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Ramos-Lorente SE, Berzal-Herranz B, Romero-López C, Berzal-Herranz A. Recruitment of the 40S ribosomal subunit by the West Nile virus 3' UTR promotes the cross-talk between the viral genomic ends for translation regulation. Virus Res 2024; 343:199340. [PMID: 38387694 PMCID: PMC10907855 DOI: 10.1016/j.virusres.2024.199340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/19/2024] [Accepted: 02/20/2024] [Indexed: 02/24/2024]
Abstract
Flaviviral RNA genomes are composed of discrete RNA structural units arranged in an ordered fashion and grouped into complex folded domains that regulate essential viral functions, e.g. replication and translation. This is achieved by adjusting the overall structure of the RNA genome via the establishment of inter- and intramolecular interactions. Translation regulation is likely the main process controlling flaviviral gene expression. Although the genomic 3' UTR is a key player in this regulation, little is known about the molecular mechanisms underlying this role. The present work provides evidence for the specific recruitment of the 40S ribosomal subunit by the 3' UTR of the West Nile virus RNA genome, showing that the joint action of both genomic ends contributes the positioning of the 40S subunit at the 5' end. The combination of structural mapping techniques revealed specific conformational requirements at the 3' UTR for 40S binding, involving the highly conserved SL-III, 5'DB, 3'DB and 3'SL elements, all involved in the translation regulation. These results point to the 40S subunit as a bridge to ensure cross-talk between both genomic ends during viral translation and support a link between 40S recruitment by the 3' UTR and translation control.
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Affiliation(s)
- Sara Esther Ramos-Lorente
- Instituto de Parasitología y Biomedicina "López-Neyra" (IPBLN), CSIC, Av. del Conocimiento 17, 18016 Armilla Granada, Spain
| | - Beatriz Berzal-Herranz
- Instituto de Parasitología y Biomedicina "López-Neyra" (IPBLN), CSIC, Av. del Conocimiento 17, 18016 Armilla Granada, Spain
| | - Cristina Romero-López
- Instituto de Parasitología y Biomedicina "López-Neyra" (IPBLN), CSIC, Av. del Conocimiento 17, 18016 Armilla Granada, Spain.
| | - Alfredo Berzal-Herranz
- Instituto de Parasitología y Biomedicina "López-Neyra" (IPBLN), CSIC, Av. del Conocimiento 17, 18016 Armilla Granada, Spain.
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2
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Zhang X, Li Y, Cao Y, Wu Y, Cheng G. The Role of Noncoding RNA in the Transmission and Pathogenicity of Flaviviruses. Viruses 2024; 16:242. [PMID: 38400018 PMCID: PMC10892091 DOI: 10.3390/v16020242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/28/2024] [Accepted: 01/31/2024] [Indexed: 02/25/2024] Open
Abstract
Noncoding RNAs (ncRNAs) constitute a class of RNA molecules that lack protein-coding capacity. ncRNAs frequently modulate gene expression through specific interactions with target proteins or messenger RNAs, thereby playing integral roles in a wide array of cellular processes. The Flavivirus genus comprises several significant members, such as dengue virus (DENV), Zika virus (ZIKV), and yellow fever virus (YFV), which have caused global outbreaks, resulting in high morbidity and mortality in human populations. The life cycle of arthropod-borne flaviviruses encompasses their transmission between hematophagous insect vectors and mammalian hosts. During this process, a complex three-way interplay occurs among the pathogen, vector, and host, with ncRNAs exerting a critical regulatory influence. ncRNAs not only constitute a crucial regulatory mechanism that has emerged from the coevolution of viruses and their hosts but also hold potential as antiviral targets for controlling flavivirus epidemics. This review introduces the biogenesis of flavivirus-derived ncRNAs and summarizes the regulatory roles of ncRNAs in viral replication, vector-mediated viral transmission, antiviral innate immunity, and viral pathogenicity. A profound comprehension of the interplay between ncRNAs and flaviviruses will help formulate efficacious prophylactic and therapeutic strategies against flavivirus-related diseases.
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Affiliation(s)
- Xianwen Zhang
- Shenzhen Bay Laboratory, Institute of Infectious Diseases, Shenzhen 518000, China
| | - Yuhan Li
- New Cornerstone Science Laboratory, Tsinghua University-Peking University Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China; (Y.L.); (Y.C.)
| | - Yingyi Cao
- New Cornerstone Science Laboratory, Tsinghua University-Peking University Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China; (Y.L.); (Y.C.)
| | - Ying Wu
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Medical School, Wuhan University, Wuhan 430072, China;
| | - Gong Cheng
- New Cornerstone Science Laboratory, Tsinghua University-Peking University Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China; (Y.L.); (Y.C.)
- Institute of Pathogenic Organisms, Shenzhen Center for Disease Control and Prevention, Shenzhen 518055, China
- Southwest United Graduate School, Kunming 650092, China
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3
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Liu Y, Guan W, Liu H. Subgenomic Flaviviral RNAs of Dengue Viruses. Viruses 2023; 15:2306. [PMID: 38140548 PMCID: PMC10747610 DOI: 10.3390/v15122306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 11/15/2023] [Accepted: 11/22/2023] [Indexed: 12/24/2023] Open
Abstract
Subgenomic flaviviral RNAs (sfRNAs) are produced during flavivirus infections in both arthropod and vertebrate cells. They are undegraded products originating from the viral 3' untranslated region (3' UTR), a result of the action of the host 5'-3' exoribonuclease, Xrn1, when it encounters specific RNA structures known as Xrn1-resistant RNAs (xrRNAs) within the viral 3' UTR. Dengue viruses generate three to four distinct species of sfRNAs through the presence of two xrRNAs and two dumbbell structures (DBs). The tertiary structures of xrRNAs have been characterized to form a ringlike structure around the 5' end of the viral RNA, effectively inhibiting the activity of Xrn1. The most important role of DENV sfRNAs is to inhibit host antiviral responses by interacting with viral and host proteins, thereby influencing viral pathogenicity, replicative fitness, epidemiological fitness, and transmission. In this review, we aimed to summarize the biogenesis, structures, and functions of DENV sfRNAs, exploring their implications for viral interference.
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Affiliation(s)
- Yi Liu
- Hubei Jiangxia Laboratory, Wuhan 430200, China
| | - Wuxiang Guan
- Hubei Jiangxia Laboratory, Wuhan 430200, China
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430207, China
| | - Haibin Liu
- Hubei Jiangxia Laboratory, Wuhan 430200, China
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430207, China
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4
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Fiacre L, Lowenski S, Bahuon C, Dumarest M, Lambrecht B, Dridi M, Albina E, Richardson J, Zientara S, Jiménez-Clavero MÁ, Pardigon N, Gonzalez G, Lecollinet S. Evaluation of NS4A, NS4B, NS5 and 3'UTR Genetic Determinants of WNV Lineage 1 Virulence in Birds and Mammals. Viruses 2023; 15:v15051094. [PMID: 37243180 DOI: 10.3390/v15051094] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 04/21/2023] [Accepted: 04/25/2023] [Indexed: 05/28/2023] Open
Abstract
West Nile virus (WNV) is amplified in an enzootic cycle involving birds as amplifying hosts. Because they do not develop high levels of viremia, humans and horses are considered to be dead-end hosts. Mosquitoes, especially from the Culex genus, are vectors responsible for transmission between hosts. Consequently, understanding WNV epidemiology and infection requires comparative and integrated analyses in bird, mammalian, and insect hosts. So far, markers of WNV virulence have mainly been determined in mammalian model organisms (essentially mice), while data in avian models are still missing. WNV Israel 1998 (IS98) is a highly virulent strain that is closely genetically related to the strain introduced into North America in 1999, NY99 (genomic sequence homology > 99%). The latter probably entered the continent at New York City, generating the most impactful WNV outbreak ever documented in wild birds, horses, and humans. In contrast, the WNV Italy 2008 strain (IT08) induced only limited mortality in birds and mammals in Europe during the summer of 2008. To test whether genetic polymorphism between IS98 and IT08 could account for differences in disease spread and burden, we generated chimeric viruses between IS98 and IT08, focusing on the 3' end of the genome (NS4A, NS4B, NS5, and 3'UTR regions) where most of the non-synonymous mutations were detected. In vitro and in vivo comparative analyses of parental and chimeric viruses demonstrated a role for NS4A/NS4B/5'NS5 in the decreased virulence of IT08 in SPF chickens, possibly due to the NS4B-E249D mutation. Additionally, significant differences between the highly virulent strain IS98 and the other three viruses were observed in mice, implying the existence of additional molecular determinants of virulence in mammals, such as the amino acid changes NS5-V258A, NS5-N280K, NS5-A372V, and NS5-R422K. As previously shown, our work also suggests that genetic determinants of WNV virulence can be host-dependent.
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Affiliation(s)
- Lise Fiacre
- Animal Health Laboratory, L'alimentation et L'environnement (INRAE), Institut National de Recherche pour L'agriculture, École Vétérinaire d'Alfort (ENVA), Agence Nationale de Sécurité Sanitaire de L'alimentation, de L'environnement et du Travail (ANSES), UMR Virology, 94700 Maisons-Alfort, France
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), UMR ASTRE, 97170 Petit-Bourg, France
- ASTRE, CIRAD, INRAe, University of Montpellier, 34000 Montpellier, France
| | - Steeve Lowenski
- Animal Health Laboratory, L'alimentation et L'environnement (INRAE), Institut National de Recherche pour L'agriculture, École Vétérinaire d'Alfort (ENVA), Agence Nationale de Sécurité Sanitaire de L'alimentation, de L'environnement et du Travail (ANSES), UMR Virology, 94700 Maisons-Alfort, France
| | - Céline Bahuon
- Animal Health Laboratory, L'alimentation et L'environnement (INRAE), Institut National de Recherche pour L'agriculture, École Vétérinaire d'Alfort (ENVA), Agence Nationale de Sécurité Sanitaire de L'alimentation, de L'environnement et du Travail (ANSES), UMR Virology, 94700 Maisons-Alfort, France
| | - Marine Dumarest
- Animal Health Laboratory, L'alimentation et L'environnement (INRAE), Institut National de Recherche pour L'agriculture, École Vétérinaire d'Alfort (ENVA), Agence Nationale de Sécurité Sanitaire de L'alimentation, de L'environnement et du Travail (ANSES), UMR Virology, 94700 Maisons-Alfort, France
| | | | - Maha Dridi
- SCIENSANO, Avian Virology and Immunology, 1180 Brussels, Belgium
| | - Emmanuel Albina
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), UMR ASTRE, 97170 Petit-Bourg, France
- ASTRE, CIRAD, INRAe, University of Montpellier, 34000 Montpellier, France
| | - Jennifer Richardson
- Animal Health Laboratory, L'alimentation et L'environnement (INRAE), Institut National de Recherche pour L'agriculture, École Vétérinaire d'Alfort (ENVA), Agence Nationale de Sécurité Sanitaire de L'alimentation, de L'environnement et du Travail (ANSES), UMR Virology, 94700 Maisons-Alfort, France
| | - Stéphan Zientara
- Animal Health Laboratory, L'alimentation et L'environnement (INRAE), Institut National de Recherche pour L'agriculture, École Vétérinaire d'Alfort (ENVA), Agence Nationale de Sécurité Sanitaire de L'alimentation, de L'environnement et du Travail (ANSES), UMR Virology, 94700 Maisons-Alfort, France
| | - Miguel-Ángel Jiménez-Clavero
- Centro de Investigación en Sanidad Animal (CISA-INIA), CSIC, Carretera Algete-El Casar s/n, 28130 Valdeolmos, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), 28001 Madrid, Spain
| | | | - Gaëlle Gonzalez
- Animal Health Laboratory, L'alimentation et L'environnement (INRAE), Institut National de Recherche pour L'agriculture, École Vétérinaire d'Alfort (ENVA), Agence Nationale de Sécurité Sanitaire de L'alimentation, de L'environnement et du Travail (ANSES), UMR Virology, 94700 Maisons-Alfort, France
| | - Sylvie Lecollinet
- Animal Health Laboratory, L'alimentation et L'environnement (INRAE), Institut National de Recherche pour L'agriculture, École Vétérinaire d'Alfort (ENVA), Agence Nationale de Sécurité Sanitaire de L'alimentation, de L'environnement et du Travail (ANSES), UMR Virology, 94700 Maisons-Alfort, France
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5
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Li D, Lu HT, Ding YZ, Wang HJ, Ye JL, Qin CF, Liu ZY. Specialized cis-Acting RNA Elements Balance Genome Cyclization to Ensure Efficient Replication of Yellow Fever Virus. J Virol 2023; 97:e0194922. [PMID: 37017533 PMCID: PMC10134800 DOI: 10.1128/jvi.01949-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 03/13/2023] [Indexed: 04/06/2023] Open
Abstract
Genome cyclization is essential for viral RNA (vRNA) replication of the vertebrate-infecting flaviviruses, and yet its regulatory mechanisms are not fully understood. Yellow fever virus (YFV) is a notorious pathogenic flavivirus. Here, we demonstrated that a group of cis-acting RNA elements in YFV balance genome cyclization to govern efficient vRNA replication. It was shown that the downstream of the 5'-cyclization sequence hairpin (DCS-HP) is conserved in the YFV clade and is important for efficient YFV propagation. By using two different replicon systems, we found that the function of the DCS-HP is determined primarily by its secondary structure and, to a lesser extent, by its base-pair composition. By combining in vitro RNA binding and chemical probing assays, we found that the DCS-HP orchestrates the balance of genome cyclization through two different mechanisms, as follows: the DCS-HP assists the correct folding of the 5' end in a linear vRNA to promote genome cyclization, and it also limits the overstabilization of the circular form through a potential crowding effect, which is influenced by the size and shape of the DCS-HP structure. We also provided evidence that an A-rich sequence downstream of the DCS-HP enhances vRNA replication and contributes to the regulation of genome cyclization. Interestingly, diversified regulatory mechanisms of genome cyclization, involving both the downstream of the 5'-cyclization sequence (CS) and the upstream of the 3'-CS elements, were identified among different subgroups of the mosquito-borne flaviviruses. In summary, our work highlighted how YFV precisely controls the balance of genome cyclization to ensure viral replication. IMPORTANCE Yellow fever virus (YFV), the prototype of the Flavivirus genus, can cause devastating yellow fever disease. Although it is preventable by vaccination, there are still tens of thousands of yellow fever cases per year, and no approved antiviral medicine is available. However, the understandings about the regulatory mechanisms of YFV replication are obscure. In this study, by a combination of bioinformatics, reverse genetics, and biochemical approaches, it was shown that the downstream of the 5'-cyclization sequence hairpin (DCS-HP) promotes efficient YFV replication by modulating the conformational balance of viral RNA. Interestingly, we found specialized combinations for the downstream of the 5'-cyclization sequence (CS) and upstream of the 3'-CS elements in different groups of the mosquito-borne flaviviruses. Moreover, possible evolutionary relationships among the various downstream of the 5'-CS elements were implied. This work highlighted the complexity of RNA-based regulatory mechanisms in the flaviviruses and will facilitate the design of RNA structure-targeted antiviral therapies.
