- a M P Chumakov Institute of Poliomyelitis and Viral Encephalitides ; Moscow Russia
| | - Marina S Kolesnikova
- a M P Chumakov Institute of Poliomyelitis and Viral Encephalitides ; Moscow Russia
| | | | - Olga V Isaeva
- a M P Chumakov Institute of Poliomyelitis and Viral Encephalitides ; Moscow Russia
| | - Vadim I Agol
- a M P Chumakov Institute of Poliomyelitis and Viral Encephalitides ; Moscow Russia.,b M V Lomonosov Moscow State University ; Moscow Russia
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19
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Smithee S, Tracy S, Chapman NM. Reversion to wildtype of a mutated and nonfunctional coxsackievirus B3CRE(2C). Virus Res 2016; 220:136-49. [PMID: 27130630 DOI: 10.1016/j.virusres.2016.04.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 04/15/2016] [Accepted: 04/18/2016] [Indexed: 11/25/2022]
Abstract
The cis-acting replication element (CRE) in the 2C protein coding region [CRE(2C)] of enteroviruses (EV) facilitates the addition of two uridine residues (uridylylation) onto the virus-encoded protein VPg in order for it to serve as the RNA replication primer. We demonstrated that coxsackievirus B3 (CVB3) is replication competent in the absence of a native (uridylylating) CRE(2C) and also demonstrated that lack of a functional CRE(2C) led to generation of 5' terminal genomic deletions in the CVB3 CRE-knock-out (CVB3-CKO) population. We asked whether reversion of the mutated CRE(2C) occurred, thus permitting sustained replication, and when were 5' terminal deletions generated during replication. Virions were isolated from HeLa cells previously electroporated with infectious CVB3-CKO T7 transcribed RNA or from hearts and spleens of mice after transfection with CVB3-CKO RNA. Viral RNA was isolated in order to amplify the CRE(2C) coding region and the genomic 5' terminal sequences. Sequence analysis revealed reversion of the CVB3-CKO sequence to wildtype occurs by 8 days post-electroporation of HeLa cells and by 20days post-transfection in mice. However, 5' terminal deletions evolve prior to these times. Reversion of the CRE(2C) mutations to wildtype despite loss of the genomic 5' termini is consistent with the hypothesis that an intact CRE(2C) is inherently vital to EV replication even when it is not enabling efficient positive strand initiation.
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Affiliation(s)
- Shane Smithee
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA; Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA 30033, USA
| | - Steven Tracy
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Nora M Chapman
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA.
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20
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Construction of a subgenomic CV-B3 replicon expressing emerald green fluorescent protein to assess viral replication of a cardiotropic enterovirus strain in cultured human cells. J Virol Methods 2016; 230:1-8. [PMID: 26800776 DOI: 10.1016/j.jviromet.2016.01.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Revised: 01/13/2016] [Accepted: 01/15/2016] [Indexed: 11/21/2022]
Abstract
Coxsackieviruses B (CV-B) (Picornaviridae) are a common infectious cause of acute myocarditis in children and young adults, a disease, which is a precursor to 10-20% of chronic myocarditis and dilated cardiomyopathy (DCM) cases. The mechanisms involved in the disease progression from acute to chronic myocarditis phase and toward the DCM clinical stage are not fully understood but are influenced by both viral and host factors. Subgenomic replicons of CV-B can be used to assess viral replication mechanisms in human cardiac cells and evaluate the effects of potential antiviral drugs on viral replication activities. Our objectives were to generate a reporter replicon from a cardiotropic prototype CV-B3/28 strain and to characterize its replication properties into human cardiac primary cells. To obtain this replicon, a cDNA plasmid containing the full CV-B3/28 genome flanked by a hammerhead ribozyme sequence and an MluI restriction site was generated and used as a platform for the insertion of sequences encoding emerald green fluorescent protein (EmGFP) in place of those encoding VP3. In vitro transcribed RNA from this plasmid was transfected into HeLa cells and human primary cardiac cells and was able to produce EmGFP and VP1-containing polypeptides. Moreover, non-structural protein biological activity was assessed by the specific cleavage of eIF4G1 by viral 2A(pro). Viral RNA replication was indirectly demonstrated by inhibition assays, fluoxetine was added to cell culture and prevented the EmGFP synthesis. Our results indicated that the EmGFP CV-B3 replicon was able to replicate and translate as well as the CV-B3/28 prototype strain. Our EmGFP CV-B3 replicon will be a valuable tool to readily investigate CV-B3 replication activities in human target cell models.
