1
|
Andrzejewska-Romanowska A, Gumna J, Tykwińska E, Pachulska-Wieczorek K. Mapping the structural landscape of the yeast Ty3 retrotransposon RNA genome. Nucleic Acids Res 2024:gkae494. [PMID: 38864374 DOI: 10.1093/nar/gkae494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 04/30/2024] [Accepted: 05/29/2024] [Indexed: 06/13/2024] Open
Abstract
Long terminal repeat (LTR)-retrotransposons are significant contributors to the evolution and diversity of eukaryotic genomes. Their RNA genomes (gRNA) serve as a template for protein synthesis and reverse transcription to a DNA copy, which can integrate into the host genome. Here, we used the SHAPE-MaP strategy to explore Ty3 retrotransposon gRNA structure in yeast and under cell-free conditions. Our study reveals the structural dynamics of Ty3 gRNA and the well-folded core, formed independently of the cellular environment. Based on the detailed map of Ty3 gRNA structure, we characterized the structural context of cis-acting sequences involved in reverse transcription and frameshifting. We also identified a novel functional sequence as a potential initiator for Ty3 gRNA dimerization. Our data indicate that the dimer is maintained by direct interaction between short palindromic sequences at the 5' ends of the two Ty3 gRNAs, resembling the model characteristic for other retroelements like HIV-1 and Ty1. This work points out a range of cell-dependent and -independent Ty3 gRNA structural changes that provide a solid background for studies on RNA structure-function relationships important for retroelement biology.
Collapse
Affiliation(s)
- Angelika Andrzejewska-Romanowska
- Department of RNA Structure and Function, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Julita Gumna
- Department of RNA Structure and Function, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Ewa Tykwińska
- Department of RNA Structure and Function, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Katarzyna Pachulska-Wieczorek
- Department of RNA Structure and Function, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| |
Collapse
|
2
|
Tipo J, Gottipati K, Choi KH. High-resolution RNA tertiary structures in Zika virus stem-loop A for the development of inhibitory small molecules. RNA (NEW YORK, N.Y.) 2024; 30:609-623. [PMID: 38383158 PMCID: PMC11098461 DOI: 10.1261/rna.079796.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 01/30/2024] [Indexed: 02/23/2024]
Abstract
Flaviviruses such as Zika (ZIKV) and dengue virus (DENV) are positive-sense RNA viruses belonging to Flaviviridae The flavivirus genome contains a 5' end stem-loop promoter sequence known as stem-loop A (SLA) that is recognized by the flavivirus polymerase NS5 during viral RNA synthesis and 5' guanosine cap methylation. The crystal structures of ZIKV and DENV SLAs show a well-defined fold, consisting of a bottom stem, side loop, and top stem-loop, providing unique interaction sites for small molecule inhibitors to disrupt the promoter function. To facilitate the identification of small molecule binding sites in flavivirus SLA, we determined high-resolution structures of the bottom and top stems of ZIKV SLA, which contain a single U- or G-bulge, respectively. Both bulge nucleotides exhibit multiple orientations, from folded back on the adjacent nucleotide to flipped out of the helix, and are stabilized by stacking or base triple interactions. These structures suggest that even a single unpaired nucleotide can provide flexibility to RNA structures, and its conformation is mainly determined by the stabilizing chemical environment. To facilitate discovery of small molecule inhibitors that interfere with the functions of ZIKV SLA, we screened and identified compounds that bind to the bottom and top stems of ZIKV SLA.
Collapse
Affiliation(s)
- Jerricho Tipo
- Department of Pharmacology and Toxicology, The University of Texas Medical Branch, Galveston, Texas 77555, USA
| | - Keerthi Gottipati
- Department of Biochemistry and Molecular Biology, and Sealy Center for Structural Biology, The University of Texas Medical Branch, Galveston, Texas 77555, USA
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, USA
| | - Kyung H Choi
- Department of Biochemistry and Molecular Biology, and Sealy Center for Structural Biology, The University of Texas Medical Branch, Galveston, Texas 77555, USA
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, USA
| |
Collapse
|
3
|
Ismat F, Tariq A, Shaheen A, Ullah R, Raheem K, Muddassar M, Mahboob S, Abbas W, Iqbal M, Rahman M. Inhibition of NS2B-NS3 protease from all four serotypes of dengue virus by punicalagin, punicalin and ellagic acid identified from Punica granatum. J Biomol Struct Dyn 2024:1-16. [PMID: 38373021 DOI: 10.1080/07391102.2024.2314258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Accepted: 01/29/2024] [Indexed: 02/20/2024]
Abstract
Despite a major threat to the public health in tropical and subtropical regions, dengue virus (DENV) infections are untreatable. Therefore, efforts are needed to investigate cost-effective therapeutic agents that could cure DENV infections in future. The NS2B-NS3 protease encoded by the genome of DENV is considered a critical target for the development of anti-dengue drugs. The objective of the current study was to find out a specific inhibitor of the NS2B-NS3 proteases from all four serotypes of DENV. To begin with, nine plant extracts with a medicinal history were evaluated for their role in inhibiting the NS2B-NS3 proteases by Fluorescence Resonance Energy Transfer (FRET) assay. Among the tested extracts, Punica granatum was found to be the most effective one. The metabolic profiling of this extract revealed the presence of several active compounds, including ellagic acid, punicalin and punicalagin, which are well-established antiviral agents. Further evaluation of IC50 values of these three antiviral molecules revealed punicalagin as the most potent anti-NS2B-NS3 protease drug with IC50 of 0.91 ± 0.10, 0.75 ± 0.05, 0.42 ± 0.03, 1.80 ± 0.16 µM against proteases from serotypes 1, 2, 3 and 4, respectively. The docking studies demonstrated that these compounds interacted at the active site of the enzyme, mainly with His and Ser residues. Molecular dynamics simulations analysis also showed the structural stability of the NS2B-NS3 proteases in the presence of punicalagin. In summary, this study concludes that the punicalagin can act as an effective inhibitor against NS2B-NS3 proteases from all four serotypes of DENV.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Fouzia Ismat
- Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Punjab, Pakistan
| | - Anam Tariq
- Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Punjab, Pakistan
| | - Aqsa Shaheen
- Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Punjab, Pakistan
- Department of Biochemistry and Biotechnology, University of Gujrat, Hafiz Hayat Campus, Gujrat, Pakistan
| | - Raheem Ullah
- Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Punjab, Pakistan
| | - Kayode Raheem
- Department of Bioscience, COMSATS University Islamabad, Islamabad, Pakistan
| | - Muhammad Muddassar
- Department of Bioscience, COMSATS University Islamabad, Islamabad, Pakistan
| | - Sadia Mahboob
- Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Punjab, Pakistan
| | - Wasim Abbas
- Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Punjab, Pakistan
| | - Mazhar Iqbal
- Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Punjab, Pakistan
| | - Moazur Rahman
- Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Punjab, Pakistan
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| |
Collapse
|
4
|
Abram QH, Landry BN, Wang AB, Kothe RF, Hauch HC, Sagan SM. The myriad roles of RNA structure in the flavivirus life cycle. RNA Biol 2024; 21:14-30. [PMID: 38797925 PMCID: PMC11135854 DOI: 10.1080/15476286.2024.2357857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/16/2024] [Indexed: 05/29/2024] Open
Abstract
As positive-sense RNA viruses, the genomes of flaviviruses serve as the template for all stages of the viral life cycle, including translation, replication, and infectious particle production. Yet, they encode just 10 proteins, suggesting that the structure and dynamics of the viral RNA itself helps shepherd the viral genome through these stages. Herein, we highlight advances in our understanding of flavivirus RNA structural elements through the lens of their impact on the viral life cycle. We highlight how RNA structures impact translation, the switch from translation to replication, negative- and positive-strand RNA synthesis, and virion assembly. Consequently, we describe three major themes regarding the roles of RNA structure in flavivirus infections: 1) providing a layer of specificity; 2) increasing the functional capacity; and 3) providing a mechanism to support genome compaction. While the interactions described herein are specific to flaviviruses, these themes appear to extend more broadly across RNA viruses.
Collapse
Affiliation(s)
- Quinn H. Abram
- Department of Biochemistry, McGill University, Montreal, QC, Canada
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Breanna N. Landry
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC, Canada
- Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada
| | - Alex B. Wang
- Department of Biochemistry, McGill University, Montreal, QC, Canada
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Ronja F. Kothe
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Hannah C.H. Hauch
- Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada
| | - Selena M. Sagan
- Department of Biochemistry, McGill University, Montreal, QC, Canada
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC, Canada
- Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada
| |
Collapse
|
5
|
Liao KC, Xie X, Sundstrom AKB, Lim XN, Tan KK, Zhang Y, Zou J, Bifani AM, Poh HX, Chen JJ, Ng WC, Lim SY, Ooi EE, Sessions OM, Tay Y, Shi PY, Huber RG, Wan Y. Dengue and Zika RNA-RNA interactomes reveal pro- and anti-viral RNA in human cells. Genome Biol 2023; 24:279. [PMID: 38053173 DOI: 10.1186/s13059-023-03110-9] [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: 04/18/2023] [Accepted: 11/15/2023] [Indexed: 12/07/2023] Open
Abstract
BACKGROUND Identifying host factors is key to understanding RNA virus pathogenicity. Besides proteins, RNAs can interact with virus genomes to impact replication. RESULTS Here, we use proximity ligation sequencing to identify virus-host RNA interactions for four strains of Zika virus (ZIKV) and one strain of dengue virus (DENV-1) in human cells. We find hundreds of coding and non-coding RNAs that bind to DENV and ZIKV viruses. Host RNAs tend to bind to single-stranded regions along the virus genomes according to hybridization energetics. Compared to SARS-CoV-2 interactors, ZIKV-interacting host RNAs tend to be downregulated upon virus infection. Knockdown of several short non-coding RNAs, including miR19a-3p, and 7SK RNA results in a decrease in viral replication, suggesting that they act as virus-permissive factors. In addition, the 3'UTR of DYNLT1 mRNA acts as a virus-restrictive factor by binding to the conserved dumbbell region on DENV and ZIKV 3'UTR to decrease virus replication. We also identify a conserved set of host RNAs that interacts with DENV, ZIKV, and SARS-CoV-2, suggesting that these RNAs are broadly important for RNA virus infection. CONCLUSIONS This study demonstrates that host RNAs can impact virus replication in permissive and restrictive ways, expanding our understanding of host factors and RNA-based gene regulation during viral pathogenesis.