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Affiliation(s)
- Dan Li
- The Centre for Infection and Immunity Studies, School of Medicine, Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Hai-Tao Lu
- The Centre for Infection and Immunity Studies, School of Medicine, Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Yu-Zhen Ding
- The Centre for Infection and Immunity Studies, School of Medicine, Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Hong-Jiang Wang
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
- The Chinese People’s Liberation Army Strategic Support Force Characteristic Medical Center, Beijing, China
| | - Jing-Long Ye
- The Centre for Infection and Immunity Studies, School of Medicine, Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Cheng-Feng Qin
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Zhong-Yu Liu
- The Centre for Infection and Immunity Studies, School of Medicine, Sun Yat-sen University, Shenzhen, Guangdong, China
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6
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Romero-López C, Roda-Herreros M, Berzal-Herranz B, Ramos-Lorente SE, Berzal-Herranz A. Inter- and Intramolecular RNA–RNA Interactions Modulate the Regulation of Translation Mediated by the 3′ UTR in West Nile Virus. Int J Mol Sci 2023; 24:ijms24065337. [PMID: 36982407 PMCID: PMC10049277 DOI: 10.3390/ijms24065337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 03/06/2023] [Accepted: 03/08/2023] [Indexed: 03/14/2023] Open
Abstract
RNA viruses rely on genomic structural elements to accomplish the functions necessary to complete the viral cycle. These elements participate in a dynamic network of RNA–RNA interactions that determine the overall folding of the RNA genome and may be responsible for the fine regulation of viral replication and translation as well as the transition between them. The genomes of members of the genus Flavivirus are characterized by a complexly folded 3′ UTR with a number of RNA structural elements that are conserved across isolates of each species. The present work provides evidence of intra- and intermolecular RNA–RNA interactions involving RNA structural elements in the 3′ UTR of the West Nile virus genome. The intermolecular interactions can be visualized in vitro by the formation of molecular dimers involving the participation of at least the SLI and 3′DB elements. Certainly, the 3′ UTR of dengue virus, which lacks the SLI element, forms molecular dimers in lower quantities via a single interaction site, probably 3′DB. The functional analysis of sequence or deletion mutants revealed an inverse relationship between 3′ UTR dimerization and viral translation efficiency in cell cultures. A network of RNA–RNA interactions involving 3′ UTR structural elements might therefore exist, helping to regulate viral translation.
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7
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Berzal-Herranz A, Berzal-Herranz B, Ramos-Lorente SE, Romero-López C. The Genomic 3′ UTR of Flaviviruses Is a Translation Initiation Enhancer. Int J Mol Sci 2022; 23:ijms23158604. [PMID: 35955738 PMCID: PMC9369090 DOI: 10.3390/ijms23158604] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 07/24/2022] [Accepted: 07/31/2022] [Indexed: 12/21/2022] Open
Abstract
Viruses rely on the cellular machinery of host cells to synthesize their proteins, and have developed different mechanisms enabling them to compete with cellular mRNAs for access to it. The genus Flavivirus is a large group of positive, single-stranded RNA viruses that includes several important human pathogens, such as West Nile, Dengue and Zika virus. The genome of flaviviruses bears a type 1 cap structure at its 5′ end, needed for the main translation initiation mechanism. Several members of the genus also use a cap-independent translation mechanism. The present work provides evidence that the WNV 5′ end also promotes a cap-independent translation initiation mechanism in mammalian and insect cells, reinforcing the hypothesis that this might be a general strategy of flaviviruses. In agreement with previous reports, we show that this mechanism depends on the presence of the viral genomic 3′ UTR. The results also show that the 3′ UTR of the WNV genome enhances translation of the cap-dependent mechanism. Interestingly, WNV 3′ UTR can be replaced by the 3′ UTR of other flaviviruses and the translation enhancing effect is maintained, suggesting a molecular mechanism that does not involve direct RNA-RNA interactions to be at work. In addition, the deletion of specific structural elements of the WNV 3′ UTR leads to increased cap-dependent and cap-independent translation. These findings suggest the 3′ UTR to be involved in a fine-tuned translation regulation mechanism.
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Xu B, Zhu Y, Cao C, Chen H, Jin Q, Li G, Ma J, Yang SL, Zhao J, Zhu J, Ding Y, Fang X, Jin Y, Kwok CK, Ren A, Wan Y, Wang Z, Xue Y, Zhang H, Zhang QC, Zhou Y. Recent advances in RNA structurome. SCIENCE CHINA. LIFE SCIENCES 2022; 65:1285-1324. [PMID: 35717434 PMCID: PMC9206424 DOI: 10.1007/s11427-021-2116-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 04/01/2022] [Indexed: 12/27/2022]
Abstract
RNA structures are essential to support RNA functions and regulation in various biological processes. Recently, a range of novel technologies have been developed to decode genome-wide RNA structures and novel modes of functionality across a wide range of species. In this review, we summarize key strategies for probing the RNA structurome and discuss the pros and cons of representative technologies. In particular, these new technologies have been applied to dissect the structural landscape of the SARS-CoV-2 RNA genome. We also summarize the functionalities of RNA structures discovered in different regulatory layers-including RNA processing, transport, localization, and mRNA translation-across viruses, bacteria, animals, and plants. We review many versatile RNA structural elements in the context of different physiological and pathological processes (e.g., cell differentiation, stress response, and viral replication). Finally, we discuss future prospects for RNA structural studies to map the RNA structurome at higher resolution and at the single-molecule and single-cell level, and to decipher novel modes of RNA structures and functions for innovative applications.
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Affiliation(s)
- Bingbing Xu
- MOE Laboratory of Biosystems Homeostasis & Protection, Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yanda Zhu
- MOE Laboratory of Biosystems Homeostasis & Protection, Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Changchang Cao
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Hao Chen
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China
| | - Qiongli Jin
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Guangnan Li
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Junfeng Ma
- Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Siwy Ling Yang
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, A*STAR, Singapore, Singapore
| | - Jieyu Zhao
- Department of Chemistry, and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Jianghui Zhu
- MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology and Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
| | - Yiliang Ding
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom.
| | - Xianyang Fang
- Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
| | - Yongfeng Jin
- MOE Laboratory of Biosystems Homeostasis & Protection, Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
| | - Chun Kit Kwok
- Department of Chemistry, and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China.
- Shenzhen Research Institute of City University of Hong Kong, Shenzhen, 518057, China.
| | - Aiming Ren
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China.
| | - Yue Wan
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, A*STAR, Singapore, Singapore.
| | - Zhiye Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
| | - Yuanchao Xue
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100101, China.
| | - Huakun Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun, 130024, China.
| | - Qiangfeng Cliff Zhang
- MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology and Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China.
| | - Yu Zhou
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
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Zhang YN, Li N, Zhang QY, Liu J, Zhan SL, Gao L, Zeng XY, Yu F, Zhang HQ, Li XD, Deng CL, Shi PY, Yuan ZM, Yuan SP, Ye HQ, Zhang B. Rational design of West Nile virus vaccine through large replacement of 3' UTR with internal poly(A). EMBO Mol Med 2021; 13:e14108. [PMID: 34351689 PMCID: PMC8422072 DOI: 10.15252/emmm.202114108] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 06/30/2021] [Accepted: 07/09/2021] [Indexed: 11/29/2022] Open
Abstract
The genus Flavivirus comprises numerous emerging and re-emerging arboviruses causing human illness. Vaccines are the best approach to prevent flavivirus diseases. But pathogen diversities are always one of the major hindrances for timely development of new vaccines when confronting unpredicted flavivirus outbreaks. We used West Nile virus (WNV) as a model to develop a new live-attenuated vaccine (LAV), WNV-poly(A), by replacing 5' portion (corresponding to SL and DB domains in WNV) of 3'-UTR with internal poly(A) tract. WNV-poly(A) not only propagated efficiently in Vero cells, but also was highly attenuated in mouse model. A single-dose vaccination elicited robust and long-lasting immune responses, conferring full protection against WNV challenge. Such "poly(A)" vaccine strategy may be promising for wide application in the development of flavivirus LAVs because of its general target regions in flaviviruses.
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Affiliation(s)
- Ya-Nan Zhang
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Na Li
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Qiu-Yan Zhang
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Jing Liu
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Shun-Li Zhan
- Beijing Shunlei Biotechnology Co. Ltd., Beijing, China
| | - Lei Gao
- Beijing Shunlei Biotechnology Co. Ltd., Beijing, China
| | - Xiang-Yue Zeng
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Fang Yu
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Hong-Qing Zhang
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Xiao-Dan Li
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Cheng-Lin Deng
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Pei-Yong Shi
- University of Texas Medical Branch, Galveston, TX, USA
| | - Zhi-Ming Yuan
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | | | - Han-Qing Ye
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Bo Zhang
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
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10
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Su Y, Lin T, Liu C, Cheng C, Han X, Jiang X. microRNAs, the Link Between Dengue Virus and the Host Genome. Front Microbiol 2021; 12:714409. [PMID: 34456895 PMCID: PMC8385664 DOI: 10.3389/fmicb.2021.714409] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 07/16/2021] [Indexed: 12/22/2022] Open
Abstract
Dengue virus (DENV) is a small envelope virus of Flaviviridae that is mainly transmitted by Aedes aegypti and Aedes albopictus. It can cause dengue fever with mild clinical symptoms or even life-threatening dengue hemorrhagic fever (DHF) and dengue shock syndrome (DSS). At present, there are no specific drugs or mature vaccine products to treat DENV. microRNAs (miRNAs) are a class of important non-coding small molecular RNAs that regulate gene expression at the post-transcriptional level. It is involved in and regulates a series of important life processes, such as growth and development, cell differentiation, cell apoptosis, anti-virus, and anti-tumor. miRNAs also play important roles in interactions between host and viral genome transcriptomes. Host miRNAs can directly target the genome of the virus or regulate host factors to promote or inhibit virus replication. Understanding the expression and function of miRNAs during infection with DENV and the related signal molecules of the miRNA-mediated regulatory network will provide new insights for the development of miRNA-based therapies.