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21
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Mutational Disruption of cis-Acting Replication Element 2C in Coxsackievirus B3 Leads to 5'-Terminal Genomic Deletions. J Virol 2015; 89:11761-72. [PMID: 26355088 PMCID: PMC4645312 DOI: 10.1128/jvi.01308-15] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 09/01/2015] [Indexed: 12/14/2022] Open
Abstract
UNLABELLED Following natural human or experimental murine infections and in cell culture, coxsackievirus B (CVB) RNA can persist for weeks in the absence of a cytopathic effect, yet viral RNA remains detectable. Our earlier studies demonstrated that this persistence produced viral RNA with up to 49 nucleotide deletions at the genomic 5' terminus which partially degraded the cloverleaf (or domain I), an RNA structure required for efficient viral replication. A cis-acting replication element (CRE) in the 2C protein-coding region [CRE(2C)] templates the addition of two uridine residues to the virus genome-encoded RNA replication primer VPg prior to positive-strand synthesis. Because our previous work also demonstrated that the genomes of CVB with a 5'-terminal deletion (CVB-TD) have VPg covalently linked, even though they rarely terminate in the canonical UU donated by CRE(2C)-mediated uridylylation of VPg, we hypothesized that a functional (uridylylating) CRE(2C) would be unnecessary for CVB-TD replication. Using the same 16 mutations in the CVB3 CRE(2C) structure that were considered lethal for this virus by others, we demonstrate here both in infected cell cultures and in mice that wild-type (wt) and CVB3-TD strains carrying these mutations with a nonuridylylating CRE(2C) are viable. While the wt genome with the mutated CRE(2C) displays suppressed replication levels similar to those observed in a CVB3-TD strain, mutation of the CRE(2C) function in a CVB3-TD strain does not further decrease replication. Finally, we show that replication of the parental CVB3 strain containing the mutated CRE(2C) drives the de novo generation of genomic deletions at the 5' terminus. IMPORTANCE In this report, we demonstrate that while CVB can replicate without a uridylylating CRE(2C), the replication rate suffers significantly. Further, deletions at the 5' terminus of the genome are generated in this virus population, with this virus population supplanting the wild-type population. This demonstrates that VPg can prime without being specifically uridylylated and that this priming is error prone, resulting in the loss of sequence information from the 5' terminus. These findings have significance when considering the replication of human enteroviruses, and we believe that these data are unattainable in a cell-free system due to the poor replication of these CRE-deficient viruses.
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22
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Tracy S, Smithee S, Alhazmi A, Chapman N. Coxsackievirus can persist in murine pancreas by deletion of 5' terminal genomic sequences. J Med Virol 2014; 87:240-7. [PMID: 25111164 DOI: 10.1002/jmv.24039] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/08/2014] [Indexed: 12/15/2022]
Abstract
Enterovirus infections are generally acute and rapidly cleared by the host immune response. Enteroviruses can at times persist in immunologically intact individuals after the rise of the type-specific neutralizing immune response. The mechanism of enterovirus persistence was shown in group B coxsackieviruses (CVB) to be due to naturally-occurring deletions at the 5' terminus of the genome which variably impact the stem-loop secondary structure called domain I. These deletions result in much slower viral replication and a loss of measurable cytopathic effect when such 5' terminally deleted (TD) viruses are assayed in cell culture. The existence and persistence of CVB-TD long after the acute phase of infection has been documented in hearts of experimentally inoculated mice and naturally infected humans but to date, the existence of TD enteroviral populations have not been documented in any other organ. Enteroviral infections have been shown to impact type 1 diabetes (T1D) onset in humans as well as in the non-obese diabetic mouse model of T1D. The first step to studying the potential impact of CVB-TD on T1D etiology is to determine whether CVB-TD populations can arise in the pancreas. After inoculation of NOD diabetic mice with CVB, viral RNA persists in the absence of cytopathic virus in pancreas weeks past the acute infectious period. Analysis of viral genomic 5' termini by RT-PCR showed CVB-TD populations displace the parental population during persistent replication in murine pancreata.