Collapse
Affiliation(s)
- Kuo-Chieh Liao
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, Singapore, 138672, Singapore
| | - Xuping Xie
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Anna Karin Beatrice Sundstrom
- Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Xin Ni Lim
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, Singapore, 138672, Singapore
| | - Kiat Kee Tan
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, Singapore, 138672, Singapore
| | - Yu Zhang
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, Singapore, 138672, Singapore
| | - Jing Zou
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Amanda Makha Bifani
- Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Hui Xian Poh
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, Singapore, 138672, Singapore
| | - Jia Jia Chen
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Wy Ching Ng
- Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Su Ying Lim
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, Singapore, 138672, Singapore
| | - Eng Eong Ooi
- Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, 8 College Road, Singapore, 169857, Singapore
| | - October M Sessions
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, 117549, Singapore
- Department of Pharmacy, National University of Singapore, Singapore, 117559, Singapore
| | - Yvonne Tay
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA.
| | - Roland G Huber
- Biomolecular Function Discovery, Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Matrix #07-01, Singapore, 138671, Singapore.
| | - Yue Wan
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, Singapore, 138672, Singapore.
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore.
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
| |
Collapse
|
6
|
Estofolete CF, Versiani AF, Dourado FS, Milhim BHGA, Pacca CC, Silva GCD, Zini N, dos Santos BF, Gandolfi FA, Mistrão NFB, Garcia PHC, Rocha RS, Gehrke L, Bosch I, Marques RE, Teixeira MM, da Fonseca FG, Vasilakis N, Nogueira ML. Influence of previous Zika virus infection on acute dengue episode. PLoS Negl Trop Dis 2023; 17:e0011710. [PMID: 37943879 PMCID: PMC10662752 DOI: 10.1371/journal.pntd.0011710] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 11/21/2023] [Accepted: 10/05/2023] [Indexed: 11/12/2023] Open
Abstract
BACKGROUND The co-circulation of flaviviruses in tropical regions has led to the hypothesis that immunity generated by a previous dengue infection could promote severe disease outcomes in subsequent infections by heterologous serotypes. This study investigated the influence of antibodies generated by previous Zika infection on the clinical outcomes of dengue infection. METHODOLOGY/PRINCIPAL FINDINGS We enrolled 1,043 laboratory confirmed dengue patients and investigated their prior infection to Zika or dengue. Severe forms of dengue disease were more frequent in patients with previous Zika infection, but not in those previously exposed to dengue. CONCLUSIONS/SIGNIFICANCE Our findings suggest that previous Zika infection may represent a risk factor for subsequent severe dengue disease, but we did not find evidence of antibody-dependent enhancement (higher viral titer or pro-inflammatory cytokine overexpression) contributing to exacerbation of the subsequent dengue infection.
Collapse
Affiliation(s)
- Cassia F. Estofolete
- Laboratório de Pesquisas em Virologia (LPV), Faculdade de Medicina de São José do Rio Preto (FAMERP); São José do Rio Preto, Sao Paulo, Brazil
| | - Alice F. Versiani
- Laboratório de Pesquisas em Virologia (LPV), Faculdade de Medicina de São José do Rio Preto (FAMERP); São José do Rio Preto, Sao Paulo, Brazil
- Department of Pathology, University of Texas Medical Branch; Galveston, Texas, United States of America
| | - Fernanda S. Dourado
- Laboratório de Pesquisas em Virologia (LPV), Faculdade de Medicina de São José do Rio Preto (FAMERP); São José do Rio Preto, Sao Paulo, Brazil
| | - Bruno H. G. A. Milhim
- Laboratório de Pesquisas em Virologia (LPV), Faculdade de Medicina de São José do Rio Preto (FAMERP); São José do Rio Preto, Sao Paulo, Brazil
| | - Carolina C. Pacca
- Laboratório de Pesquisas em Virologia (LPV), Faculdade de Medicina de São José do Rio Preto (FAMERP); São José do Rio Preto, Sao Paulo, Brazil
| | - Gislaine C. D. Silva
- Laboratório de Pesquisas em Virologia (LPV), Faculdade de Medicina de São José do Rio Preto (FAMERP); São José do Rio Preto, Sao Paulo, Brazil
| | - Nathalia Zini
- Laboratório de Pesquisas em Virologia (LPV), Faculdade de Medicina de São José do Rio Preto (FAMERP); São José do Rio Preto, Sao Paulo, Brazil
| | - Barbara F. dos Santos
- Laboratório de Pesquisas em Virologia (LPV), Faculdade de Medicina de São José do Rio Preto (FAMERP); São José do Rio Preto, Sao Paulo, Brazil
| | - Flora A. Gandolfi
- Laboratório de Pesquisas em Virologia (LPV), Faculdade de Medicina de São José do Rio Preto (FAMERP); São José do Rio Preto, Sao Paulo, Brazil
| | - Natalia F. B. Mistrão
- Laboratório de Pesquisas em Virologia (LPV), Faculdade de Medicina de São José do Rio Preto (FAMERP); São José do Rio Preto, Sao Paulo, Brazil
| | - Pedro H. C. Garcia
- Laboratório de Pesquisas em Virologia (LPV), Faculdade de Medicina de São José do Rio Preto (FAMERP); São José do Rio Preto, Sao Paulo, Brazil
| | - Rodrigo S. Rocha
- Laboratório de Pesquisas em Virologia (LPV), Faculdade de Medicina de São José do Rio Preto (FAMERP); São José do Rio Preto, Sao Paulo, Brazil
| | - Lee Gehrke
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology; Cambridge, Massachusetts, United States of America
- Department of Microbiology, Harvard Medical School; Boston, Massachusetts, United States of America
| | - Irene Bosch
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology; Cambridge, Massachusetts, United States of America
| | - Rafael E. Marques
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM); Campinas, Sao Paulo, Brazil
| | - Mauro M. Teixeira
- Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais; Belo Horizonte, Minas Gerais, Brazil
| | - Flavio G. da Fonseca
- Laboratório de Virologia Básica e Aplicada, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais; Belo Horizonte, Minas Gerais, Brazil
- Centro de Tecnoogia em Vacinas da UFMG, Universidade Federal de Minas Gerais; Belo Horizonte, Minas Gerais, Brazil
| | - Nikos Vasilakis
- Department of Pathology, University of Texas Medical Branch; Galveston, Texas, United States of America
- Center for Vector-Borne and Zoonotic Diseases, University of Texas Medical Branch; Galveston, Texas, United States of America
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch; Galveston, Texas, United States of America
- Center for Tropical Diseases, University of Texas Medical Branch; Galveston, Texas, United States of America
- Institute for Human Infection and Immunity, University of Texas Medical Branch; Galveston, Texas, United States of America
| | - Maurício L. Nogueira
- Laboratório de Pesquisas em Virologia (LPV), Faculdade de Medicina de São José do Rio Preto (FAMERP); São José do Rio Preto, Sao Paulo, Brazil
- Department of Pathology, University of Texas Medical Branch; Galveston, Texas, United States of America
| |
Collapse
|
7
|
Chin WX, Kong HY, Zhu IXY, Teo ZY, Faruk R, Lee RCH, Ho SX, Aw ZQ, Yi B, Hou XJ, Tan AKY, Yogarajah T, Huber RG, Cai Y, Wan Y, Chu JJH. Flavivirus genome recoding by codon optimisation confers genetically stable in vivo attenuation in both mice and mosquitoes. PLoS Pathog 2023; 19:e1011753. [PMID: 37883598 PMCID: PMC10629665 DOI: 10.1371/journal.ppat.1011753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 11/07/2023] [Accepted: 10/14/2023] [Indexed: 10/28/2023] Open
Abstract
Virus genome recoding is an attenuation method that confers genetically stable attenuation by rewriting a virus genome with numerous silent mutations. Prior flavivirus genome recoding attempts utilised codon deoptimisation approaches. However, these codon deoptimisation approaches act in a species dependent manner and were unable to confer flavivirus attenuation in mosquito cells or in mosquito animal models. To overcome these limitations, we performed flavivirus genome recoding using the contrary approach of codon optimisation. The genomes of flaviviruses such as dengue virus type 2 (DENV2) and Zika virus (ZIKV) contain functional RNA elements that regulate viral replication. We hypothesised that flavivirus genome recoding by codon optimisation would introduce silent mutations that disrupt these RNA elements, leading to decreased replication efficiency and attenuation. We chose DENV2 and ZIKV as representative flaviviruses and recoded them by codon optimising their genomes for human expression. Our study confirms that this recoding approach of codon optimisation does translate into reduced replication efficiency in mammalian, human, and mosquito cells as well as in vivo attenuation in both mice and mosquitoes. In silico modelling and RNA SHAPE analysis confirmed that DENV2 recoding resulted in the extensive disruption of genomic structural elements. Serial passaging of recoded DENV2 resulted in the emergence of rescue or adaptation mutations, but no reversion mutations. These rescue mutations were unable to rescue the delayed replication kinetics and in vivo attenuation of recoded DENV2, demonstrating that recoding confers genetically stable attenuation. Therefore, our recoding approach is a reliable attenuation method with potential applications for developing flavivirus vaccines.