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Affiliation(s)
- Yinghua Su
- College of Biological Science and Engineering, Fuzhou University, Fujian, China
| | - Ting Lin
- College of Biological Science and Engineering, Fuzhou University, Fujian, China
| | - Chun Liu
- College of Biological Science and Engineering, Fuzhou University, Fujian, China
| | - Cui Cheng
- College of Biological Science and Engineering, Fuzhou University, Fujian, China
| | - Xiao Han
- College of Biological Science and Engineering, Fuzhou University, Fujian, China
| | - Xiwen Jiang
- DAAN Gene Co., Ltd. of Sun Yat-sen University, Guangdong, China
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11
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Akiyama BM, Graham ME, O′Donoghue Z, Beckham J, Kieft J. Three-dimensional structure of a flavivirus dumbbell RNA reveals molecular details of an RNA regulator of replication. Nucleic Acids Res 2021; 49:7122-7138. [PMID: 34133732 PMCID: PMC8266583 DOI: 10.1093/nar/gkab462] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 05/07/2021] [Accepted: 05/17/2021] [Indexed: 11/14/2022] Open
Abstract
Mosquito-borne flaviviruses (MBFVs) including dengue, West Nile, yellow fever, and Zika viruses have an RNA genome encoding one open reading frame flanked by 5' and 3' untranslated regions (UTRs). The 3' UTRs of MBFVs contain regions of high sequence conservation in structured RNA elements known as dumbbells (DBs). DBs regulate translation and replication of the viral RNA genome, functions proposed to depend on the formation of an RNA pseudoknot. To understand how DB structure provides this function, we solved the x-ray crystal structure of the Donggang virus DB to 2.1Å resolution and used structural modeling to reveal the details of its three-dimensional fold. The structure confirmed the predicted pseudoknot and molecular modeling revealed how conserved sequences form a four-way junction that appears to stabilize the pseudoknot. Single-molecule FRET suggests that the DB pseudoknot is a stable element that can regulate the switch between translation and replication during the viral lifecycle by modulating long-range RNA conformational changes.
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Affiliation(s)
- Benjamin M Akiyama
- Department of Biochemistry and Molecular Genetics, Aurora, CO 80045, USA
| | - Monica E Graham
- Department of Immunology and Microbiology, Aurora, CO 80045, USA
| | - Zoe O′Donoghue
- Department of Immunology and Microbiology, Aurora, CO 80045, USA
| | - J David Beckham
- Department of Immunology and Microbiology, Aurora, CO 80045, USA
- Department of Medicine Division of Infectious Diseases, Aurora, CO 80045, USA
| | - Jeffrey S Kieft
- Department of Biochemistry and Molecular Genetics, Aurora, CO 80045, USA
- RNA BioScience Initiative, University of Colorado Denver School of Medicine, Aurora, CO 80045, USA
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12
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Mechanisms Underlying Host Range Variation in Flavivirus: From Empirical Knowledge to Predictive Models. J Mol Evol 2021; 89:329-340. [PMID: 34059925 DOI: 10.1007/s00239-021-10013-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Accepted: 05/13/2021] [Indexed: 12/22/2022]
Abstract
Preventing and controlling epidemics caused by vector-borne viruses are particularly challenging due to their diverse pool of hosts and highly adaptive nature. Many vector-borne viruses belong to the Flavivirus genus, whose members vary greatly in host range and specificity. Members of the Flavivirus genus can be categorized to four main groups: insect-specific viruses that are maintained solely in arthropod populations, mosquito-borne viruses and tick-borne viruses that are transmitted to vertebrate hosts by mosquitoes or ticks via blood feeding, and those with no-known vector. The mosquito-borne group encompasses the yellow fever, dengue, and West Nile viruses, all of which are globally spread and cause severe morbidity in humans. The Flavivirus genus is genetically diverse, and its members are subject to different host-specific and vector-specific selective constraints, which do not always align. Thus, understanding the underlying genetic differences that led to the diversity in host range within this genus is an important aspect in deciphering the mechanisms that drive host compatibility and can aid in the constant arms-race against viral threats. Here, we review the phylogenetic relationships between members of the genus, their infection bottlenecks, and phenotypic and genomic differences. We further discuss methods that utilize these differences for prediction of host shifts in flaviviruses and can contribute to viral surveillance efforts.
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13
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Molecular Insights into the Flavivirus Replication Complex. Viruses 2021; 13:v13060956. [PMID: 34064113 PMCID: PMC8224304 DOI: 10.3390/v13060956] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 05/17/2021] [Accepted: 05/17/2021] [Indexed: 12/11/2022] Open
Abstract
Flaviviruses are vector-borne RNA viruses, many of which are clinically relevant human viral pathogens, such as dengue, Zika, Japanese encephalitis, West Nile and yellow fever viruses. Millions of people are infected with these viruses around the world each year. Vaccines are only available for some members of this large virus family, and there are no effective antiviral drugs to treat flavivirus infections. The unmet need for vaccines and therapies against these flaviviral infections drives research towards a better understanding of the epidemiology, biology and immunology of flaviviruses. In this review, we discuss the basic biology of the flavivirus replication process and focus on the molecular aspects of viral genome replication. Within the virus-induced intracellular membranous compartments, flaviviral RNA genome replication takes place, starting from viral poly protein expression and processing to the assembly of the virus RNA replication complex, followed by the delivery of the progeny viral RNA to the viral particle assembly sites. We attempt to update the latest understanding of the key molecular events during this process and highlight knowledge gaps for future studies.
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14
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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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15
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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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16
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Genetic Variation in the Domain II, 3' Untranslated Region of Human and Mosquito Derived Dengue Virus Strains in Sri Lanka. Viruses 2021; 13:v13030421. [PMID: 33807922 PMCID: PMC8001906 DOI: 10.3390/v13030421] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/25/2021] [Accepted: 02/26/2021] [Indexed: 02/07/2023] Open
Abstract
Genetic variations in dengue virus (DENV) play a distinct role in epidemic emergence. The DENV 3′ UTR has become a recent interest in research. The objective of the study was to examine the genetic variation in the domain II, 3′ UTR region of human and mosquito-derived DENV. DENV-infected human sera were orally infected to laboratory reared Aedes aegypti mosquitoes. The domain II, 3′ UTR of each human- and mosquito-derived sample was amplified. The nucleotide sequence variation, phylogenetic and secondary structure analysis was carried out incorporating respective regions of so far recorded Sri Lankan and the reference genotype strains of the DENV3 and DENV1 serotypes. The human- and mosquito-derived domain II, 3′ UTR were identical in nucleotide sequences within the serotypes isolated, indicating the conserved nature of the region during host switch. The sequence analysis revealed distinct variations in study isolates compared to so far recorded Sri Lankan isolates. However, despite single nucleotide variations, the maintenance of structural integrity was evident in related strains within the serotypes in the secondary structure analysis. The phylogenetic analysis revealed distinct clade segregation of the study sequences from so far reported Sri Lankan isolates and illustrated the phylogenetic relations of the study sequences to the available global isolates of respective serotypes.
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17
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Harima H, Orba Y, Torii S, Qiu Y, Kajihara M, Eto Y, Matsuta N, Hang'ombe BM, Eshita Y, Uemura K, Matsuno K, Sasaki M, Yoshii K, Nakao R, Hall WW, Takada A, Abe T, Wolfinger MT, Simuunza M, Sawa H. An African tick flavivirus forming an independent clade exhibits unique exoribonuclease-resistant RNA structures in the genomic 3'-untranslated region. Sci Rep 2021; 11:4883. [PMID: 33649491 PMCID: PMC7921595 DOI: 10.1038/s41598-021-84365-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 02/15/2021] [Indexed: 12/16/2022] Open
Abstract
Tick-borne flaviviruses (TBFVs) infect mammalian hosts through tick bites and can cause various serious illnesses, such as encephalitis and hemorrhagic fevers, both in humans and animals. Despite their importance to public health, there is limited epidemiological information on TBFV infection in Africa. Herein, we report that a novel flavivirus, Mpulungu flavivirus (MPFV), was discovered in a Rhipicephalus muhsamae tick in Zambia. MPFV was found to be genetically related to Ngoye virus detected in ticks in Senegal, and these viruses formed a unique lineage in the genus Flavivirus. Analyses of dinucleotide contents of flaviviruses indicated that MPFV was similar to those of other TBFVs with a typical vertebrate genome signature, suggesting that MPFV may infect vertebrate hosts. Bioinformatic analyses of the secondary structures in the 3′-untranslated regions (UTRs) revealed that MPFV exhibited unique exoribonuclease-resistant RNA (xrRNA) structures. Utilizing biochemical approaches, we clarified that two xrRNA structures of MPFV in the 3′-UTR could prevent exoribonuclease activity. In summary, our findings provide new information regarding the geographical distribution of TBFV and xrRNA structures in the 3′-UTR of flaviviruses.
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Affiliation(s)
- Hayato Harima
- Hokudai Center for Zoonosis Control in Zambia, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Yasuko Orba
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan.,International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Shiho Torii
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Yongjin Qiu
- Hokudai Center for Zoonosis Control in Zambia, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Masahiro Kajihara
- Division of Global Epidemiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Yoshiki Eto
- Division of Global Epidemiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Naoya Matsuta
- Department of Electrical and Information Engineering, Graduate School of Science and Technology, Niigata University, Niigata, Japan
| | - Bernard M Hang'ombe
- Department of Para-Clinical Studies, School of Veterinary Medicine, The University of Zambia, Lusaka, Zambia.,Africa Center of Excellence for Infectious Diseases of Humans and Animals, The University of Zambia, Lusaka, Zambia
| | - Yuki Eshita
- Hokudai Center for Zoonosis Control in Zambia, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Kentaro Uemura
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan.,Drug Discovery and Disease Research Laboratory, Shionogi & Co., Ltd., Osaka, Japan
| | - Keita Matsuno
- International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan.,Unit of Risk Analysis and Management, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Michihito Sasaki
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Kentaro Yoshii
- Laboratory of Public Health, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan.,National Research Center for the Control and Prevention of Infectious Diseases (CCPID), Nagasaki University, Nagasaki, Japan
| | - Ryo Nakao
- Laboratory of Parasitology, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - William W Hall
- International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan.,National Virus Reference Laboratory, School of Medicine, University College Dublin, Dublin, Ireland.,Centre for Research in Infectious Diseases, School of Medicine, University College Dublin, Dublin, Ireland.,Global Virus Network, Baltimore, MD, USA
| | - Ayato Takada
- International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan.,Division of Global Epidemiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan.,Africa Center of Excellence for Infectious Diseases of Humans and Animals, The University of Zambia, Lusaka, Zambia.,Department of Disease Control, School of Veterinary Medicine, The University of Zambia, Lusaka, Zambia
| | - Takashi Abe
- Department of Electrical and Information Engineering, Graduate School of Science and Technology, Niigata University, Niigata, Japan
| | - Michael T Wolfinger
- Department of Theoretical Chemistry, University of Vienna, Vienna, Austria.,Research Group Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria
| | - Martin Simuunza
- Africa Center of Excellence for Infectious Diseases of Humans and Animals, The University of Zambia, Lusaka, Zambia.,Department of Disease Control, School of Veterinary Medicine, The University of Zambia, Lusaka, Zambia
| | - Hirofumi Sawa
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan. .,International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan. .,Africa Center of Excellence for Infectious Diseases of Humans and Animals, The University of Zambia, Lusaka, Zambia. .,Global Virus Network, Baltimore, MD, USA. .,Department of Disease Control, School of Veterinary Medicine, The University of Zambia, Lusaka, Zambia.