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Affiliation(s)
- Steven Tracy
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska
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Prusa J, Missak J, Kittrell J, Evans JJ, Tapprich WE. Major alteration in coxsackievirus B3 genomic RNA structure distinguishes a virulent strain from an avirulent strain. Nucleic Acids Res 2014; 42:10112-21. [PMID: 25074382 PMCID: PMC4150801 DOI: 10.1093/nar/gku706] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Coxsackievirus B3 (CV-B3) is a cardiovirulent enterovirus that utilizes a 5′ untranslated region (5′UTR) to complete critical viral processes. Here, we directly compared the structure of a 5′UTR from a virulent strain with that of a naturally occurring avirulent strain. Using chemical probing analysis, we identified a structural difference between the two 5′UTRs in the highly substituted stem-loop II region (SLII). For the remainder of the 5′UTR, we observed conserved structure. Comparative sequence analysis of 170 closely related enteroviruses revealed that the SLII region lacks conservation. To investigate independent folding and function, two chimeric CV-B3 strains were created by exchanging nucleotides 104–184 and repeating the 5′UTR structural analysis. Neither the parent SLII nor the remaining domains of the background 5′UTR were structurally altered by the exchange, supporting an independent mechanism of folding and function. We show that the attenuated 5′UTR lacks structure in the SLII cardiovirulence determinant.
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Affiliation(s)
- Jerome Prusa
- Biology Department, University of Nebraska at Omaha, Omaha, NE 68182, USA
| | - Johanna Missak
- Department of Family Medicine, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Jeff Kittrell
- Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - John J Evans
- Department of Pathology, University of Colorado Anshutz Medical Campus, Denver, CO 80045, USA
| | - William E Tapprich
- Biology Department, University of Nebraska at Omaha, Omaha, NE 68182, USA
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Ogram SA, Boone CD, McKenna R, Flanegan JB. Amiloride inhibits the initiation of Coxsackievirus and poliovirus RNA replication by inhibiting VPg uridylylation. Virology 2014; 464-465:87-97. [PMID: 25058507 DOI: 10.1016/j.virol.2014.06.025] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Revised: 06/02/2014] [Accepted: 06/17/2014] [Indexed: 12/24/2022]
Abstract
The mechanism of amiloride inhibition of Coxsackievirus B3 (CVB3) and poliovirus type 1 (PV1) RNA replication was investigated using membrane-associated RNA replication complexes. Amiloride was shown to inhibit viral RNA replication and VPgpUpU synthesis. However, the drug had no effect on polymerase elongation activity during either (-) strand or (+) strand synthesis. These findings indicated that amiloride inhibited the initiation of RNA synthesis by inhibiting VPg uridylylation. In addition, in silico binding studies showed that amiloride docks in the VPg binding site on the back of the viral RNA polymerase, 3D(pol). Since VPg binding at this site on PV1 3D(pol) was previously shown to be required for VPg uridylylation, our results suggest that amiloride inhibits VPg binding to 3D(pol). In summary, our findings are consistent with a model in which amiloride inhibits VPgpUpU synthesis and viral RNA replication by competing with VPg for binding to 3D(pol).
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Affiliation(s)
- Sushma A Ogram
- Department of Biochemistry and Molecular Biology, University of Florida, College of Medicine, Gainesville, FL 32610-0245, USA
| | - Christopher D Boone
- Department of Biochemistry and Molecular Biology, University of Florida, College of Medicine, Gainesville, FL 32610-0245, USA
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, University of Florida, College of Medicine, Gainesville, FL 32610-0245, USA
| | - James B Flanegan
- Department of Biochemistry and Molecular Biology, University of Florida, College of Medicine, Gainesville, FL 32610-0245, USA.