Collapse
Affiliation(s)
- Wei-Xin Chin
- Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology and Immunology and Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore
| | - Hao Yuin Kong
- NUSMed Biosafety Level 3 Core Facility, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Isabelle Xin Yu Zhu
- Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology and Immunology and Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore
| | - Zi Yun Teo
- Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology and Immunology and Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore
| | - Regina Faruk
- Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology and Immunology and Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore
| | - Regina Ching Hua Lee
- Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology and Immunology and Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore
| | - Si Xian Ho
- Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology and Immunology and Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore
| | - Zhen Qin Aw
- NUSMed Biosafety Level 3 Core Facility, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Bowen Yi
- NUSMed Biosafety Level 3 Core Facility, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Xin Jun Hou
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Antson Kiat Yee Tan
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Thinesshwary Yogarajah
- Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology and Immunology and Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore
| | - Roland G. Huber
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Yu Cai
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Yue Wan
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Justin Jang Hann Chu
- Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology and Immunology and Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore
- NUSMed Biosafety Level 3 Core Facility, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore
| |
Collapse
|
8
|
Mathez G, Cagno V. Small Molecules Targeting Viral RNA. Int J Mol Sci 2023; 24:13500. [PMID: 37686306 PMCID: PMC10487773 DOI: 10.3390/ijms241713500] [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: 08/02/2023] [Revised: 08/25/2023] [Accepted: 08/28/2023] [Indexed: 09/10/2023] Open
Abstract
The majority of antivirals available target viral proteins; however, RNA is emerging as a new and promising antiviral target due to the presence of highly structured RNA in viral genomes fundamental for their replication cycle. Here, we discuss methods for the identification of RNA-targeting compounds, starting from the determination of RNA structures either from purified RNA or in living cells, followed by in silico screening on RNA and phenotypic assays to evaluate viral inhibition. Moreover, we review the small molecules known to target the programmed ribosomal frameshifting element of SARS-CoV-2, the internal ribosomal entry site of different viruses, and RNA elements of HIV.
Collapse
Affiliation(s)
| | - Valeria Cagno
- Institute of Microbiology, University Hospital of Lausanne, University of Lausanne, 1011 Lausanne, Switzerland
| |
Collapse
|
9
|
Jakob C, Lovate GL, Desirò D, Gießler L, Smyth R, Marquet R, Lamkiewicz K, Marz M, Schwemmle M, Bolte H. Sequential disruption of SPLASH-identified vRNA-vRNA interactions challenges their role in influenza A virus genome packaging. Nucleic Acids Res 2023; 51:6479-6494. [PMID: 37224537 PMCID: PMC10325904 DOI: 10.1093/nar/gkad442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 05/02/2023] [Accepted: 05/10/2023] [Indexed: 05/26/2023] Open
Abstract
A fundamental step in the influenza A virus (IAV) replication cycle is the coordinated packaging of eight distinct genomic RNA segments (i.e. vRNAs) into a viral particle. Although this process is thought to be controlled by specific vRNA-vRNA interactions between the genome segments, few functional interactions have been validated. Recently, a large number of potentially functional vRNA-vRNA interactions have been detected in purified virions using the RNA interactome capture method SPLASH. However, their functional significance in coordinated genome packaging remains largely unclear. Here, we show by systematic mutational analysis that mutant A/SC35M (H7N7) viruses lacking several prominent SPLASH-identified vRNA-vRNA interactions involving the HA segment package the eight genome segments as efficiently as the wild-type virus. We therefore propose that the vRNA-vRNA interactions identified by SPLASH in IAV particles are not necessarily critical for the genome packaging process, leaving the underlying molecular mechanism elusive.
Collapse
Affiliation(s)
- Celia Jakob
- Institute of Virology, Medical Center – University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Gabriel L Lovate
- RNA Bioinformatics and High-Throughput Analysis, Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, Germany
| | - Daniel Desirò
- Department of Biochemistry, University of Cambridge, CambridgeCB2 1QW, UK
| | - Lara Gießler
- Institute of Virology, Medical Center – University of Freiburg, Freiburg, Germany
| | - Redmond P Smyth
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
- Julius-Maximilians-Universität Würzburg, Faculty of Medicine, Würzburg, Germany
| | - Roland Marquet
- Architecture et Réactivité de l’ARN, Université de Strasbourg, CNRS, IBMC, Strasbourg, France
| | - Kevin Lamkiewicz
- RNA Bioinformatics and High-Throughput Analysis, Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, Germany
- German Center for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Germany
- European Virus Bioinformatics Center (EVBC), Jena, Germany
| | - Manja Marz
- RNA Bioinformatics and High-Throughput Analysis, Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, Germany
- German Center for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Germany
- European Virus Bioinformatics Center (EVBC), Jena, Germany
- FLI Leibniz Institute for Age Research, Jena, Germany
| | - Martin Schwemmle
- Institute of Virology, Medical Center – University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Hardin Bolte
- Institute of Virology, Medical Center – University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| |
Collapse
|
10
|
Kim IJ, Tighe MP, Clark MJ, Gromowski GD, Lanthier PA, Travis KL, Bernacki DT, Cookenham TS, Lanzer KG, Szaba FM, Tamhankar MA, Ross CN, Tardif SD, Layne-Colon D, Dick EJ, Gonzalez O, Giraldo Giraldo MI, Patterson JL, Blackman MA. Impact of prior dengue virus infection on Zika virus infection during pregnancy in marmosets. Sci Transl Med 2023; 15:eabq6517. [PMID: 37285402 DOI: 10.1126/scitranslmed.abq6517] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 05/18/2023] [Indexed: 06/09/2023]
Abstract
Zika virus (ZIKV) infection during pregnancy causes severe developmental defects in newborns, termed congenital Zika syndrome (CZS). Factors contributing to a surge in ZIKV-associated CZS are poorly understood. One possibility is that ZIKV may exploit the antibody-dependent enhancement of infection mechanism, mediated by cross-reactive antibodies from prior dengue virus (DENV) infection, which may exacerbate ZIKV infection during pregnancy. In this study, we investigated the impact of prior DENV infection or no DENV infection on ZIKV pathogenesis during pregnancy in a total of four female common marmosets with five or six fetuses per group. The results showed that negative-sense viral RNA copies increased in the placental and fetal tissues of DENV-immune dams but not in DENV-naïve dams. In addition, viral proteins were prevalent in endothelial cells, macrophages, and neonatal Fc receptor-expressing cells in the placental trabeculae and in neuronal cells in the brains of fetuses from DENV-immune dams. DENV-immune marmosets maintained high titers of cross-reactive ZIKV-binding antibodies that were poorly neutralizing, raising the possibility that these antibodies might be involved in the exacerbation of ZIKV infection. These findings need to be verified in a larger study, and the mechanism involved in the exacerbation of ZIKV infection in DENV-immune marmosets needs further investigation. However, the results suggest a potential negative impact of preexisting DENV immunity on subsequent ZIKV infection during pregnancy in vivo.
Collapse
Affiliation(s)
- In-Jeong Kim
- Trudeau Institute Inc., Saranac Lake, NY 12983, USA
| | | | | | - Gregory D Gromowski
- Viral Diseases Branch, Center of Infectious Disease Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | | | | | | | | | | | | | - Manasi A Tamhankar
- Southwest National Primate Center, Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | - Corrina N Ross
- Southwest National Primate Center, Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | - Suzette D Tardif
- Southwest National Primate Center, Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | - Donna Layne-Colon
- Southwest National Primate Center, Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | - Edward J Dick
- Southwest National Primate Center, Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | - Olga Gonzalez
- Southwest National Primate Center, Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | - Maria I Giraldo Giraldo
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Jean L Patterson
- Southwest National Primate Center, Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | | |
Collapse
|
11
|
Boon PLS, Martins AS, Lim XN, Enguita FJ, Santos NC, Bond PJ, Wan Y, Martins IC, Huber RG. Dengue Virus Capsid Protein Facilitates Genome Compaction and Packaging. Int J Mol Sci 2023; 24:ijms24098158. [PMID: 37175867 PMCID: PMC10179140 DOI: 10.3390/ijms24098158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 04/24/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023] Open
Abstract
Dengue virus (DENV) is a single-stranded (+)-sense RNA virus that infects humans and mosquitoes, posing a significant health risk in tropical and subtropical regions. Mature virions are composed of an icosahedral shell of envelope (E) and membrane (M) proteins circumscribing a lipid bilayer, which in turn contains a complex of the approximately 11 kb genomic RNA with capsid (C) proteins. Whereas the structure of the envelope is clearly defined, the structure of the packaged genome in complex with C proteins remains elusive. Here, we investigated the interactions of C proteins with viral RNA, in solution and inside mature virions, via footprinting and cross-linking experiments. We demonstrated that C protein interaction with DENV genomes saturates at an RNA:C protein ratio below 1:250. Moreover, we also showed that the length of the RNA genome interaction sites varies, in a multimodal distribution, consistent with the C protein binding to each RNA site mostly in singlets or pairs (and, in some instances, higher numbers). We showed that interaction sites are preferentially sites with low base pairing, as previously measured by 2'-acetylation analyzed by primer extension (SHAPE) reactivity indicating structuredness. We found a clear association pattern emerged: RNA-C protein binding sites are strongly associated with long-range RNA-RNA interaction sites, particularly inside virions. This, in turn, explains the need for C protein in viral genome packaging: the protein has a chief role in coordinating these key interactions, promoting proper packaging of viral RNA. Such sites are, thus, highly consequential for viral assembly, and, as such, may be targeted in future drug development strategies against these and related viruses.