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18
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Abstract
Recent studies have renewed interest in developing novel antiviral therapeutics and vaccines based on defective interfering particles (DIPs)—a subset of viral deletion mutants that conditionally replicate. Identifying and engineering DIPs require that viral cis- and trans-acting elements be accurately mapped. It has long been known that noncoding genomic regions can be obligate cis elements acted upon in trans by gene products. In viruses, cis elements regulate gene expression, encapsidation, and other maturation processes, but mapping these elements relies on targeted iterative deletion or laborious prospecting for rare spontaneously occurring mutants. Here, we introduce a method to comprehensively map viral cis and trans elements at single-nucleotide resolution by high-throughput random deletion. Variable-size deletions are randomly generated by transposon integration, excision, and exonuclease chewback and then barcoded for tracking via sequencing (i.e., random deletion library sequencing [RanDeL-seq]). Using RanDeL-seq, we generated and screened >23,000 HIV-1 variants to generate a single-base resolution map of HIV-1’s cis and trans elements. The resulting landscape recapitulated HIV-1’s known cis-acting elements (i.e., long terminal repeat [LTR], Ψ, and Rev response element [RRE]) and, surprisingly, indicated that HIV-1’s central DNA flap (i.e., central polypurine tract [cPPT] to central termination sequence [CTS]) is as critical as the LTR, Ψ, and RRE for long-term passage. Strikingly, RanDeL-seq identified a previously unreported ∼300-bp region downstream of RRE extending to splice acceptor 7 that is equally critical for sustained viral passage. RanDeL-seq was also used to construct and screen a library of >90,000 variants of Zika virus (ZIKV). Unexpectedly, RanDeL-seq indicated that ZIKV’s cis-acting regions are larger than the untranscribed (UTR) termini, encompassing a large fraction of the nonstructural genes. Collectively, RanDeL-seq provides a versatile framework for generating viral deletion mutants, enabling discovery of replication mechanisms and development of novel antiviral therapeutics, particularly for emerging viral infections.
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19
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Fiacre L, Pagès N, Albina E, Richardson J, Lecollinet S, Gonzalez G. Molecular Determinants of West Nile Virus Virulence and Pathogenesis in Vertebrate and Invertebrate Hosts. Int J Mol Sci 2020; 21:ijms21239117. [PMID: 33266206 PMCID: PMC7731113 DOI: 10.3390/ijms21239117] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/23/2020] [Accepted: 11/26/2020] [Indexed: 12/12/2022] Open
Abstract
West Nile virus (WNV), like the dengue virus (DENV) and yellow fever virus (YFV), are major arboviruses belonging to the Flavivirus genus. WNV is emerging or endemic in many countries around the world, affecting humans and other vertebrates. Since 1999, it has been considered to be a major public and veterinary health problem, causing diverse pathologies, ranging from a mild febrile state to severe neurological damage and death. WNV is transmitted in a bird–mosquito–bird cycle, and can occasionally infect humans and horses, both highly susceptible to the virus but considered dead-end hosts. Many studies have investigated the molecular determinants of WNV virulence, mainly with the ultimate objective of guiding vaccine development. Several vaccines are used in horses in different parts of the world, but there are no licensed WNV vaccines for humans, suggesting the need for greater understanding of the molecular determinants of virulence and antigenicity in different hosts. Owing to technical and economic considerations, WNV virulence factors have essentially been studied in rodent models, and the results cannot always be transported to mosquito vectors or to avian hosts. In this review, the known molecular determinants of WNV virulence, according to invertebrate (mosquitoes) or vertebrate hosts (mammalian and avian), are presented and discussed. This overview will highlight the differences and similarities found between WNV hosts and models, to provide a foundation for the prediction and anticipation of WNV re-emergence and its risk of global spread.
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Affiliation(s)
- Lise Fiacre
- UMR 1161 Virology, ANSES, INRAE, ENVA, ANSES Animal Health Laboratory, EURL for Equine Diseases, 94704 Maisons-Alfort, France; (L.F.); (J.R.); (G.G.)
- CIRAD, UMR ASTRE, F-97170 Petit Bourg, Guadeloupe, France; (N.P.); (E.A.)
- ASTRE, University Montpellier, CIRAD, INRAE, F-34398 Montpellier, France
| | - Nonito Pagès
- CIRAD, UMR ASTRE, F-97170 Petit Bourg, Guadeloupe, France; (N.P.); (E.A.)
- ASTRE, University Montpellier, CIRAD, INRAE, F-34398 Montpellier, France
| | - Emmanuel Albina
- CIRAD, UMR ASTRE, F-97170 Petit Bourg, Guadeloupe, France; (N.P.); (E.A.)
- ASTRE, University Montpellier, CIRAD, INRAE, F-34398 Montpellier, France
| | - Jennifer Richardson
- UMR 1161 Virology, ANSES, INRAE, ENVA, ANSES Animal Health Laboratory, EURL for Equine Diseases, 94704 Maisons-Alfort, France; (L.F.); (J.R.); (G.G.)
| | - Sylvie Lecollinet
- UMR 1161 Virology, ANSES, INRAE, ENVA, ANSES Animal Health Laboratory, EURL for Equine Diseases, 94704 Maisons-Alfort, France; (L.F.); (J.R.); (G.G.)
- Correspondence: ; Tel.: +33-1-43967376
| | - Gaëlle Gonzalez
- UMR 1161 Virology, ANSES, INRAE, ENVA, ANSES Animal Health Laboratory, EURL for Equine Diseases, 94704 Maisons-Alfort, France; (L.F.); (J.R.); (G.G.)
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20
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Taylor MK, Williams EP, Wongsurawat T, Jenjaroenpun P, Nookaew I, Jonsson CB. Amplicon-Based, Next-Generation Sequencing Approaches to Characterize Single Nucleotide Polymorphisms of Orthohantavirus Species. Front Cell Infect Microbiol 2020; 10:565591. [PMID: 33163416 PMCID: PMC7591466 DOI: 10.3389/fcimb.2020.565591] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 09/08/2020] [Indexed: 12/26/2022] Open
Abstract
Whole-genome sequencing (WGS) of viruses from patient or environmental samples can provide tremendous insight into the epidemiology, drug resistance or evolution of a virus. However, we face two common hurdles in obtaining robust sequence information; the low copy number of viral genomes in specimens and the error introduced by WGS techniques. To optimize detection and minimize error in WGS of hantaviruses, we tested four amplification approaches and different amplicon pooling methods for library preparation and examined these preparations using two sequencing platforms, Illumina MiSeq and Oxford Nanopore Technologies MinION. First, we tested and optimized primers used for whole segment PCR or one kilobase amplicon amplification for even coverage using RNA isolated from the supernatant of virus-infected cells. Once optimized we assessed two sources of total RNA, virus-infected cells and supernatant from the virus-infected cells, with four variations of primer pooling for amplicons, and six different amplification approaches. We show that 99-100% genome coverage was obtained using a one-step RT-PCR reaction with one forward and reverse primer. Using a two-step RT-PCR with three distinct tiling approaches for the three genomic segments (vRNAs), we optimized primer pooling approaches for PCR amplification to achieve a greater number of aligned reads, average depth of genome, and genome coverage. The single nucleotide polymorphisms identified from MiSeq and MinION sequencing suggested intrinsic mutation frequencies of ~10-5-10-7 per genome and 10-4-10-5 per genome, respectively. We noted no difference in the coverage or accuracy when comparing WGS results with amplicons amplified from RNA extracted from infected cells or supernatant of these infected cells. Our results show that high-throughput diagnostics requiring the identification of hantavirus species or strains can be performed using MiSeq or MinION using a one-step approach. However, the two-step MiSeq approach outperformed the MinION in coverage depth and accuracy, and hence would be superior for assessment of genomes for epidemiology or evolutionary questions using the methods developed herein.
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Affiliation(s)
- Mariah K. Taylor
- Department of Microbiology, Immunology and Biochemistry, The University of Tennessee Health Science Center, Memphis, TN, United States
| | - Evan P. Williams
- Department of Microbiology, Immunology and Biochemistry, The University of Tennessee Health Science Center, Memphis, TN, United States
| | - Thidathip Wongsurawat
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Piroon Jenjaroenpun
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Intawat Nookaew
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Colleen B. Jonsson
- Department of Microbiology, Immunology and Biochemistry, The University of Tennessee Health Science Center, Memphis, TN, United States
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21
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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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22
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Cerikan B, Goellner S, Neufeldt CJ, Haselmann U, Mulder K, Chatel-Chaix L, Cortese M, Bartenschlager R. A Non-Replicative Role of the 3' Terminal Sequence of the Dengue Virus Genome in Membranous Replication Organelle Formation. Cell Rep 2020; 32:107859. [PMID: 32640225 PMCID: PMC7351112 DOI: 10.1016/j.celrep.2020.107859] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 04/11/2020] [Accepted: 06/12/2020] [Indexed: 12/14/2022] Open
Abstract
Dengue virus (DENV) and Zika virus (ZIKV), members of the Flavivirus genus, rearrange endoplasmic reticulum membranes to induce invaginations known as vesicle packets (VPs), which are the assumed sites for viral RNA replication. Mechanistic information on VP biogenesis has so far been difficult to attain due to the necessity of studying their formation under conditions of viral replication, where perturbations reducing replication will inevitably impact VP formation. Here, we report a replication-independent expression system, designated pIRO (plasmid-induced replication organelle formation) that induces bona fide DENV and ZIKV VPs that are morphologically indistinguishable from those in infected cells. Using this system, we demonstrate that sequences in the 3' terminal RNA region of the DENV, but not the ZIKV genome, contribute to VP formation in a non-replicative manner. These results validate the pIRO system that opens avenues for mechanistically dissecting virus replication from membrane reorganization.
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Affiliation(s)
- Berati Cerikan
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, Heidelberg, Germany
| | - Sarah Goellner
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, Heidelberg, Germany
| | - Christopher John Neufeldt
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, Heidelberg, Germany
| | - Uta Haselmann
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, Heidelberg, Germany
| | - Klaas Mulder
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, Heidelberg, Germany
| | - Laurent Chatel-Chaix
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, Heidelberg, Germany
| | - Mirko Cortese
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, Heidelberg, Germany
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, Heidelberg, Germany; German Center for Infection Research (DZIF), Heidelberg Partner Site, University, 69120 Heidelberg, Germany.
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23
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Hannemann H. Viral replicons as valuable tools for drug discovery. Drug Discov Today 2020; 25:1026-1033. [PMID: 32272194 PMCID: PMC7136885 DOI: 10.1016/j.drudis.2020.03.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 02/28/2020] [Accepted: 03/13/2020] [Indexed: 12/15/2022]
Abstract
RNA viruses can cause severe diseases such as dengue, Lassa, chikungunya and Ebola. Many of these viruses can only be propagated under high containment levels, necessitating the development of low containment surrogate systems such as subgenomic replicons and minigenome systems. Replicons are self-amplifying recombinant RNA molecules expressing proteins sufficient for their own replication but which do not produce infectious virions. Replicons can persist in cells and are passed on during cell division, enabling quick, efficient and high-throughput testing of drug candidates that act on viral transcription, translation and replication. This review will explore the history and potential for drug discovery of hepatitis C virus, dengue virus, respiratory syncytial virus, Ebola virus and norovirus replicon and minigenome systems.
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Affiliation(s)
- Holger Hannemann
- The Native Antigen Company, Langford Locks, Kidlington OX5 1LH, UK.