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25
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The structural and phylogenetic profile of the 3' terminus of coxsackievirus B3 negative strand. Virus Res 2014; 188:81-9. [PMID: 24675276 DOI: 10.1016/j.virusres.2014.03.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Revised: 03/14/2014] [Accepted: 03/16/2014] [Indexed: 11/20/2022]
Abstract
In the replication process of RNA(+) viruses both the positive-strand template and the newly synthesized negative strand appear in a double-stranded form, RF. It has been shown for poliovirus that prior to the initiation of positive-strand synthesis, the 5'-terminus of the positive strand must adopt a cloverleaf structure. When that happens, the 3'-terminal region of the negative strand is released from the RF form and is able to form into its own defined structure. In order to determine the secondary structure of this region, a comprehensive approach consisting of experimental mapping methods, phylogenetic analysis and computer predictions was applied. Here we propose the first structural model of the 3'-terminal region of the coxsackievirus B3 (CV-B3) negative strand, approximately 450 nucleotides in length. The region folds into three highly defined structural domains, I'-III'. The most 3'-terminal part of this region is domain I', which folds into a cloverleaf structure similar to that found in the viral RNA strand of positive-polarity. Remarkably, this motif is conserved among all analyzed viral isolates of CV-B3 despite the observed sequence diversity. Several other conserved structural motifs within the 3'-terminal region of the viral negative strand were also identified. The structure of this region may be crucial for the replication complex assembly.
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26
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Luo Z, Dong X, Li Y, Zhang Q, Kim C, Song Y, Kang L, Liu Y, Wu K, Wu J. PolyC-binding protein 1 interacts with 5'-untranslated region of enterovirus 71 RNA in membrane-associated complex to facilitate viral replication. PLoS One 2014; 9:e87491. [PMID: 24489926 PMCID: PMC3906175 DOI: 10.1371/journal.pone.0087491] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Accepted: 12/26/2013] [Indexed: 01/01/2023] Open
Abstract
Enterovirus 71 (EV71) is one causative agent of hand, foot, and mouth disease (HFMD), which may lead to severe neurological disorders and mortality in children. EV71 genome is a positive single-stranded RNA containing a single open reading frame (ORF) flanked by 5'-untranslated region (5'UTR) and 3'UTR. The 5'UTR is fundamentally important for virus replication by interacting with cellular proteins. Here, we revealed that poly(C)-binding protein 1 (PCBP1) specifically binds to the 5'UTR of EV71. Detailed studies indicated that the RNA-binding K-homologous 1 (KH1) domain of PCBP1 is responsible for its binding to the stem-loop I and IV of EV71 5'UTR. Interestingly, we revealed that PCBP1 is distributed in the nucleus and cytoplasm of uninfected cells, but mainly localized in the cytoplasm of EV71-infected cells due to interaction and co-localization with the viral RNA. Furthermore, sub-cellular distribution analysis showed that PCBP1 is located in ER-derived membrane, in where virus replication occurred in the cytoplasm of EV71-infected cells, suggesting PCBP1 is recruited in a membrane-associated replication complex. In addition, we found that the binding of PCBP1 to 5'UTR resulted in enhancing EV71 viral protein expression and virus production so as to facilitate viral replication. Thus, we revealed a novel mechanism in which PCBP1 as a positive regulator involved in regulation of EV71 replication in the host specialized membrane-associated replication complex, which provides an insight into cellular factors involved in EV71 replication.