Collapse
Affiliation(s)
- Priscilla L S Boon
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore 138671, Singapore
- Department of Biological Sciences (DBS), National University of Singapore (NUS), 16 Science Drive 4, Singapore 117558, Singapore
| | - Ana S Martins
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisbon, Portugal
| | - Xin Ni Lim
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore 138672, Singapore
| | - Francisco J Enguita
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisbon, Portugal
| | - Nuno C Santos
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisbon, Portugal
| | - Peter J Bond
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore 138671, Singapore
- Department of Biological Sciences (DBS), National University of Singapore (NUS), 16 Science Drive 4, Singapore 117558, Singapore
| | - Yue Wan
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore 138672, Singapore
| | - Ivo C Martins
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisbon, Portugal
| | - Roland G Huber
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore 138671, Singapore
| |
Collapse
|
12
|
Mirska B, Woźniak T, Lorent D, Ruszkowska A, Peterson JM, Moss WN, Mathews DH, Kierzek R, Kierzek E. In vivo secondary structural analysis of Influenza A virus genomic RNA. Cell Mol Life Sci 2023; 80:136. [PMID: 37131079 PMCID: PMC10153785 DOI: 10.1007/s00018-023-04764-1] [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: 10/28/2022] [Revised: 03/19/2023] [Accepted: 03/19/2023] [Indexed: 05/04/2023]
Abstract
Influenza A virus (IAV) is a respiratory virus that causes epidemics and pandemics. Knowledge of IAV RNA secondary structure in vivo is crucial for a better understanding of virus biology. Moreover, it is a fundament for the development of new RNA-targeting antivirals. Chemical RNA mapping using selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) coupled with Mutational Profiling (MaP) allows for the thorough examination of secondary structures in low-abundance RNAs in their biological context. So far, the method has been used for analyzing the RNA secondary structures of several viruses including SARS-CoV-2 in virio and in cellulo. Here, we used SHAPE-MaP and dimethyl sulfate mutational profiling with sequencing (DMS-MaPseq) for genome-wide secondary structure analysis of viral RNA (vRNA) of the pandemic influenza A/California/04/2009 (H1N1) strain in both in virio and in cellulo environments. Experimental data allowed the prediction of the secondary structures of all eight vRNA segments in virio and, for the first time, the structures of vRNA5, 7, and 8 in cellulo. We conducted a comprehensive structural analysis of the proposed vRNA structures to reveal the motifs predicted with the highest accuracy. We also performed a base-pairs conservation analysis of the predicted vRNA structures and revealed many highly conserved vRNA motifs among the IAVs. The structural motifs presented herein are potential candidates for new IAV antiviral strategies.
Collapse
Affiliation(s)
- Barbara Mirska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Tomasz Woźniak
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszynska 32, 60-479, Poznan, Poland
| | - Dagny Lorent
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Agnieszka Ruszkowska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Jake M Peterson
- Roy J. Carver Department of Biophysics, Biochemistry and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| | - Walter N Moss
- Roy J. Carver Department of Biophysics, Biochemistry and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| | - David H Mathews
- Department of Biochemistry & Biophysics and Center for RNA Biology, School of Medicine and Dentistry, University of Rochester, 601 Elmwood Avenue, Box 712, Rochester, NY, 14642, USA
| | - Ryszard Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Elzbieta Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland.
| |
Collapse
|
13
|
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.
Collapse
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
| |
Collapse
|
14
|
Boerneke MA, Gokhale NS, Horner SM, Weeks KM. Structure-first identification of RNA elements that regulate dengue virus genome architecture and replication. Proc Natl Acad Sci U S A 2023; 120:e2217053120. [PMID: 37011200 PMCID: PMC10104495 DOI: 10.1073/pnas.2217053120] [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: 10/05/2022] [Accepted: 03/02/2023] [Indexed: 04/05/2023] Open
Abstract
The genomes of RNA viruses encode the information required for replication in host cells both in their linear sequence and in complex higher-order structures. A subset of these RNA genome structures show clear sequence conservation, and have been extensively described for well-characterized viruses. However, the extent to which viral RNA genomes contain functional structural elements-unable to be detected by sequence alone-that nonetheless are critical to viral fitness is largely unknown. Here, we devise a structure-first experimental strategy and use it to identify 22 structure-similar motifs across the coding sequences of the RNA genomes for the four dengue virus serotypes. At least 10 of these motifs modulate viral fitness, revealing a significant unnoticed extent of RNA structure-mediated regulation within viral coding sequences. These viral RNA structures promote a compact global genome architecture, interact with proteins, and regulate the viral replication cycle. These motifs are also thus constrained at the levels of both RNA structure and protein sequence and are potential resistance-refractory targets for antivirals and live-attenuated vaccines. Structure-first identification of conserved RNA structure enables efficient discovery of pervasive RNA-mediated regulation in viral genomes and, likely, other cellular RNAs.
Collapse
Affiliation(s)
- Mark A. Boerneke
- Department of Chemistry, University of North Carolina, Chapel Hill, NC27599-3290
| | - Nandan S. Gokhale
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC27710
| | - Stacy M. Horner
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC27710
- Department of Medicine, Duke University Medical Center, Durham, NC27710
| | - Kevin M. Weeks
- Department of Chemistry, University of North Carolina, Chapel Hill, NC27599-3290
| |
Collapse
|
15
|
Allan MF, Brivanlou A, Rouskin S. RNA levers and switches controlling viral gene expression. Trends Biochem Sci 2023; 48:391-406. [PMID: 36710231 DOI: 10.1016/j.tibs.2022.12.002] [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: 09/12/2022] [Revised: 11/27/2022] [Accepted: 12/15/2022] [Indexed: 01/29/2023]
Abstract
RNA viruses are diverse and abundant pathogens that are responsible for numerous human diseases. RNA viruses possess relatively compact genomes and have therefore evolved multiple mechanisms to maximize their coding capacities, often by encoding overlapping reading frames. These reading frames are then decoded by mechanisms such as alternative splicing and ribosomal frameshifting to produce multiple distinct proteins. These solutions are enabled by the ability of the RNA genome to fold into 3D structures that can mimic cellular RNAs, hijack host proteins, and expose or occlude regulatory protein-binding motifs to ultimately control key process in the viral life cycle. We highlight recent findings focusing on less conventional mechanisms of gene expression and new discoveries on the role of RNA structures.
Collapse
Affiliation(s)
- Matthew F Allan
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Amir Brivanlou
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
| | - Silvi Rouskin
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA.
| |
Collapse
|
16
|
Chiang TK, Kimchi O, Dhaliwal HK, Villarreal DA, Vasquez FF, Manoharan VN, Brenner MP, Garmann RF. Measuring intramolecular connectivity in long RNA molecules using two-dimensional DNA patch-probe arrays. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.12.532302. [PMID: 36993626 PMCID: PMC10055002 DOI: 10.1101/2023.03.12.532302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
We describe a simple method to infer intramolecular connections in a population of long RNA molecules in vitro. First we add DNA oligonucleotide "patches" that perturb the RNA connections, then we use a microarray containing a complete set of DNA oligonucleotide "probes" to record where perturbations occur. The pattern of perturbations reveals couplings between different regions of the RNA sequence, from which we infer connections as well as their prevalences in the population. We validate this patch-probe method using the 1,058-nucleotide RNA genome of satellite tobacco mosaic virus (STMV), which has previously been shown to have multiple long-range connections. Our results not only indicate long duplexes that agree with previous structures but also reveal the prevalence of competing connections. Together, these results suggest that globally-folded and locally-folded structures coexist in solution. We show that the prevalence of connections changes when pseudouridine, an important component of natural and synthetic RNA molecules, is substituted for uridine in STMV RNA.