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24
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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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25
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Hosseini S, Muñoz-Soto RB, Oliva-Ramírez J, Vázquez-Villegas P, Aghamohammadi N, Rodriguez-Garcia A, Martinez-Chapa SO. Latest Updates in Dengue Fever Therapeutics: Natural, Marine and Synthetic Drugs. Curr Med Chem 2020; 27:719-744. [DOI: 10.2174/0929867325666180629124709] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 05/25/2018] [Accepted: 06/01/2018] [Indexed: 11/22/2022]
Abstract
In this paper, we review the history of Dengue, the mechanism of infection, the
molecular characteristics and components of Dengue, the mechanism of entry to the target
cells, cyclization of the genome and replication process, as well as translation of the proteins
for virus assembly. The major emphasis of this work is on natural products and plant extracts,
which were used for as palliative or adjuvant treatment of Dengue. This review article also
summarizes the latest findings in regards to the marine products as effective drugs to target
different symptoms of Dengue. Furthermore, an update on synthetic drugs for treating Dengue
is provided in this review. As a novel alternative, we describe monoclonal antibody therapy
for Dengue management and treatment.
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Affiliation(s)
- Samira Hosseini
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey, N.L. 64849, Mexico
| | - Rodrigo B. Muñoz-Soto
- Tecnologico de Monterrey, Campus Ciudad de México, Escuela de Ingeniería y Ciencias, Calle del Puente 222, Mexico City, Mexico
| | - Jacqueline Oliva-Ramírez
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Ave. Lago de Guadalupe Km 3.5, Cd Lopez Mateos, Atizapan, Estado de Mexico, Mexico
| | | | - Nasrin Aghamohammadi
- Centre for Occupational and Environmental Health, Department of Social and Preventive Medicine, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Aida Rodriguez-Garcia
- Universidad Autonoma de Nuevo Leon, Facultad de Ciencias Biologicas, Instituto de Biotecnología. Ave. Pedro de Alba S/N, Ciudad Universitaria, San Nicolás de los Garza, N.L. 66455, Mexico
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26
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de Wispelaere M, Carocci M, Burri DJ, Neidermyer WJ, Olson CM, Roggenbach I, Liang Y, Wang J, Whelan SPJ, Gray NS, Yang PL. A broad-spectrum antiviral molecule, QL47, selectively inhibits eukaryotic translation. J Biol Chem 2020; 295:1694-1703. [PMID: 31914414 PMCID: PMC7008383 DOI: 10.1074/jbc.ra119.011132] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 12/16/2019] [Indexed: 12/13/2022] Open
Abstract
Small-molecule inhibitors of translation are critical tools to study the molecular mechanisms of protein synthesis. In this study, we sought to characterize how QL47, a host-targeted, small-molecule antiviral agent, inhibits steady-state viral protein expression. We demonstrate that this small molecule broadly inhibits both viral and host protein synthesis and targets a translation step specific to eukaryotic cells. We show that QL47 inhibits protein neosynthesis initiated by both canonical cap-driven and noncanonical initiation strategies, most likely by targeting an early step in translation elongation. Our findings thus establish QL47 as a new small-molecule inhibitor that can be utilized to probe the eukaryotic translation machinery and that can be further developed as a new therapeutic agent.
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Affiliation(s)
- Mélissanne de Wispelaere
- Department of Microbiology and Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115
| | - Margot Carocci
- Department of Microbiology and Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115
| | - Dominique J Burri
- Department of Microbiology and Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115
| | - William J Neidermyer
- Department of Microbiology and Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115
| | - Calla M Olson
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215
| | - Imme Roggenbach
- Department of Microbiology and Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115
| | - Yanke Liang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215
| | - Jinhua Wang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215
| | - Sean P J Whelan
- Department of Microbiology and Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115
| | - Nathanael S Gray
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215
| | - Priscilla L Yang
- Department of Microbiology and Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115.
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27
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Kendall C, Khalid H, Müller M, Banda DH, Kohl A, Merits A, Stonehouse NJ, Tuplin A. Structural and phenotypic analysis of Chikungunya virus RNA replication elements. Nucleic Acids Res 2019; 47:9296-9312. [PMID: 31350895 PMCID: PMC6753490 DOI: 10.1093/nar/gkz640] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 07/09/2019] [Accepted: 07/16/2019] [Indexed: 02/06/2023] Open
Abstract
Chikungunya virus (CHIKV) is a re-emerging, pathogenic Alphavirus transmitted to humans by Aedes spp. mosquitoes. We have mapped the RNA structure of the 5′ region of the CHIKV genome using selective 2′-hydroxyl acylation analysed by primer extension (SHAPE) to investigate intramolecular base-pairing at single-nucleotide resolution. Taking a structure-led reverse genetic approach, in both infectious virus and sub-genomic replicon systems, we identified six RNA replication elements essential to efficient CHIKV genome replication - including novel elements, either not previously analysed in other alphaviruses or specific to CHIKV. Importantly, through a reverse genetic approach we demonstrate that the replication elements function within the positive-strand genomic copy of the virus genome, in predominantly structure-dependent mechanisms during efficient replication of the CHIKV genome. Comparative analysis in human and mosquito-derived cell lines reveal that a novel element within the 5′UTR is essential for efficient replication in both host systems, while those in the adjacent nsP1 encoding region are specific to either vertebrate or invertebrate host cells. In addition to furthering our knowledge of fundamental aspects of the molecular virology of this important human pathogen, we foresee that results from this study will be important for rational design of a genetically stable attenuated vaccine.
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Affiliation(s)
- Catherine Kendall
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Henna Khalid
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Marietta Müller
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Dominic H Banda
- University of Ghent, Corneel Heymanslaan 10, B-9000 Ghent, Belgium
| | - Alain Kohl
- MRC-Centre for Virus Research, University of Glasgow, Glasgow, G61 1QH, UK
| | - Andres Merits
- Institute of Technology, University of Tartu, Tartu 50411, Estonia
| | - Nicola J Stonehouse
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Andrew Tuplin
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
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28
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Hodge K, Kamkaew M, Pisitkun T, Chimnaronk S. Flavors of Flaviviral RNA Structure: towards an Integrated View of RNA Function from Translation through Encapsidation. Bioessays 2019; 41:e1900003. [PMID: 31210384 PMCID: PMC7161798 DOI: 10.1002/bies.201900003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 05/02/2019] [Indexed: 01/03/2023]
Abstract
For many viruses, RNA is the holder of genetic information and serves as the template for both replication and translation. While host and viral proteins play important roles in viral decision‐making, the extent to which viral RNA (vRNA) actively participates in translation and replication might be surprising. Here, the focus is on flaviviruses, which include common human scourges such as dengue, West Nile, and Zika viruses, from an RNA‐centric viewpoint. In reviewing more recent findings, an attempt is made to fill knowledge gaps and revisit some canonical views of vRNA structures involved in replication. In particular, alternative views are offered on the nature of the flaviviral promoter and genome cyclization, and the feasibility of refining in vitro‐derived models with modern RNA probing and sequencing methods is pointed out. By tracing vRNA structures from translation through encapsidation, a dynamic molecule closely involved in the self‐regulation of viral replication is revealed.
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Affiliation(s)
- Kenneth Hodge
- The Systems Biology Center, Research Affairs, Faculty of Medicine, Chulalongkorn University, 1873 Rama 4 Road, Pathumwan, Bangkok, 10330, Thailand
| | - Maliwan Kamkaew
- Laboratory of RNA Biology, Institute of Molecular Biosciences, Mahidol University, Salaya Campus, Nakhon Pathom, 73170, Thailand
| | - Trairak Pisitkun
- The Systems Biology Center, Research Affairs, Faculty of Medicine, Chulalongkorn University, 1873 Rama 4 Road, Pathumwan, Bangkok, 10330, Thailand
| | - Sarin Chimnaronk
- Laboratory of RNA Biology, Institute of Molecular Biosciences, Mahidol University, Salaya Campus, Nakhon Pathom, 73170, Thailand
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29
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Ochsenreiter R, Hofacker IL, Wolfinger MT. Functional RNA Structures in the 3'UTR of Tick-Borne, Insect-Specific and No-Known-Vector Flaviviruses. Viruses 2019; 11:E298. [PMID: 30909641 PMCID: PMC6466055 DOI: 10.3390/v11030298] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 03/19/2019] [Accepted: 03/20/2019] [Indexed: 12/21/2022] Open
Abstract
Untranslated regions (UTRs) of flaviviruses contain a large number of RNA structural elements involved in mediating the viral life cycle, including cyclisation, replication, and encapsidation. Here we report on a comparative genomics approach to characterize evolutionarily conserved RNAs in the 3 ' UTR of tick-borne, insect-specific and no-known-vector flaviviruses in silico. Our data support the wide distribution of previously experimentally characterized exoribonuclease resistant RNAs (xrRNAs) within tick-borne and no-known-vector flaviviruses and provide evidence for the existence of a cascade of duplicated RNA structures within insect-specific flaviviruses. On a broader scale, our findings indicate that viral 3 ' UTRs represent a flexible scaffold for evolution to come up with novel xrRNAs.
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Affiliation(s)
- Roman Ochsenreiter
- Department of Theoretical Chemistry, University of Vienna, Währingerstraße 17, 1090 Vienna, Austria.
| | - Ivo L Hofacker
- Department of Theoretical Chemistry, University of Vienna, Währingerstraße 17, 1090 Vienna, Austria.
- Research Group BCB, Faculty of Computer Science, University of Vienna, Währingerstraße 29, 1090 Vienna, Austria.
| | - Michael T Wolfinger
- Department of Theoretical Chemistry, University of Vienna, Währingerstraße 17, 1090 Vienna, Austria.
- Research Group BCB, Faculty of Computer Science, University of Vienna, Währingerstraße 29, 1090 Vienna, Austria.
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Kraft JJ, Peterson MS, Cho SK, Wang Z, Hui A, Rakotondrafara AM, Treder K, Miller CL, Miller WA. The 3' Untranslated Region of a Plant Viral RNA Directs Efficient Cap-Independent Translation in Plant and Mammalian Systems. Pathogens 2019; 8:E28. [PMID: 30823456 PMCID: PMC6471432 DOI: 10.3390/pathogens8010028] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 02/03/2019] [Accepted: 02/23/2019] [Indexed: 11/29/2022] Open
Abstract
Many plant viral RNA genomes lack a 5' cap, and instead are translated via a cap-independent translation element (CITE) in the 3' untranslated region (UTR). The panicum mosaic virus-like CITE (PTE), found in many plant viral RNAs, binds and requires the cap-binding translation initiation factor eIF4E to facilitate translation. eIF4E is structurally conserved between plants and animals, so we tested cap-independent translation efficiency of PTEs of nine plant viruses in plant and mammalian systems. The PTE from thin paspalum asymptomatic virus (TPAV) facilitated efficient cap-independent translation in wheat germ extract, rabbit reticulocyte lysate, HeLa cell lysate, and in oat and mammalian (BHK) cells. Human eIF4E bound the TPAV PTE but not a PTE that did not stimulate cap-independent translation in mammalian extracts or cells. Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) footprinting revealed that both human and wheat eIF4E protected the conserved guanosine (G)-rich domain in the TPAV PTE pseudoknot. The central G plays a key role, as it was found to be required for translation and protection from SHAPE modification by eIF4E. These results provide insight on how plant viruses gain access to the host's translational machinery, an essential step in infection, and raise the possibility that similar PTE-like mechanisms may exist in mRNAs of mammals or their viruses.
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Affiliation(s)
- Jelena J Kraft
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011, USA.
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA.
| | - Mariko S Peterson
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA.
- Yerkes National Primate Research Center, Emory Vaccine Center 2009, 954 Gatewood Rd NE, Atlanta, GA 30329, USA.
| | - Sung Ki Cho
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011, USA.
- Dura-Line, 1355 Carden Farm Dr., Clinton, TN 37716, USA.
| | - Zhaohui Wang
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011, USA.
- Department of Orthopaedic Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA.
| | - Alice Hui
- Interdepartmental Plant Biology Program, Iowa State University, Ames, IA 50011, USA.
| | | | - Krzysztof Treder
- Laboratory of Molecular Diagnostic and Biochemistry, Bonin Research Center, Plant Breeding and Acclimatization Institute⁻National Research Institute, 76-009 Bonin, Poland.
| | - Cathy L Miller
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA.
| | - W Allen Miller
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011, USA.
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA.
- Interdepartmental Plant Biology Program, Iowa State University, Ames, IA 50011, USA.