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Affiliation(s)
- Zhen Luo
- State Key Laboratory of Virology and College of Life Sciences, Wuhan University, Wuhan, Hubei, China
| | - Xingchen Dong
- State Key Laboratory of Virology and College of Life Sciences, Wuhan University, Wuhan, Hubei, China
| | - Youxing Li
- State Key Laboratory of Virology and College of Life Sciences, Wuhan University, Wuhan, Hubei, China
| | - Qi Zhang
- State Key Laboratory of Virology and College of Life Sciences, Wuhan University, Wuhan, Hubei, China
| | - Cholho Kim
- State Key Laboratory of Virology and College of Life Sciences, Wuhan University, Wuhan, Hubei, China
| | - Yu Song
- State Key Laboratory of Virology and College of Life Sciences, Wuhan University, Wuhan, Hubei, China
| | - Lei Kang
- State Key Laboratory of Virology and College of Life Sciences, Wuhan University, Wuhan, Hubei, China
| | - Yingle Liu
- State Key Laboratory of Virology and College of Life Sciences, Wuhan University, Wuhan, Hubei, China
| | - Kailang Wu
- State Key Laboratory of Virology and College of Life Sciences, Wuhan University, Wuhan, Hubei, China
- * E-mail: (JW); (KW)
| | - Jianguo Wu
- State Key Laboratory of Virology and College of Life Sciences, Wuhan University, Wuhan, Hubei, China
- Chinese-French Liver Disease Research Institute, Zhongnan Hospital, Wuhan University, Wuhan, Hubei, China
- * E-mail: (JW); (KW)
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27
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Abstract
The genomic RNA of poliovirus and closely related picornaviruses perform template and non-template functions during viral RNA replication. The non-template functions are mediated by cis-active RNA sequences that bind viral and cellular proteins to form RNP complexes. The RNP complexes mediate temporally dynamic, long-range interactions in the viral genome and ensure the specificity of replication. The 5' cloverleaf (5' CL)-RNP complex serves as a key cis-active element in all of the non-template functions of viral RNA. The 5'CL-RNP complex is proposed to interact with the cre-RNP complex during VPgpUpU synthesis, the 3'NTR-poly(A) RNP complex during negative-strand initiation and the 30 end negative-strand-RNP complex during positive-strand initiation. Co-ordinating these long-range interactions is important in regulating each step in the replication cycle.
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Affiliation(s)
- Sushma A Ogram
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610, United States
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28
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Conservation of a triple-helix-forming RNA stability element in noncoding and genomic RNAs of diverse viruses. Cell Rep 2012; 2:26-32. [PMID: 22840393 DOI: 10.1016/j.celrep.2012.05.020] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Revised: 04/19/2012] [Accepted: 05/23/2012] [Indexed: 01/17/2023] Open
Abstract
Abundant expression of the long noncoding (lnc) PAN (polyadenylated nuclear) RNA by the human oncogenic gammaherpesvirus Kaposi's sarcoma-associated herpesvirus (KSHV) depends on a cis-element called the expression and nuclear retention element (ENE). The ENE upregulates PAN RNA by inhibiting its rapid nuclear decay through triple-helix formation with the poly(A) tail. Using structure-based bioinformatics, we identified six ENE-like elements in evolutionarily diverse viral genomes. Five are in double-stranded DNA viruses, including mammalian herpesviruses, insect polydnaviruses, and a protist mimivirus. One is in an insect picorna-like positive-strand RNA virus, suggesting that the ENE can counteract cytoplasmic as well as nuclear RNA decay pathways. Functionality of four of the ENEs was demonstrated by increased accumulation of an intronless polyadenylated reporter transcript in human cells. Identification of these ENEs enabled the discovery of PAN RNA homologs in two additional gammaherpesviruses, RRV and EHV2. Our findings demonstrate that searching for structural elements can lead to rapid identification of lncRNAs.
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29
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Castilla V, Scolaro LA. Involvement of heterogeneous nuclear ribonucleoproteins in viral multiplication. Future Virol 2012. [DOI: 10.2217/fvl.12.48] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The study of virus–host interactions is a major goal in molecular virology and provides new effective targets for antiviral therapies. Heterogeneous nuclear ribonucleoproteins (hnRNPs) constitute a group of cellular RNA-binding proteins localized predominantly within the nucleus, which participate in gene transcription and subsequent RNA post-transcriptional modifications. The interaction between hnRNPs and viral components was extensively demonstrated, as well as the ability of virus infections to alter the intracellular localization or the level of expression of different hnRNPs. The involvement of these proteins in the replication of numerous viruses including members from the Retroviridae, Flaviviridae, Coronaviridae, Arenaviridae, Rhabdoviridae, Papillomaviridae, Orthomyxoviridae, Picornaviridae, Togaviridae and Herpesviridae families, has been reported. In order to gain an increased understanding of the interactions between virus and cell that result in the productive infection of the latter, in this review we discuss the main findings about the role of hnRNPs in different steps of viral replication, such as RNA synthesis, translation, RNA processing and egress of newly assembled progeny virus.