Collapse
|
17
|
Chen R, Francese R, Wang N, Li F, Sun X, Xu B, Liu J, Liu Z, Donalisio M, Lembo D, Zhou GC. Exploration of novel hexahydropyrrolo[1,2-e]imidazol-1-one derivatives as antiviral agents against ZIKV and USUV. Eur J Med Chem 2023; 248:115081. [PMID: 36623328 DOI: 10.1016/j.ejmech.2022.115081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 12/28/2022] [Accepted: 12/29/2022] [Indexed: 01/05/2023]
Abstract
Zika virus (ZIKV) and Usutu virus (USUV) are two emerging flaviviruses mostly transmitted by mosquitos. ZIKV is associated with microcephaly in newborns and the less-known USUV, with its reported neurotropism and its extensive spread in Europe, represents a growing concern for human health. There is still no approved vaccine or specific antiviral against ZIKV and USUV infections. The main goal of this study is to investigate the anti-ZIKV and anti-USUV activity of a new library of compounds and to preliminarily investigate the mechanism of action of the selected hit compounds in vitro. Two potent anti-ZIKV and anti-USUV agents, namely ZDL-115 and ZDL-116, were discovered, both presenting low cytotoxicity, cell-line independent antiviral activity in the low micromolar range and ability of reducing viral progeny production. The analysis of the structure-activity relationship (SAR) revealed that introduction of 2-deoxyribose to 3-arene was fundamental to enhance the solubility and improve the antiviral action. Additionally, we demonstrated that ZDL-115 and ZDL-116 are significantly active against both viruses when added on cells for at least 24 h prior to viral inoculation or immediately post-infection. The docking analysis showed that ZDL-116 could target the host vitamin D receptor (VDR) and viral proteins. Future experiments will be focused on compound modification to discover analogues that are more potent and on the clarification of the mechanism of action and the specific drug target. The discovery and the development of a novel anti-flavivirus drug will have a significant impact in a context where there are no fully effective antiviral drugs or vaccines for most flaviviruses.
Collapse
Affiliation(s)
- Ran Chen
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, 211816, Jiangsu, China; Xitaihu Lake Industrial College, Nanjing Tech University, Changzhou, 213149, Jiangsu, China
| | - Rachele Francese
- Laboratory of Molecular Virology and Antiviral Research, Department of Clinical and Biological Sciences, University of Turin, S. Luigi Gonzaga Hospital, 10043 Orbassano, Turin, Italy
| | - Na Wang
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Feng Li
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, 211816, Jiangsu, China
| | - Xia Sun
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, 211816, Jiangsu, China
| | - Bin Xu
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, 211816, Jiangsu, China
| | - Jinsong Liu
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Zhuyun Liu
- School of Pharmacy, Taizhou Polytechnic College, Taizhou, 225300, Jiangsu, China
| | - Manuela Donalisio
- Laboratory of Molecular Virology and Antiviral Research, Department of Clinical and Biological Sciences, University of Turin, S. Luigi Gonzaga Hospital, 10043 Orbassano, Turin, Italy
| | - David Lembo
- Laboratory of Molecular Virology and Antiviral Research, Department of Clinical and Biological Sciences, University of Turin, S. Luigi Gonzaga Hospital, 10043 Orbassano, Turin, Italy.
| | - Guo-Chun Zhou
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, 211816, Jiangsu, China; Xitaihu Lake Industrial College, Nanjing Tech University, Changzhou, 213149, Jiangsu, China.
| |
Collapse
|
18
|
Chen T, Yang H, Liu P, Hamiti M, Zhang X, Xu Y, Quan W, Zhang Y, Yu W, Jiao L, Du T, Xi J, Yin B, Zhou W, Lu S, Peng X. Splicing factor SF3B3, a NS5-binding protein, restricts ZIKV infection by targeting GCH1. Virol Sin 2022; 38:222-232. [PMID: 36572150 PMCID: PMC10176263 DOI: 10.1016/j.virs.2022.12.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 12/09/2022] [Indexed: 12/24/2022] Open
Abstract
Zika virus (ZIKV), a positive-sense single-stranded RNA virus, causes congenital ZIKV syndrome in children and Guillain-Barré Syndrome (GBS) in adults. ZIKV expresses nonstructural protein 5 (NS5), a large protein that is essential for viral replication. ZIKV NS5 confers the ability to evade interferon (IFN) signalling; however, the exact mechanism remains unclear. In this study, we employed affinity pull-down and liquid chromatography-tandem mass spectrometry (LC-MS/MS) analyses and found that splicing factor 3b subunit 3 (SF3B3) is associated with the NS5-Flag pull-down complex through interaction with NS5. Functional assays showed that SF3B3 overexpression inhibited ZIKV replication by promoting IFN-stimulated gene (ISG) expression whereas silencing of SF3B3 inhibited expression of ISGs to promote ZIKV replication. GTP cyclohydrolase I (GCH1) is the first and rate-limiting enzyme in tetrahydrobiopterin (BH4) biosynthesis. NS5 upregulates the expression of GCH1 during ZIKV infection. And GCH1 marginally promoted ZIKV replication via the IFN pathway. Additionally, GCH1 expression is related to the regulation of SF3B3. Overexpression of the SF3B3 protein effectively reduced GCH1 protein levels, whereas SF3B3 knockdown increased its levels. These findings indicated that ZIKV NS5 binding protein SF3B3 contributed to the host immune response against ZIKV replication by modulating the expression of GCH1.
Collapse
Affiliation(s)
- Tanxiu Chen
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, 650031, China; Department of Science and Education, Jiangxi Key Laboratory of Translational Cancer Research, Jiangxi Cancer Hospital, Nanchang, 330029, China
| | - Hao Yang
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, 650031, China
| | - Penghui Liu
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, 650031, China
| | - Moliduer Hamiti
- The State Key Laboratory of Medical Molecular Biology, Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Medical Primate Research Center, Neuroscience Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Xintian Zhang
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, 650031, China
| | - Yi Xu
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, 650031, China
| | - Wenqi Quan
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, 650031, China
| | - Yong Zhang
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, 650031, China
| | - Wenhai Yu
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, 650031, China
| | - Li Jiao
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, 650031, China
| | - Tingfu Du
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, 650031, China
| | - Juemin Xi
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, 650031, China
| | - Bin Yin
- The State Key Laboratory of Medical Molecular Biology, Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Medical Primate Research Center, Neuroscience Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Wei Zhou
- Department of Science and Education, Jiangxi Key Laboratory of Translational Cancer Research, Jiangxi Cancer Hospital, Nanchang, 330029, China
| | - Shuaiyao Lu
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, 650031, China.
| | - Xiaozhong Peng
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, 650031, China; The State Key Laboratory of Medical Molecular Biology, Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Medical Primate Research Center, Neuroscience Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
| |
Collapse
|
19
|
Haack PA, Harmrolfs K, Bader CD, Garcia R, Gunesch AP, Haid S, Popoff A, Voltz A, Kim H, Bartenschlager R, Pietschmann T, Müller R. Thiamyxins: Structure and Biosynthesis of Myxobacterial RNA-Virus Inhibitors. Angew Chem Int Ed Engl 2022; 61:e202212946. [PMID: 36208117 PMCID: PMC10100342 DOI: 10.1002/anie.202212946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Indexed: 11/07/2022]
Abstract
During our search for novel myxobacterial natural products, we discovered the thiamyxins: thiazole- and thiazoline-rich non-ribosomal peptide-polyketide hybrids with potent antiviral activity. We isolated four congeners of this unprecedented natural product family with the non-cyclized thiamyxin D fused to a glycerol unit at the C-terminus. Alongside their structure elucidation, we present a concise biosynthesis model based on biosynthetic gene cluster analysis and isotopically labelled precursor feeding. We report incorporation of a 2-(hydroxymethyl)-4-methylpent-3-enoic acid moiety by a GCN5-related N-acetyltransferase-like decarboxylase domain featuring polyketide synthase. The thiamyxins show potent inhibition of RNA viruses in cell culture models of corona, zika and dengue virus infection. Their potency up to a half maximal inhibitory concentration of 560 nM combined with milder cytotoxic effects on human cell lines indicate the potential for further development of the thiamyxins.
Collapse
Affiliation(s)
- Patrick A Haack
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Saarbrücken, Germany.,German center for infection research (DZIF), Braunschweig, Germany
| | - Kirsten Harmrolfs
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Saarbrücken, Germany.,German center for infection research (DZIF), Braunschweig, Germany
| | - Chantal D Bader
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Saarbrücken, Germany.,German center for infection research (DZIF), Braunschweig, Germany
| | - Ronald Garcia
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Saarbrücken, Germany.,German center for infection research (DZIF), Braunschweig, Germany
| | - Antonia P Gunesch
- Institute of Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Medical School Hannover (MHH) and the Helmholtz Centre for Infection Research (HZI), Hannover, Germany.,German Center for Infection Research, Hannover-Braunschweig Partner Site, and Cluster of Excellence RESIST (EXC 2155), Hannover, Germany
| | - Sibylle Haid
- Institute of Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Medical School Hannover (MHH) and the Helmholtz Centre for Infection Research (HZI), Hannover, Germany.,German Center for Infection Research, Hannover-Braunschweig Partner Site, and Cluster of Excellence RESIST (EXC 2155), Hannover, Germany
| | - Alexander Popoff
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Saarbrücken, Germany.,German center for infection research (DZIF), Braunschweig, Germany
| | - Alexander Voltz
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Saarbrücken, Germany.,German center for infection research (DZIF), Braunschweig, Germany
| | - Heeyoung Kim
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, German Center for Infection Research, Heidelberg Partner Site and Division of Virus-Associated Carcinogenesis, German Cancer Research Center (DKFZ), German Center for Infection Research (DZIF), Heidelberg, Germany
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, German Center for Infection Research, Heidelberg Partner Site and Division of Virus-Associated Carcinogenesis, German Cancer Research Center (DKFZ), German Center for Infection Research (DZIF), Heidelberg, Germany
| | - Thomas Pietschmann
- Institute of Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Medical School Hannover (MHH) and the Helmholtz Centre for Infection Research (HZI), Hannover, Germany.,German Center for Infection Research, Hannover-Braunschweig Partner Site, and Cluster of Excellence RESIST (EXC 2155), Hannover, Germany
| | - Rolf Müller
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Saarbrücken, Germany.,German center for infection research (DZIF), Braunschweig, Germany
| |
Collapse
|
20
|
Ng WC, Kwek SS, Sun B, Yousefi M, Ong EZ, Tan HC, Puschnik AS, Chan KR, Ooi YS, Ooi EE. A fast-growing dengue virus mutant reveals a dual role of STING in response to infection. Open Biol 2022; 12:220227. [PMID: 36514984 PMCID: PMC9748785 DOI: 10.1098/rsob.220227] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The four dengue viruses (DENVs) have evolved multiple mechanisms to ensure its survival. Among these mechanisms is the ability to regulate its replication rate, which may contribute to avoiding premature immune activation that limit infection dissemination: DENVs associated with dengue epidemics have shown slower replication rate than pre-epidemic strains. Correspondingly, wild-type DENVs replicate more slowly than their clinically attenuated derivatives. To understand how DENVs 'make haste slowly', we generated and screened for DENV2 mutants with accelerated replication that also induced high type-I interferon (IFN) expression in infected cells. We chanced upon a single NS2B-I114T amino acid substitution, in an otherwise highly conserved amino acid residue. Accelerated DENV2 replication damaged host DNA as mutant infection was dependent on host DNA damage repair factors, namely RAD21, EID3 and NEK5. DNA damage induced cGAS/STING signalling and activated early type-I IFN response that inhibited infection dissemination. Unexpectedly, STING activation also supported mutant DENV replication in infected cells through STING-induced autophagy. Our findings thus show that DENV NS2B has multi-faceted role in controlling DENV replication rate and immune evasion and suggest that the dual role of STING in supporting virus replication within infected cells but inhibiting infection dissemination could be particularly advantageous for live attenuated vaccine development.