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Reyes-Ruiz JM, Osuna-Ramos JF, Bautista-Carbajal P, Jaworski E, Soto-Acosta R, Cervantes-Salazar M, Angel-Ambrocio AH, Castillo-Munguía JP, Chávez-Munguía B, De Nova-Ocampo M, Routh A, Del Ángel RM, Salas-Benito JS. Mosquito cells persistently infected with dengue virus produce viral particles with host-dependent replication. Virology 2019; 531:1-18. [PMID: 30844508 DOI: 10.1016/j.virol.2019.02.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 02/22/2019] [Accepted: 02/26/2019] [Indexed: 11/26/2022]
Abstract
Dengue viruses (DENV) are important arboviruses that can establish a persistent infection in its mosquito vector Aedes. Mosquitoes have a short lifetime in nature which makes trying to study the processes that take place during persistent viral infections in vivo. Therefore, C6/36 cells have been used to study this type of infection. C6/36 cells persistently infected with DENV 2 produce virions that cannot infect BHK -21 cells. We hypothesized that the following passages in mosquito cells have a deleterious impact on DENV fitness in vertebrate cells. Here, we demonstrated that the viral particles released from persistently infected cells were infectious to mosquito but not to vertebrate cells. This host restriction occurs at the replication level and is associated with several mutations in the DENV genome. In summary, our findings provide new information about viral replication fitness in a host-dependent manner.
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Affiliation(s)
- José Manuel Reyes-Ruiz
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico
| | - Juan Fidel Osuna-Ramos
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico
| | - Patricia Bautista-Carbajal
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico
| | - Elizabeth Jaworski
- Department of Biochemistry and Molecular Biology, The University of Texas, Medical Branch, Galveston, TX 77555, USA
| | - Rubén Soto-Acosta
- Department of Biochemistry and Molecular Biology, The University of Texas, Medical Branch, Galveston, TX 77555, USA
| | - Margot Cervantes-Salazar
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico
| | | | - Juan Pablo Castillo-Munguía
- Maestría en Ciencias en Biomedicina Molecular, Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, Mexico
| | - Bibiana Chávez-Munguía
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico
| | - Mónica De Nova-Ocampo
- Maestría en Ciencias en Biomedicina Molecular, Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, Mexico
| | - Andrew Routh
- Department of Biochemistry and Molecular Biology, The University of Texas, Medical Branch, Galveston, TX 77555, USA; Sealy Center for Structural Biology and Molecular Biophysics, The University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Rosa María Del Ángel
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico.
| | - Juan Santiago Salas-Benito
- Maestría en Ciencias en Biomedicina Molecular, Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, Mexico; Doctorado en Ciencias en Biotecnología, Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, Mexico.
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Abstract
Flaviviruses include a diverse group of medically important viruses that cycle between mosquitoes and humans. During this natural process of switching hosts, each species imposes different selective forces on the viral population. Using dengue virus (DENV) as model, we found that paralogous RNA structures originating from duplications in the viral 3' untranslated region (UTR) are under different selective pressures in the two hosts. These RNA structures, known as dumbbells (DB1 and DB2), were originally proposed to be enhancers of viral replication. Analysis of viruses obtained from infected mosquitoes showed selection of mutations that mapped in DB2. Recombinant viruses carrying the identified variations confirmed that these mutations greatly increase viral replication in mosquito cells, with low or no impact in human cells. Use of viruses lacking each of the DB structures revealed opposite viral phenotypes. While deletion of DB1 reduced viral replication about 10-fold, viruses lacking DB2 displayed a great increase of fitness in mosquitoes, confirming a functional diversification of these similar RNA elements. Mechanistic analysis indicated that DB1 and DB2 differentially modulate viral genome cyclization and RNA replication. We found that a pseudoknot formed within DB2 competes with long-range RNA-RNA interactions that are necessary for minus-strand RNA synthesis. Our results support a model in which a functional diversification of duplicated RNA elements in the viral 3' UTR is driven by host-specific requirements. This study provides new ideas for understanding molecular aspects of the evolution of RNA viruses that naturally jump between different species.IMPORTANCE Flaviviruses constitute the most relevant group of arthropod-transmitted viruses, including important human pathogens such as the dengue, Zika, yellow fever, and West Nile viruses. The natural alternation of these viruses between vertebrate and invertebrate hosts shapes the viral genome population, which leads to selection of different viral variants with potential implications for epidemiological fitness and pathogenesis. However, the selective forces and mechanisms acting on the viral RNA during host adaptation are still largely unknown. Here, we found that two almost identical tandem RNA structures present at the viral 3' untranslated region are under different selective pressures in the two hosts. Mechanistic studies indicated that the two RNA elements, known as dumbbells, contain sequences that overlap essential RNA cyclization elements involved in viral RNA synthesis. The data support a model in which the duplicated RNA structures differentially evolved to accommodate distinct functions for viral replication in the two hosts.
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Ahmad Z, Poh CL. The Conserved Molecular Determinants of Virulence in Dengue Virus. Int J Med Sci 2019; 16:355-365. [PMID: 30911269 PMCID: PMC6428985 DOI: 10.7150/ijms.29938] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 12/17/2018] [Indexed: 12/22/2022] Open
Abstract
Dengue virus belongs to the Flaviviridae family which also includes viruses such as the Zika, West Nile and yellow fever virus. Dengue virus generally causes mild disease, however, more severe forms of the dengue virus infection, dengue haemorrhagic fever (DHF) and dengue haemorrhagic fever with shock syndrome (DSS) can also occur, resulting in multiple organ failure and even death, especially in children. The only dengue vaccine available in the market, CYD-TDV offers limited coverage for vaccinees from 9-45 years of age and is only recommended for individuals with prior dengue exposure. A number of mutations that were shown to attenuate virulence of dengue virus in vitro and/or in vivo have been identified in the literature. The mutations which fall within the conserved regions of all four dengue serotypes are discussed. This review hopes to provide information leading to the construction of a live attenuated dengue vaccine that is suitable for all ages, irrespective of the infecting dengue serotype and prior dengue exposure.
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Affiliation(s)
- Zuleeza Ahmad
- Centre for Virus and Vaccine Research, School of Science and Technology, Sunway University, 47500 Subang Jaya, Selangor, Malaysia
| | - Chit Laa Poh
- Centre for Virus and Vaccine Research, School of Science and Technology, Sunway University, 47500 Subang Jaya, Selangor, Malaysia
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34
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Mazeaud C, Freppel W, Chatel-Chaix L. The Multiples Fates of the Flavivirus RNA Genome During Pathogenesis. Front Genet 2018. [PMID: 30564270 DOI: 10.3389/fgene.2018.00595/full] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/26/2023] Open
Abstract
The Flavivirus genus comprises many viruses (including dengue, Zika, West Nile and yellow fever viruses) which constitute important public health concerns worldwide. For several of these pathogens, neither antivirals nor vaccines are currently available. In addition to this unmet medical need, flaviviruses are of particular interest since they constitute an excellent model for the study of spatiotemporal regulation of RNA metabolism. Indeed, with no DNA intermediate or nuclear step, the flaviviral life cycle entirely relies on the cytoplasmic fate of a single RNA species, namely the genomic viral RNA (vRNA) which contains all the genetic information necessary for optimal viral replication. From a single open reading frame, the vRNA encodes a polyprotein which is processed to generate the mature viral proteins. In addition to coding for the viral polyprotein, the vRNA serves as a template for RNA synthesis and is also selectively packaged into newly assembled viral particles. Notably, vRNA translation, replication and encapsidation must be tightly coordinated in time and space via a fine-tuned equilibrium as these processes cannot occur simultaneously and hence, are mutually exclusive. As such, these dynamic processes involve several vRNA secondary and tertiary structures as well as RNA modifications. Finally, the vRNA can be detected as a foreign molecule by cytosolic sensors which trigger upon activation antiviral signaling pathways and the production of antiviral factors such as interferons and interferon-stimulated genes. However, to create an environment favorable to infection, flaviviruses have evolved mechanisms to dampen these antiviral processes, notably through the production of a specific vRNA degradation product termed subgenomic flavivirus RNA (sfRNA). In this review, we discuss the current understanding of the fates of flavivirus vRNA and how this is regulated at the molecular level to achieve an optimal replication within infected cells.
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Affiliation(s)
- Clément Mazeaud
- Institut National de la Recherche Scientifique, Centre INRS-Institut Armand-Frappier, Laval, QC, Canada
| | - Wesley Freppel
- Institut National de la Recherche Scientifique, Centre INRS-Institut Armand-Frappier, Laval, QC, Canada
| | - Laurent Chatel-Chaix
- Institut National de la Recherche Scientifique, Centre INRS-Institut Armand-Frappier, Laval, QC, Canada
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35
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Balasubramanian A, Pilankatta R, Teramoto T, Sajith AM, Nwulia E, Kulkarni A, Padmanabhan R. Inhibition of dengue virus by curcuminoids. Antiviral Res 2018; 162:71-78. [PMID: 30529358 DOI: 10.1016/j.antiviral.2018.12.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 11/21/2018] [Accepted: 12/02/2018] [Indexed: 01/01/2023]
Abstract
The dengue virus is considered to be a globally important human pathogen prevalent in tropical and subtropical regions of the world. According to a recent estimate, the disease burden due to DENV infections is ∼390 million infections per year globally in ∼100 countries including the southern US, Puerto Rico and Hawaii, resulting in nearly ∼25,000 deaths mostly among children. Despite the significant morbidity and mortality that results from DENV infections, there is currently no effective chemotherapeutic treatment for DENV infections. We identified curcumin as an inhibitor of DENV2 NS2B/NS3protease in a previous high-throughput screening (HTS) campaign. We synthesized four analogues of curcumin (curcuminoids) and tested the in vitro protease inhibition activity and inhibition of replication by cell-based assays. The results revealed that curcumin is a weak inhibitor of the viral protease. However, the analogues exhibited more potent inhibition of DENV infectivity in plaque assays suggesting that the cellular pathway(s) required for viral replication and/or assembly are targeted by these compounds. Further analysis shows that inhibition of genes involved in lipid biosynthesis, and of actin polymerization by curcuminoids, are likely to be involved as their mode of action in DENV2-infected cells. Three of the curcumin derivatives possess good selectivity indices (SI) (>10) when compared to the parent curcumin.
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Affiliation(s)
| | - Rajendra Pilankatta
- Department of Microbiology and Immunology, Georgetown University, Washington, D.C, USA
| | - Tadahisa Teramoto
- Department of Microbiology and Immunology, Georgetown University, Washington, D.C, USA
| | - Ayyiliath M Sajith
- Department of Psychiatry and Behavioral Sciences, College of Medicine, Howard University, Washington, D.C, USA
| | - Evaristus Nwulia
- Department of Psychiatry and Behavioral Sciences, College of Medicine, Howard University, Washington, D.C, USA
| | - Amol Kulkarni
- Department of Pharmaceutical Sciences, College of Pharmacy, Howard University, Washington, D.C, USA.
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36
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Mazeaud C, Freppel W, Chatel-Chaix L. The Multiples Fates of the Flavivirus RNA Genome During Pathogenesis. Front Genet 2018; 9:595. [PMID: 30564270 PMCID: PMC6288177 DOI: 10.3389/fgene.2018.00595] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 11/15/2018] [Indexed: 12/11/2022] Open
Abstract
The Flavivirus genus comprises many viruses (including dengue, Zika, West Nile and yellow fever viruses) which constitute important public health concerns worldwide. For several of these pathogens, neither antivirals nor vaccines are currently available. In addition to this unmet medical need, flaviviruses are of particular interest since they constitute an excellent model for the study of spatiotemporal regulation of RNA metabolism. Indeed, with no DNA intermediate or nuclear step, the flaviviral life cycle entirely relies on the cytoplasmic fate of a single RNA species, namely the genomic viral RNA (vRNA) which contains all the genetic information necessary for optimal viral replication. From a single open reading frame, the vRNA encodes a polyprotein which is processed to generate the mature viral proteins. In addition to coding for the viral polyprotein, the vRNA serves as a template for RNA synthesis and is also selectively packaged into newly assembled viral particles. Notably, vRNA translation, replication and encapsidation must be tightly coordinated in time and space via a fine-tuned equilibrium as these processes cannot occur simultaneously and hence, are mutually exclusive. As such, these dynamic processes involve several vRNA secondary and tertiary structures as well as RNA modifications. Finally, the vRNA can be detected as a foreign molecule by cytosolic sensors which trigger upon activation antiviral signaling pathways and the production of antiviral factors such as interferons and interferon-stimulated genes. However, to create an environment favorable to infection, flaviviruses have evolved mechanisms to dampen these antiviral processes, notably through the production of a specific vRNA degradation product termed subgenomic flavivirus RNA (sfRNA). In this review, we discuss the current understanding of the fates of flavivirus vRNA and how this is regulated at the molecular level to achieve an optimal replication within infected cells.