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Affiliation(s)
- Viviana Castilla
- Laboratorio de Virología, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Luis A Scolaro
- Laboratorio de Virología, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
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30
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Tsueng G, Tabor-Godwin JM, Gopal A, Ruller CM, Deline S, An N, Frausto RF, Milner R, Crocker SJ, Whitton JL, Feuer R. Coxsackievirus preferentially replicates and induces cytopathic effects in undifferentiated neural progenitor cells. J Virol 2011; 85:5718-32. [PMID: 21471247 PMCID: PMC3126326 DOI: 10.1128/jvi.02261-10] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2010] [Accepted: 03/25/2011] [Indexed: 12/21/2022] Open
Abstract
Enteroviruses, including coxsackieviruses, exhibit significant tropism for the central nervous system, and these viruses are commonly associated with viral meningitis and encephalitis. Previously, we described the ability of coxsackievirus B3 (CVB3) to infect proliferating neuronal progenitor cells located in the neonatal subventricular zone and persist in the adult murine central nervous system (CNS). Here, we demonstrate that cultured murine neurospheres, which comprise neural stem cells and their progeny at different stages of development, were highly susceptible to CVB3 infection. Neurospheres, or neural progenitor and stem cells (NPSCs), isolated from neonatal C57BL/6 mice, supported high levels of infectious virus production and high viral protein expression levels following infection with a recombinant CVB3 expressing enhanced green fluorescent protein (eGFP) protein. Similarly, NPSCs isolated from neonatal actin-promoter-GFP transgenic mice (actin-GFP NPSCs) were highly susceptible to infection with a recombinant CVB3 expressing DsRed (Discosoma sp. red fluorescent protein). Both nestin-positive and NG2(+) progenitor cells within neurospheres were shown to preferentially express high levels of viral protein as soon as 24 h postinfection (p.i.). By day 3 p.i., viral protein expression and viral titers increased dramatically in NPSCs with resultant cytopathic effects (CPE) and eventual cell death. In contrast, reduced viral replication, lower levels of CPE, and diminished viral protein expression levels were observed in NPSCs differentiated for 5 or 16 days in the presence of fetal bovine serum (FBS). Despite the presence of CPE and high levels of cell death following early CVB3 infection, surviving neurospheres were readily observed and continued to express detectable levels of viral protein as long as 37 days after initial infection. Also, CVB3 infection of actin-GFP NPSCs increased the percentage of cells expressing neuronal class III β-tubulin following their differentiation in the presence of FBS. These results suggest that neural stem cells may be preferentially targeted by CVB3 and that neurogenic regions of the CNS may support persistent viral replication in the surviving host. In addition, normal progenitor cell differentiation may be altered in the host following infection.
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Affiliation(s)
- Ginger Tsueng
- Cell and Molecular Biology Joint Doctoral Program, Department of Biology, San Diego State University, San Diego, California 92182-4614
| | - Jenna M. Tabor-Godwin
- Cell and Molecular Biology Joint Doctoral Program, Department of Biology, San Diego State University, San Diego, California 92182-4614
| | - Aparajita Gopal
- Cell and Molecular Biology Joint Doctoral Program, Department of Biology, San Diego State University, San Diego, California 92182-4614
| | - Chelsea M. Ruller
- Cell and Molecular Biology Joint Doctoral Program, Department of Biology, San Diego State University, San Diego, California 92182-4614
| | - Steven Deline
- Cell and Molecular Biology Joint Doctoral Program, Department of Biology, San Diego State University, San Diego, California 92182-4614
| | - Naili An
- Cell and Molecular Biology Joint Doctoral Program, Department of Biology, San Diego State University, San Diego, California 92182-4614
| | - Ricardo F. Frausto
- Department of Immunology and Microbial Science, SP30-2110, The Scripps Research Institute, La Jolla, California 92037
| | - Richard Milner
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla California 92037
| | - Stephen J. Crocker
- Department of Immunology and Microbial Science, SP30-2110, The Scripps Research Institute, La Jolla, California 92037
| | - J. Lindsay Whitton
- Department of Immunology and Microbial Science, SP30-2110, The Scripps Research Institute, La Jolla, California 92037
| | - Ralph Feuer
- Cell and Molecular Biology Joint Doctoral Program, Department of Biology, San Diego State University, San Diego, California 92182-4614
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