Collapse
Affiliation(s)
- Wy Ching Ng
- Programme in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore 169857, Singapore
| | - Swee Sen Kwek
- Programme in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore 169857, Singapore
| | - Bo Sun
- Programme in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore 169857, Singapore
| | - Meisam Yousefi
- Programme in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore 169857, Singapore
| | - Eugenia Z. Ong
- Programme in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore 169857, Singapore,Viral Research and Experimental Medicine Center, SingHealth Duke-NUS Academic Medical Center, Singapore 169856, Singapore
| | - Hwee Cheng Tan
- Programme in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore 169857, Singapore
| | | | - Kuan Rong Chan
- Programme in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore 169857, Singapore
| | - Yaw Shin Ooi
- Programme in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore 169857, Singapore
| | - Eng Eong Ooi
- Programme in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore 169857, Singapore,Viral Research and Experimental Medicine Center, SingHealth Duke-NUS Academic Medical Center, Singapore 169856, Singapore,Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore,Saw Swee Hock School of Public Health, National University of Singapore, Singapore 117549, Singapore
| |
Collapse
|
21
|
Dos Santos Nascimento IJ, da Silva Rodrigues ÉE, da Silva MF, de Araújo-Júnior JX, de Moura RO. Advances in Computational Methods to Discover New NS2B-NS3 Inhibitors Useful Against Dengue and Zika Viruses. Curr Top Med Chem 2022; 22:2435-2462. [PMID: 36415099 DOI: 10.2174/1568026623666221122121330] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/20/2022] [Accepted: 09/27/2022] [Indexed: 11/24/2022]
Abstract
The Flaviviridae virus family consists of the genera Hepacivirus, Pestivirus, and Flavivirus, with approximately 70 viral types that use arthropods as vectors. Among these diseases, dengue (DENV) and zika virus (ZIKV) serotypes stand out, responsible for thousands of deaths worldwide. Due to the significant increase in cases, the World Health Organization (WHO) declared DENV a potential threat for 2019 due to being transmitted by infected travelers. Furthermore, ZIKV also has a high rate of transmissibility, highlighted in the outbreak in 2015, generating consequences such as Guillain-Barré syndrome and microcephaly. According to clinical outcomes, those infected with DENV can be asymptomatic, and in other cases, it can be lethal. On the other hand, ZIKV has severe neurological symptoms in newborn babies and adults. More serious symptoms include microcephaly, brain calcifications, intrauterine growth restriction, and fetal death. Despite these worrying data, no drug or vaccine is approved to treat these diseases. In the drug discovery process, one of the targets explored against these diseases is the NS2B-NS3 complex, which presents the catalytic triad His51, Asp75, and Ser135, with the function of cleaving polyproteins, with specificity for basic amino acid residues, Lys- Arg, Arg-Arg, Arg-Lys or Gln-Arg. Since NS3 is highly conserved in all DENV serotypes and plays a vital role in viral replication, this complex is an excellent drug target. In recent years, computer-aided drug discovery (CADD) is increasingly essential in drug discovery campaigns, making the process faster and more cost-effective, mainly explained by discovering new drugs against DENV and ZIKV. Finally, the main advances in computational methods applied to discover new compounds against these diseases will be presented here. In fact, molecular dynamics simulations and virtual screening is the most explored approach, providing several hit and lead compounds that can be used in further optimizations. In addition, fragment-based drug design and quantum chemistry/molecular mechanics (QM/MM) provides new insights for developing anti-DENV/ZIKV drugs. We hope that this review offers further helpful information for researchers worldwide and stimulates the use of computational methods to find a promising drug for treating DENV and ZIKV.
Collapse
Affiliation(s)
- Igor José Dos Santos Nascimento
- Department of Pharmacy, Estácio of Alagoas College, Maceió, Brazil.,Department of Pharmacy, Cesmac University Center, Maceió, Brazil.,Department of Pharmacy, Drug Development and Synthesis Laboratory, State University of Paraíba, Campina Grande, Brazil
| | | | - Manuele Figueiredo da Silva
- Laboratory of Medicinal Chemistry, Pharmaceutical Sciences Institute, Federal University of Alagoas, Maceió, Brazil
| | - João Xavier de Araújo-Júnior
- Laboratory of Medicinal Chemistry, Pharmaceutical Sciences Institute, Federal University of Alagoas, Maceió, Brazil
| | - Ricardo Olimpio de Moura
- Department of Pharmacy, Drug Development and Synthesis Laboratory, State University of Paraíba, Campina Grande, Brazil
| |
Collapse
|
22
|
Effect of prior Zika and dengue virus exposure on the severity of a subsequent dengue infection in adults. Sci Rep 2022; 12:17225. [PMID: 36241869 PMCID: PMC9568574 DOI: 10.1038/s41598-022-22231-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 10/11/2022] [Indexed: 01/06/2023] Open
Abstract
Given the structural similarity between Zika and dengue viruses, prior infection from one virus is hypothesized to modulate the severity of a subsequent infection from the other virus. A previous paediatric cohort study observed that a prior Zika infection may increase the risk of a subsequent symptomatic or severe dengue infection. The Colombo Dengue study is a prospective hospital-based cohort study in Sri Lanka that recruits symptomatic adult dengue patients within the first three days of fever. Anti-Dengue Envelope and anti-Zika NS1 IgG antibodies were tested by ELISA (Euroimmun, Lubeck, Germany) in all recruited patients. Associations between pre-morbid seroprevalence for either or both infections and adverse clinical outcomes of the current dengue infection were explored. A total of 507 dengue infected patients were assessed of whom 342 (68%) and 132 (26%) patients had anti-dengue IgG and anti-Zika IgG respectively. People with combined prior dengue and zika exposure as well as prior dengue exposure alone, were at increased risk of plasma leakage, compensated and uncompensated shock, and severe dengue (p < 0·05), compared to people without prior exposure to either infection. The effect of prior Zika exposure alone could not be established due to the small the number of primary dengue infections with prior Zika exposure.
Collapse
|
23
|
RNA secondary structure packages evaluated and improved by high-throughput experiments. Nat Methods 2022; 19:1234-1242. [PMID: 36192461 PMCID: PMC9839360 DOI: 10.1038/s41592-022-01605-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 08/10/2022] [Indexed: 01/17/2023]
Abstract
Despite the popularity of computer-aided study and design of RNA molecules, little is known about the accuracy of commonly used structure modeling packages in tasks sensitive to ensemble properties of RNA. Here, we demonstrate that the EternaBench dataset, a set of more than 20,000 synthetic RNA constructs designed on the RNA design platform Eterna, provides incisive discriminative power in evaluating current packages in ensemble-oriented structure prediction tasks. We find that CONTRAfold and RNAsoft, packages with parameters derived through statistical learning, achieve consistently higher accuracy than more widely used packages in their standard settings, which derive parameters primarily from thermodynamic experiments. We hypothesized that training a multitask model with the varied data types in EternaBench might improve inference on ensemble-based prediction tasks. Indeed, the resulting model, named EternaFold, demonstrated improved performance that generalizes to diverse external datasets including complete messenger RNAs, viral genomes probed in human cells and synthetic designs modeling mRNA vaccines.