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Affiliation(s)
- Clément Mazeaud
- Institut National de la Recherche Scientifique, Centre INRS-Institut Armand-Frappier, Laval, QC, Canada
| | - Wesley Freppel
- Institut National de la Recherche Scientifique, Centre INRS-Institut Armand-Frappier, Laval, QC, Canada
| | - Laurent Chatel-Chaix
- Institut National de la Recherche Scientifique, Centre INRS-Institut Armand-Frappier, Laval, QC, Canada
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37
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Liu X, Liu Y, Zhang Q, Zhang B, Xia H, Yuan Z. Homologous RNA secondary structure duplications in 3′ untranslated region influence subgenomic RNA production and replication of dengue virus. Virology 2018; 524:114-126. [DOI: 10.1016/j.virol.2018.08.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 08/18/2018] [Accepted: 08/21/2018] [Indexed: 10/28/2022]
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38
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Ziv O, Gabryelska MM, Lun ATL, Gebert LFR, Sheu-Gruttadauria J, Meredith LW, Liu ZY, Kwok CK, Qin CF, MacRae IJ, Goodfellow I, Marioni JC, Kudla G, Miska EA. COMRADES determines in vivo RNA structures and interactions. Nat Methods 2018; 15:785-788. [PMID: 30202058 PMCID: PMC6168409 DOI: 10.1038/s41592-018-0121-0] [Citation(s) in RCA: 117] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 07/20/2018] [Indexed: 01/07/2023]
Abstract
The structural flexibility of RNA underlies fundamental biological processes, but there are no methods for exploring the multiple conformations adopted by RNAs in vivo. We developed cross-linking of matched RNAs and deep sequencing (COMRADES) for in-depth RNA conformation capture, and a pipeline for the retrieval of RNA structural ensembles. Using COMRADES, we determined the architecture of the Zika virus RNA genome inside cells, and identified multiple site-specific interactions with human noncoding RNAs.
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Affiliation(s)
- Omer Ziv
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK.
- Department of Genetics, University of Cambridge, Cambridge, UK.
| | - Marta M Gabryelska
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland, UK
| | - Aaron T L Lun
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Luca F R Gebert
- Department of Integrative Structural and Computational Biology, the Scripps Research Institute, La Jolla, CA, USA
| | - Jessica Sheu-Gruttadauria
- Department of Integrative Structural and Computational Biology, the Scripps Research Institute, La Jolla, CA, USA
| | - Luke W Meredith
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Zhong-Yu Liu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- School of Medicine (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Chun Kit Kwok
- Department of Chemistry, City University of Hong Kong, Hong Kong, China
| | - Cheng-Feng Qin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Ian J MacRae
- Department of Integrative Structural and Computational Biology, the Scripps Research Institute, La Jolla, CA, USA
| | - Ian Goodfellow
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - John C Marioni
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
- Wellcome Sanger Institute, Cambridge, UK
| | - Grzegorz Kudla
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland, UK.
| | - Eric A Miska
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK.
- Department of Genetics, University of Cambridge, Cambridge, UK.
- Wellcome Sanger Institute, Cambridge, UK.
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39
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Klitting R, Fischer C, Drexler JF, Gould EA, Roiz D, Paupy C, de Lamballerie X. What Does the Future Hold for Yellow Fever Virus? (II). Genes (Basel) 2018; 9:E425. [PMID: 30134625 PMCID: PMC6162518 DOI: 10.3390/genes9090425] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 08/13/2018] [Accepted: 08/16/2018] [Indexed: 02/06/2023] Open
Abstract
As revealed by the recent resurgence of yellow fever virus (YFV) activity in the tropical regions of Africa and South America, YFV control measures need urgent rethinking. Over the last decade, most reported outbreaks occurred in, or eventually reached, areas with low vaccination coverage but that are suitable for virus transmission, with an unprecedented risk of expansion to densely populated territories in Africa, South America and Asia. As reflected in the World Health Organization's initiative launched in 2017, it is high time to strengthen epidemiological surveillance to monitor accurately viral dissemination, and redefine vaccination recommendation areas. Vector-control and immunisation measures need to be adapted and vaccine manufacturing must be reconciled with an increasing demand. We will have to face more yellow fever (YF) cases in the upcoming years. Hence, improving disease management through the development of efficient treatments will prove most beneficial. Undoubtedly, these developments will require in-depth descriptions of YFV biology at molecular, physiological and ecological levels. This second section of a two-part review describes the current state of knowledge and gaps regarding the molecular biology of YFV, along with an overview of the tools that can be used to manage the disease at the individual, local and global levels.
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Affiliation(s)
- Raphaëlle Klitting
- Unité des Virus Émergents (UVE: Aix-Marseille Univ⁻IRD 190⁻Inserm 1207⁻IHU Méditerranée Infection), 13385 Marseille CEDEX 05, France.
| | - Carlo Fischer
- Charité-Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, 10117 Berlin, Germany.
- German Center for Infection Research (DZIF), 38124 Braunschweig, Germany.
| | - Jan F Drexler
- Charité-Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, 10117 Berlin, Germany.
- German Center for Infection Research (DZIF), 38124 Braunschweig, Germany.
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, 119991 Moscow, Russia.
| | - Ernest A Gould
- Unité des Virus Émergents (UVE: Aix-Marseille Univ⁻IRD 190⁻Inserm 1207⁻IHU Méditerranée Infection), 13385 Marseille CEDEX 05, France.
| | - David Roiz
- UMR Maladies Infectieuses et Vecteurs: Écologie, Génétique Évolution et Contrôle (MIVEGEC: IRD, CNRS, Univ. Montpellier), 34394 Montpellier, France.
| | - Christophe Paupy
- UMR Maladies Infectieuses et Vecteurs: Écologie, Génétique Évolution et Contrôle (MIVEGEC: IRD, CNRS, Univ. Montpellier), 34394 Montpellier, France.
| | - Xavier de Lamballerie
- Unité des Virus Émergents (UVE: Aix-Marseille Univ⁻IRD 190⁻Inserm 1207⁻IHU Méditerranée Infection), 13385 Marseille CEDEX 05, France.
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40
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Decreased accumulation of subgenomic RNA in human cells infected with vaccine candidate DEN4Δ30 increases viral susceptibility to type I interferon. Vaccine 2018; 36:3460-3467. [PMID: 29752023 DOI: 10.1016/j.vaccine.2018.04.087] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 04/19/2018] [Accepted: 04/20/2018] [Indexed: 11/20/2022]
Abstract
The NIH has developed live attenuated dengue virus (DENV) vaccine candidates by deletion of 30 nucleotides (Δ30) from the untranslated region of the viral genome. Although this attenuation strategy has proven to be effective in generating safe and immunogenic vaccine strains, the molecular mechanism of attenuation is largely unknown. To examine the mediators of the observed attenuation phenotype, differences in translation efficiency, genome replication, cytotoxicity, and type I interferon susceptibility were compared between wild type parental DENV and DENVΔ30 attenuated vaccine candidates. We observed that decreased accumulation of subgenomic RNA (sfRNA) from the vaccine candidates in infected human cells causes increased type I IFN susceptibility and propose this as one of the of attenuation mechanisms produced by the 3' UTR Δ30 mutation.
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41
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Barrows NJ, Campos RK, Liao KC, Prasanth KR, Soto-Acosta R, Yeh SC, Schott-Lerner G, Pompon J, Sessions OM, Bradrick SS, Garcia-Blanco MA. Biochemistry and Molecular Biology of Flaviviruses. Chem Rev 2018; 118:4448-4482. [PMID: 29652486 DOI: 10.1021/acs.chemrev.7b00719] [Citation(s) in RCA: 193] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Flaviviruses, such as dengue, Japanese encephalitis, tick-borne encephalitis, West Nile, yellow fever, and Zika viruses, are critically important human pathogens that sicken a staggeringly high number of humans every year. Most of these pathogens are transmitted by mosquitos, and not surprisingly, as the earth warms and human populations grow and move, their geographic reach is increasing. Flaviviruses are simple RNA-protein machines that carry out protein synthesis, genome replication, and virion packaging in close association with cellular lipid membranes. In this review, we examine the molecular biology of flaviviruses touching on the structure and function of viral components and how these interact with host factors. The latter are functionally divided into pro-viral and antiviral factors, both of which, not surprisingly, include many RNA binding proteins. In the interface between the virus and the hosts we highlight the role of a noncoding RNA produced by flaviviruses to impair antiviral host immune responses. Throughout the review, we highlight areas of intense investigation, or a need for it, and potential targets and tools to consider in the important battle against pathogenic flaviviruses.
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Affiliation(s)
- Nicholas J Barrows
- Department of Biochemistry and Molecular Biology , University of Texas Medical Branch , Galveston , Texas 77555 , United States.,Department of Molecular Genetics and Microbiology , Duke University , Durham , North Carolina 27710 , United States
| | - Rafael K Campos
- Department of Biochemistry and Molecular Biology , University of Texas Medical Branch , Galveston , Texas 77555 , United States.,Department of Molecular Genetics and Microbiology , Duke University , Durham , North Carolina 27710 , United States
| | - Kuo-Chieh Liao
- Programme in Emerging Infectious Diseases , Duke-NUS Medical School , Singapore 169857 , Singapore
| | - K Reddisiva Prasanth
- Department of Biochemistry and Molecular Biology , University of Texas Medical Branch , Galveston , Texas 77555 , United States
| | - Ruben Soto-Acosta
- Department of Biochemistry and Molecular Biology , University of Texas Medical Branch , Galveston , Texas 77555 , United States
| | - Shih-Chia Yeh
- Programme in Emerging Infectious Diseases , Duke-NUS Medical School , Singapore 169857 , Singapore
| | - Geraldine Schott-Lerner
- Department of Biochemistry and Molecular Biology , University of Texas Medical Branch , Galveston , Texas 77555 , United States
| | - Julien Pompon
- Programme in Emerging Infectious Diseases , Duke-NUS Medical School , Singapore 169857 , Singapore.,MIVEGEC, IRD, CNRS, Université de Montpellier , Montpellier 34090 , France
| | - October M Sessions
- Programme in Emerging Infectious Diseases , Duke-NUS Medical School , Singapore 169857 , Singapore
| | - Shelton S Bradrick
- Department of Biochemistry and Molecular Biology , University of Texas Medical Branch , Galveston , Texas 77555 , United States
| | - Mariano A Garcia-Blanco
- Department of Biochemistry and Molecular Biology , University of Texas Medical Branch , Galveston , Texas 77555 , United States.,Programme in Emerging Infectious Diseases , Duke-NUS Medical School , Singapore 169857 , Singapore
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42
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Srivarangkul P, Yuttithamnon W, Suroengrit A, Pankaew S, Hengphasatporn K, Rungrotmongkol T, Phuwapraisirisan P, Ruxrungtham K, Boonyasuppayakorn S. A novel flavanone derivative inhibits dengue virus fusion and infectivity. Antiviral Res 2018; 151:27-38. [PMID: 29360474 DOI: 10.1016/j.antiviral.2018.01.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 10/10/2017] [Accepted: 01/17/2018] [Indexed: 01/24/2023]
Abstract
Dengue infection is a global burden affecting millions of world population. Previous studies indicated that flavanones were potential dengue virus inhibitors. We discovered that a novel flavanone derivative, 5-hydroxy-7-methoxy-6-methylflavanone (FN5Y), inhibited DENV2 pH-dependent fusion in cell-based system with strong binding efficiency to DENV envelope protein at K (P83, L107, K128, L198), K' (T48, E49, A50, L198, Q200, L277), X' (Y138, V354, I357), and Y' (V97, R99, N103, K246) by molecular dynamic simulation. FN5Y inhibited DENV2 infectivity with EC50s (and selectivity index) of 15.99 ± 5.38 (>6.25), and 12.31 ± 1.64 (2.23) μM in LLC/MK2 and Vero cell lines, respectively, and inhibited DENV4 at 11.70 ± 6.04 (>8.55) μM. CC50s in LLC/MK2, HEK-293, and HepG2 cell lines at 72 h were higher than 100 μM. Time-of-addition study revealed that the maximal efficacy was achieved at early after infection corresponded with pH-dependent fusion. Inactivating the viral particle, interfering with cellular receptors, inhibiting viral protease, or the virus replication complex were not major targets of this compound. FN5Y could become a potent anti-flaviviral drug and can be structurally modified for higher potency using simulation to DENV envelope as a molecular target.
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Affiliation(s)
- Pimsiri Srivarangkul
- Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Wanchalerm Yuttithamnon
- Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Aphinya Suroengrit
- Graduate Program, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Saran Pankaew
- Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Kowit Hengphasatporn
- Bioinformatics and Computational Biology Program, Graduated School, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Thanyada Rungrotmongkol
- Bioinformatics and Computational Biology Program, Graduated School, Chulalongkorn University, Bangkok, 10330, Thailand; Structural and Computational Biology Research Group, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | | | - Kiat Ruxrungtham
- Chula Vaccine Research Center (Chula VRC), Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Siwaporn Boonyasuppayakorn
- Chula Vaccine Research Center (Chula VRC), Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand; Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand.
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43
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Rausch JW, Sztuba-Solinska J, Le Grice SFJ. Probing the Structures of Viral RNA Regulatory Elements with SHAPE and Related Methodologies. Front Microbiol 2018; 8:2634. [PMID: 29375504 PMCID: PMC5767303 DOI: 10.3389/fmicb.2017.02634] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 12/18/2017] [Indexed: 01/18/2023] Open
Abstract
Viral RNAs were selected by evolution to possess maximum functionality in a minimal sequence. Depending on the classification of the virus and the type of RNA in question, viral RNAs must alternately be replicated, spliced, transcribed, transported from the nucleus into the cytoplasm, translated and/or packaged into nascent virions, and in most cases, provide the sequence and structural determinants to facilitate these processes. One consequence of this compact multifunctionality is that viral RNA structures can be exquisitely complex, often involving intermolecular interactions with RNA or protein, intramolecular interactions between sequence segments separated by several thousands of nucleotides, or specialized motifs such as pseudoknots or kissing loops. The fluidity of viral RNA structure can also present a challenge when attempting to characterize it, as genomic RNAs especially are likely to sample numerous conformations at various stages of the virus life cycle. Here we review advances in chemoenzymatic structure probing that have made it possible to address such challenges with respect to cis-acting elements, full-length viral genomes and long non-coding RNAs that play a major role in regulating viral gene expression.
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Affiliation(s)
- Jason W Rausch
- Basic Research Laboratory, National Cancer Institute, Frederick, MD, United States
| | - Joanna Sztuba-Solinska
- Basic Research Laboratory, National Cancer Institute, Frederick, MD, United States.,Department of Biological Sciences, Auburn University, Auburn, AL, United States
| | - Stuart F J Le Grice
- Basic Research Laboratory, National Cancer Institute, Frederick, MD, United States
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44
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Lim CS, Brown CM. Know Your Enemy: Successful Bioinformatic Approaches to Predict Functional RNA Structures in Viral RNAs. Front Microbiol 2018; 8:2582. [PMID: 29354101 PMCID: PMC5758548 DOI: 10.3389/fmicb.2017.02582] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 12/11/2017] [Indexed: 12/14/2022] Open
Abstract
Structured RNA elements may control virus replication, transcription and translation, and their distinct features are being exploited by novel antiviral strategies. Viral RNA elements continue to be discovered using combinations of experimental and computational analyses. However, the wealth of sequence data, notably from deep viral RNA sequencing, viromes, and metagenomes, necessitates computational approaches being used as an essential discovery tool. In this review, we describe practical approaches being used to discover functional RNA elements in viral genomes. In addition to success stories in new and emerging viruses, these approaches have revealed some surprising new features of well-studied viruses e.g., human immunodeficiency virus, hepatitis C virus, influenza, and dengue viruses. Some notable discoveries were facilitated by new comparative analyses of diverse viral genome alignments. Importantly, comparative approaches for finding RNA elements embedded in coding and non-coding regions differ. With the exponential growth of computer power we have progressed from stem-loop prediction on single sequences to cutting edge 3D prediction, and from command line to user friendly web interfaces. Despite these advances, many powerful, user friendly prediction tools and resources are underutilized by the virology community.
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Affiliation(s)
- Chun Shen Lim
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Chris M Brown
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
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45
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Halogenated Chrysins Inhibit Dengue and Zika Virus Infectivity. Sci Rep 2017; 7:13696. [PMID: 29057920 PMCID: PMC5651866 DOI: 10.1038/s41598-017-14121-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 10/04/2017] [Indexed: 11/08/2022] Open
Abstract
Dengue virus infection is a global threat for which no specific treatment has not been established. Previous reports suggested chrysin and flavanone derivatives were potential flaviviral inhibitors. Here, we reported two halogenated chrysins, abbreviated FV13 and FV14, were highly potent against DENV1-4 and ZIKV infectivities with the FV13 EC50 values of 2.30 ± 1.04, 1.47 ± 0.86, 2.32 ± 1.46, 1.78 ± 0.72 and 1.65 ± 0.86 µM; and FV14 EC50 values of 2.30 ± 0.92, 2.19 ± 0.31, 1.02 ± 0.31, 1.29 ± 0.60 and 1.39 ± 0.11 µM, respectively. The CC50s to LLC/MK2 of FV13 and FV14 were 44.28 ± 2.90 μM, 42.51 ± 2.53 µM, respectively. Mechanism of drug action studies suggested multiple targets but maximal efficiency was achieved with early post infection treatment. This is the first report showing a high potency of halogenated chrysins for development as a broad-spectrum anti-flaviviral drug.
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46
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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: 114] [Impact Index Per Article: 16.3] [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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47
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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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48
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Balasubramanian A, Teramoto T, Kulkarni AA, Bhattacharjee AK, Padmanabhan R. Antiviral activities of selected antimalarials against dengue virus type 2 and Zika virus. Antiviral Res 2016; 137:141-150. [PMID: 27889529 DOI: 10.1016/j.antiviral.2016.11.015] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2016] [Revised: 11/21/2016] [Accepted: 11/22/2016] [Indexed: 12/23/2022]
Abstract
In a previous study, twelve antimalarial compounds, amodiaquine (AQ) and derivatives, were shown to have potent anti-dengue viral (DENV) activity by using the stable DENV2 Renilla luciferase reporter replicon expressing BHK-21 cells, infectivity (plaque), and the qRT-PCR assays. In this study, we performed molecular modeling on these compounds to determine their stereo-electronic properties required for optimal antiviral activity. Based on the similarity of calculated stereo-electronic profiles, specifically the electrostatic potential profiles of the compounds, and in silico screening of related compounds from literature, we identified three additional compounds, Quinacrine (QC), Mefloquine (MQ), and GSK369796. Analysis of their antiviral activities indicated that all three compounds have high anti-DENV activity in the DENV2 replicon expressing cells with EC50 values of 5.30 ± 1.31 μM (QC), 3.22 ± 0.37 μM (MQ), and 5.06 ± 0.86 μM (GSK369796). The infectivity assays revealed the EC50 values of 7.09 ± 1.67 μM (QC), 4.36 ± 0.31 μM (MQ) and 3.03 ± 0.35 μM (GSK369796). The mode of action of these compounds is through inhibition of autophagy, thereby affecting DENV2 replication. Moreover, these compounds also showed antiviral activity against the rapidly emerging Zika virus (ZIKV) with EC50 values of 2.27 ± 0.14 μM (QC), 3.95 ± 0.21 μM (MQ), and 2.57 ± 0.09 μM (GSK369796).
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Affiliation(s)
- Anuradha Balasubramanian
- Department of Microbiology & Immunology, Georgetown University School of Medicine, Washington DC, USA
| | - Tadahisa Teramoto
- Department of Microbiology & Immunology, Georgetown University School of Medicine, Washington DC, USA
| | - Amol A Kulkarni
- Department of Pharmaceutical Sciences, College of Pharmacy, Howard University, Washington DC, USA
| | - Apurba K Bhattacharjee
- Department of Microbiology & Immunology, Georgetown University School of Medicine, Washington DC, USA.
| | - Radhakrishnan Padmanabhan
- Department of Microbiology & Immunology, Georgetown University School of Medicine, Washington DC, USA.
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49
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Xie X, Zou J, Shan C, Yang Y, Kum DB, Dallmeier K, Neyts J, Shi PY. Zika Virus Replicons for Drug Discovery. EBioMedicine 2016; 12:156-160. [PMID: 27658737 PMCID: PMC5078599 DOI: 10.1016/j.ebiom.2016.09.013] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 09/09/2016] [Accepted: 09/13/2016] [Indexed: 01/08/2023] Open
Abstract
The current epidemic of Zika virus (ZIKV) has underscored the urgency to establish experimental systems for studying viral replication and pathogenesis, and countermeasure development. Here we report two ZIKV replicon systems: a luciferase replicon that can differentiate between viral translation and RNA synthesis; and a stable luciferase replicon carrying cell line that can be used to screen and characterize inhibitors of viral replication. The transient replicon was used to evaluate the effect of an NS5 polymerase mutation on viral RNA synthesis and to analyze a known ZIKV inhibitor. The replicon cell line was developed into a 96-well format for antiviral testing. Compare with virus infection-based assay, the replicon cell line allows antiviral screening without using infectious virus. Collectively, the replicon systems have provided critical tools for both basic and translational research. A Zika virus replicon has been developed to study antivirals and to differentiate between viral translation and replication. A cell line carrying Zika virus replicon has been developed to screen and characterize antiviral inhibitors.
Experimental systems are urgently needed to study Zika virus and to develop countermeasures. In this communication, we report the development of Zika virus replicon systems that can be used to study viral replication and pathogenesis as well as to screen and characterize antiviral inhibitors.
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Affiliation(s)
- Xuping Xie
- Department of Biochemistry & Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Jing Zou
- Department of Biochemistry & Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Chao Shan
- Department of Biochemistry & Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Yujiao Yang
- Department of Biochemistry & Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA; College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Dieudonné Buh Kum
- Department of Biochemistry & Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA; Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, University of Leuven, Leuven, Belgium
| | - Kai Dallmeier
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, University of Leuven, Leuven, Belgium
| | - Johan Neyts
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, University of Leuven, Leuven, Belgium
| | - Pei-Yong Shi
- Department of Biochemistry & Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA; Department of Pharmacology & Toxicology, Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA.
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50
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Han YS, Penthala NR, Oliveira M, Mesplède T, Xu H, Quan Y, Crooks PA, Wainberg MA. Identification of resveratrol analogs as potent anti-dengue agents using a cell-based assay. J Med Virol 2016; 89:397-407. [PMID: 27509184 DOI: 10.1002/jmv.24660] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/08/2016] [Indexed: 01/19/2023]
Abstract
Dengue virus (DENV) causes a variety of difficult-to-treat diseases that threaten almost half of the world's population. Currently, no effective vaccine or antiviral therapy is available. We have examined a series of synthetic resveratrol analogs to identify potential anti-DENV agents. Here, we demonstrate that two resveratrol analogs, PNR-4-44 and PNR-5-02, possess potent anti-DENV activity with EC50 values in the low nanomolar range. These two resveratrol analogs were shown to mainly target viral RNA translation and viral replication, but PNR-5-02 is also likely to target cellular factors inside host cells. Although the precise molecular mechanism(s) mediating anti-DENV activities have not been elucidated, further structure-guided design might lead to the development of newer improved resveratrol derivatives that might have therapeutic value. J. Med. Virol. 89:397-407, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Ying-Shan Han
- McGill University AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Narsimha Reddy Penthala
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Maureen Oliveira
- McGill University AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Thibault Mesplède
- McGill University AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Hongtao Xu
- McGill University AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Yudong Quan
- McGill University AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Peter A Crooks
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Mark A Wainberg
- McGill University AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
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