Collapse
|
24
|
Zawadzka M, Andrzejewska-Romanowska A, Gumna J, Garfinkel DJ, Pachulska-Wieczorek K. Cell Compartment-Specific Folding of Ty1 Long Terminal Repeat Retrotransposon RNA Genome. Viruses 2022; 14:2007. [PMID: 36146813 PMCID: PMC9503155 DOI: 10.3390/v14092007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 09/01/2022] [Accepted: 09/08/2022] [Indexed: 11/16/2022] Open
Abstract
The structural transitions RNAs undergo during trafficking are not well understood. Here, we used the well-developed yeast Ty1 retrotransposon to provide the first structural model of genome (g) RNA in the nucleus from a retrovirus-like transposon. Through a detailed comparison of nuclear Ty1 gRNA structure with those established in the cytoplasm, virus-like particles (VLPs), and those synthesized in vitro, we detected Ty1 gRNA structural alterations that occur during retrotransposition. Full-length Ty1 gRNA serves as the mRNA for Gag and Gag-Pol proteins and as the genome that is reverse transcribed within VLPs. We show that about 60% of base pairs predicted for the nuclear Ty1 gRNA appear in the cytoplasm, and active translation does not account for such structural differences. Most of the shared base pairs are represented by short-range interactions, whereas the long-distance pairings seem unique for each compartment. Highly structured motifs tend to be preserved after nuclear export of Ty1 gRNA. In addition, our study highlights the important role of Ty1 Gag in mediating critical RNA-RNA interactions required for retrotransposition.
Collapse
Affiliation(s)
- Małgorzata Zawadzka
- Department of Structure and Function of Retrotransposons, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Angelika Andrzejewska-Romanowska
- Department of Structure and Function of Retrotransposons, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Julita Gumna
- Department of Structure and Function of Retrotransposons, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - David J. Garfinkel
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Katarzyna Pachulska-Wieczorek
- Department of Structure and Function of Retrotransposons, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| |
Collapse
|
25
|
Yeh SC, Diosa-Toro M, Tan WL, Rachenne F, Hain A, Yeo CPX, Bribes I, Xiang BWW, Sathiamoorthy Kannan G, Manuel MC, Missé D, Mok YK, Pompon J. Characterization of dengue virus 3'UTR RNA binding proteins in mosquitoes reveals that AeStaufen reduces subgenomic flaviviral RNA in saliva. PLoS Pathog 2022; 18:e1010427. [PMID: 36121894 PMCID: PMC9531803 DOI: 10.1371/journal.ppat.1010427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 10/04/2022] [Accepted: 09/09/2022] [Indexed: 11/27/2022] Open
Abstract
Dengue viruses (DENV) are expanding global pathogens that are transmitted through the bite of mosquitoes, mostly Aedes aegypti. As RNA viruses, DENV rely on RNA-binding proteins (RBPs) to complete their life cycle. Alternatively, RBPs can act as restriction factors that prevent DENV multiplication. While the importance of RBPs is well-supported in humans, there is a dearth of information about their influence on DENV transmission by mosquitoes. Such knowledge could be harnessed to design novel, effective interventions against DENV. Here, we successfully adapted RNA-affinity chromatography coupled with mass spectrometry-a technique initially developed in mammalian cells-to identify RBPs in Ae. aegypti cells. We identified fourteen RBPs interacting with DENV serotype 2 3'UTR, which is involved in the viral multiplication and produces subgenomic flaviviral RNA (sfRNA). We validated the RNA affinity results for two RBPs by confirming that AePur binds the 3'UTR, whereas AeStaufen interacts with both 3'UTR and sfRNA. Using in vivo functional evaluation, we determined that RBPs like AeRan, AeExoRNase, and AeRNase have pro-viral functions, whereas AeGTPase, AeAtu, and AePur have anti-viral functions in mosquitoes. Furthermore, we showed that human and mosquito Pur homologs have a shared affinity to DENV2 RNA, although the anti-viral effect is specific to the mosquito protein. Importantly, we revealed that AeStaufen mediates a reduction of gRNA and sfRNA copies in several mosquito tissues, including the salivary glands and that AeStaufen-mediated sfRNA reduction diminishes the concentration of transmission-enhancing sfRNA in saliva, thereby revealing AeStaufen's role in DENV transmission. By characterizing the first RBPs that associate with DENV2 3'UTR in mosquitoes, our study unravels new pro- and anti-viral targets for the design of novel therapeutic interventions as well as provides foundation for studying the role of RBPs in virus-vector interactions.
Collapse
Affiliation(s)
- Shih-Chia Yeh
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Republic of Singapore
| | - Mayra Diosa-Toro
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Republic of Singapore
| | - Wei-Lian Tan
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Republic of Singapore
| | | | - Arthur Hain
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Republic of Singapore
| | - Celestia Pei Xuan Yeo
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Republic of Singapore
| | - Inès Bribes
- MIVEGEC, Univ. Montpellier, IRD, CNRS, Montpellier, France
| | - Benjamin Wong Wei Xiang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Republic of Singapore
| | | | - Menchie Casayuran Manuel
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Republic of Singapore
| | - Dorothée Missé
- MIVEGEC, Univ. Montpellier, IRD, CNRS, Montpellier, France
| | - Yu Keung Mok
- Department of Biological Sciences, National University of Singapore, Singapore, Republic of Singapore
| | - Julien Pompon
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Republic of Singapore
- MIVEGEC, Univ. Montpellier, IRD, CNRS, Montpellier, France
| |
Collapse
|
26
|
Dumetz F, Enright AJ, Zhao J, Kwok CK, Merrick CJ. The in vivo RNA structurome of the malaria parasite Plasmodium falciparum, a protozoan with an A/U-rich transcriptome. PLoS One 2022; 17:e0270863. [PMID: 36048819 PMCID: PMC9436142 DOI: 10.1371/journal.pone.0270863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 06/19/2022] [Indexed: 11/18/2022] Open
Abstract
Plasmodium falciparum, a protozoan parasite and causative agent of human malaria, has one of the most A/T-biased genomes sequenced to date. This may give the genome and the transcriptome unusual structural features. Recent progress in sequencing techniques has made it possible to study the secondary structures of RNA molecules at the transcriptomic level. Thus, in this study we produced the in vivo RNA structurome of a protozoan parasite with a highly A/U-biased transcriptome. We showed that it is possible to probe the secondary structures of P. falciparum RNA molecules in vivo using two different chemical probes, and obtained structures for more than half of all transcripts in the transcriptome. These showed greater stability (lower free energy) than the same structures modelled in silico, and structural features appeared to influence translation efficiency and RNA decay. Finally, we compared the P. falciparum RNA structurome with the predicted RNA structurome of an A/U-balanced species, P. knowlesi, finding a bias towards lower overall transcript stability and more hairpins and multi-stem loops in P. falciparum. This unusual protozoan RNA structurome will provide a basis for similar studies in other protozoans and also in other unusual genomes.
Collapse
Affiliation(s)
- Franck Dumetz
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Anton J. Enright
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Jieyu Zhao
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, 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, China
| | | |
Collapse
|
27
|
Singh S, Shyamal S, Panda AC. Detecting RNA-RNA interactome. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022; 13:e1715. [PMID: 35132791 DOI: 10.1002/wrna.1715] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/27/2021] [Accepted: 01/07/2022] [Indexed: 06/14/2023]
Abstract
The last decade has seen a robust increase in various types of novel RNA molecules and their complexity in gene regulation. RNA molecules play a critical role in cellular events by interacting with other biomolecules, including protein, DNA, and RNA. It has been established that RNA-RNA interactions play a critical role in several biological processes by regulating the biogenesis and function of RNA molecules. Interestingly, RNA-RNA interactions regulate the biogenesis of diverse RNA molecules, including mRNAs, microRNAs, tRNAs, and circRNAs, through splicing or backsplicing. Structured RNAs like rRNA, tRNA, and snRNAs achieve their functional conformation by intramolecular RNA-RNA interactions. In addition, functional consequences of many intermolecular RNA-RNA interactions have been extensively studied in the regulation of gene expression. Hence, it is essential to understand the mechanism and functions of RNA-RNA interactions in eukaryotes. Conventionally, RNA-RNA interactions have been identified through diverse biochemical methods for decades. The advent of high-throughput RNA-sequencing technologies has revolutionized the identification of global RNA-RNA interactome in cells and their importance in RNA structure and function in gene expression regulation. Although these technologies revealed tens of thousands of intramolecular and intermolecular RNA-RNA interactions, we further look forward to future unbiased and quantitative high-throughput technologies for detecting transcriptome-wide RNA-RNA interactions. With the ability to detect RNA-RNA interactome, we expect that future studies will reveal the higher-order structures of RNA molecules and multi-RNA hybrids impacting human health and diseases. This article is categorized under: RNA Methods > RNA Analyses In Vitro and In Silico RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems.
Collapse
Affiliation(s)
- Suman Singh
- Institute of Life Sciences, Nalco Square, Bhubaneswar, India
- Regional Center for Biotechnology, Faridabad, India
| | | | - Amaresh C Panda
- Institute of Life Sciences, Nalco Square, Bhubaneswar, India
| |
Collapse
|
28
|
Yang SL, Ponti RD, Wan Y, Huber RG. Computational and Experimental Approaches to Study the RNA Secondary Structures of RNA Viruses. Viruses 2022; 14:v14081795. [PMID: 36016417 PMCID: PMC9415818 DOI: 10.3390/v14081795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/12/2022] [Accepted: 08/13/2022] [Indexed: 11/16/2022] Open
Abstract
Most pandemics of recent decades can be traced to RNA viruses, including HIV, SARS, influenza, dengue, Zika, and SARS-CoV-2. These RNA viruses impose considerable social and economic burdens on our society, resulting in a high number of deaths and high treatment costs. As these RNA viruses utilize an RNA genome, which is important for different stages of the viral life cycle, including replication, translation, and packaging, studying how the genome folds is important to understand virus function. In this review, we summarize recent advances in computational and high-throughput RNA structure-mapping approaches and their use in understanding structures within RNA virus genomes. In particular, we focus on the genome structures of the dengue, Zika, and SARS-CoV-2 viruses due to recent significant outbreaks of these viruses around the world.
Collapse
Affiliation(s)
- Siwy Ling Yang
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore 138672, Singapore
| | - Riccardo Delli Ponti
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore 138671, Singapore
| | - Yue Wan
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore 138672, Singapore
- Correspondence: (Y.W.); (R.G.H.)
| | - Roland G. Huber
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore 138671, Singapore
- Correspondence: (Y.W.); (R.G.H.)
| |
Collapse
|
29
|
Dengue Virus NS4b N-Terminus Disordered Region Interacts with NS3 Helicase C-Terminal Subdomain to Enhance Helicase Activity. Viruses 2022; 14:v14081712. [PMID: 36016333 PMCID: PMC9412862 DOI: 10.3390/v14081712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 08/01/2022] [Accepted: 08/01/2022] [Indexed: 11/17/2022] Open
Abstract
Dengue virus replicates its single-stranded RNA genome in membrane-bound complexes formed on the endoplasmic reticulum, where viral non-structural proteins (NS) and RNA co-localize. The NS proteins interact with one another and with the host proteins. The interaction of the viral helicase and protease, NS3, with the RNA-dependent RNA polymerase, NS5, and NS4b proteins is critical for replication. In vitro, NS3 helicase activity is enhanced by interaction with NS4b. We characterized the interaction between NS3 and NS4b and explained a possible mechanism for helicase activity modulation by NS4b. Our bacterial two-hybrid assay results showed that the N-terminal 57 residues region of NS4b is enough to interact with NS3. The molecular docking of the predicted NS4b structure onto the NS3 structure revealed that the N-terminal disordered region of NS4b wraps around the C-terminal subdomain (CTD) of the helicase. Further, NS3 helicase activity is enhanced upon interaction with NS4b. Molecular dynamics simulations on the NS4b-docked NS3 crystal structure and intrinsic tryptophan fluorescence studies suggest that the interaction results in NS3 CTD domain motions. Based on the interpretation of our results in light of the mechanism explained for NS3 helicase, NS4b–NS3 interaction modulating CTD dynamics is a plausible explanation for the helicase activity enhancement.
Collapse
|
30
|
França RKADO, Silva JM, Rodrigues LS, Sokolowskei D, Brigido MM, Maranhão AQ. New Anti-Flavivirus Fusion Loop Human Antibodies with Zika Virus-Neutralizing Potential. Int J Mol Sci 2022; 23:ijms23147805. [PMID: 35887153 PMCID: PMC9321016 DOI: 10.3390/ijms23147805] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/05/2022] [Accepted: 07/11/2022] [Indexed: 02/04/2023] Open
Abstract
Zika virus infections exhibit recurrent outbreaks and can be responsible for disease complications such as congenital Zika virus syndrome. Effective therapeutic interventions are still a challenge. Antibodies can provide significant protection, although the antibody response may fail due to antibody-dependent enhancement reactions. The choice of the target antigen is a crucial part of the process to generate effective neutralizing antibodies. Human anti-Zika virus antibodies were selected by phage display technology. The antibodies were selected against a mimetic peptide based on the fusion loop region in the protein E of Zika virus, which is highly conserved among different flaviviruses. Four rounds of selection were performed using the synthetic peptide in two strategies: the first was using the acidic elution of bound phages, and the second was by applying a competing procedure. After panning, the selected VH and VL domains were determined by combining NGS and bioinformatic approaches. Three different human monoclonal antibodies were expressed as scFvs and further characterized. All showed a binding capacity to Zika (ZIKV) and showed cross-recognition with yellow fever (YFV) and dengue (DENV) viruses. Two of these antibodies, AZ1p and AZ6m, could neutralize the ZIKV infection in vitro. Due to the conservation of the fusion loop region, these new antibodies can potentially be used in therapeutic intervention against Zika virus and other flavivirus illnesses.
Collapse
Affiliation(s)
- Renato Kaylan Alves de Oliveira França
- Molecular Immunology Laboratory, Department of Cellular Biology, Institute of Biological Sciences, University of Brasilia, Brasilia 70910-900, Brazil; (R.K.A.d.O.F.); (J.M.S.); (L.S.R.); (D.S.); (A.Q.M.)
- Graduation Program in Molecular Pathology, University of Brasilia, Brasilia 70910-900, Brazil
| | - Jacyelle Medeiros Silva
- Molecular Immunology Laboratory, Department of Cellular Biology, Institute of Biological Sciences, University of Brasilia, Brasilia 70910-900, Brazil; (R.K.A.d.O.F.); (J.M.S.); (L.S.R.); (D.S.); (A.Q.M.)
| | - Lucas Silva Rodrigues
- Molecular Immunology Laboratory, Department of Cellular Biology, Institute of Biological Sciences, University of Brasilia, Brasilia 70910-900, Brazil; (R.K.A.d.O.F.); (J.M.S.); (L.S.R.); (D.S.); (A.Q.M.)
- Graduation Program in Molecular Pathology, University of Brasilia, Brasilia 70910-900, Brazil
| | - Dimitri Sokolowskei
- Molecular Immunology Laboratory, Department of Cellular Biology, Institute of Biological Sciences, University of Brasilia, Brasilia 70910-900, Brazil; (R.K.A.d.O.F.); (J.M.S.); (L.S.R.); (D.S.); (A.Q.M.)
- Graduation Program in Molecular Biology, University of Brasilia, Brasilia 70910-900, Brazil
| | - Marcelo Macedo Brigido
- Molecular Immunology Laboratory, Department of Cellular Biology, Institute of Biological Sciences, University of Brasilia, Brasilia 70910-900, Brazil; (R.K.A.d.O.F.); (J.M.S.); (L.S.R.); (D.S.); (A.Q.M.)
- Graduation Program in Molecular Pathology, University of Brasilia, Brasilia 70910-900, Brazil
- Graduation Program in Molecular Biology, University of Brasilia, Brasilia 70910-900, Brazil
- III-Immunology Investigation Institute–CNPq-MCT, São Paulo 05403-000, Brazil
- Correspondence:
| | - Andrea Queiroz Maranhão
- Molecular Immunology Laboratory, Department of Cellular Biology, Institute of Biological Sciences, University of Brasilia, Brasilia 70910-900, Brazil; (R.K.A.d.O.F.); (J.M.S.); (L.S.R.); (D.S.); (A.Q.M.)
- Graduation Program in Molecular Pathology, University of Brasilia, Brasilia 70910-900, Brazil
- Graduation Program in Molecular Biology, University of Brasilia, Brasilia 70910-900, Brazil
- III-Immunology Investigation Institute–CNPq-MCT, São Paulo 05403-000, Brazil
| |
Collapse
|
31
|
Zika Virus Replication in a Mast Cell Model is Augmented by Dengue Virus Antibody-Dependent Enhancement and Features a Selective Immune Mediator Secretory Profile. Microbiol Spectr 2022; 10:e0177222. [PMID: 35862953 PMCID: PMC9431662 DOI: 10.1128/spectrum.01772-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Antibodies generated against one dengue serotype can enhance infection of another by a phenomenon called antibody-dependent enhancement (ADE). Additionally, antigenic similarities between Zika and dengue viruses can promote Zika virus infection by way of ADE
in vitro
using these very same anti-dengue antibodies.
Collapse
|
32
|
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.
Collapse
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.
| |
Collapse
|
33
|
Delli Ponti R, Wang J, Wan Y, Huber RG. RNAvigator: A Pipeline to Identify Candidates for Functional RNA Structure Elements. FRONTIERS IN VIROLOGY 2022. [DOI: 10.3389/fviro.2022.878679] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Identifying structural elements in long and complex RNAs, such as long non-coding and RNA viruses, can shed light on the functionality and mechanisms of such RNAs. Here we present RNAvigator, a tool able to identify elements of structural importance by using experimental SHAPE data or SHAPE-like predictions in conjunction with stability and entropy assessments. RNAvigator recognizes regions that are the most stable, unambiguous, and structured on RNA molecules, and thus potentially functional. When relying on predictions, RNAvigator uses the CROSS algorithm, a neural network trained on experimental data that achieved an AUC of 0.74 on hepatitis C virus SHAPE-MaP data and which was able to improve the predictive power of Superfold. By using RNAvigator, we can identify known functional regions on the complete hepatitis C virus genome, including the regulatory regions CRE and IRES, and the 3’ UTR of dengue virus, a region known for the presence of structural elements essential for its replication, and functional regions of long non-coding RNAs such as XIST and HOTAIR. We envision that RNAvigator will be a useful tool for studying long and complex RNA molecules using known chemical probing data or, if they are not available, by employing predicted profiles.
Collapse
|
34
|
Gabryelska MM, Badrock AP, Lau JY, O'Keefe RT, Crow YJ, Kudla G. Global mapping of RNA homodimers in living cells. Genome Res 2022; 32:956-967. [PMID: 35332098 PMCID: PMC9104694 DOI: 10.1101/gr.275900.121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 03/18/2022] [Indexed: 11/25/2022]
Abstract
RNA homodimerization is important for various physiological processes, including the assembly of membraneless organelles, RNA subcellular localization, and packaging of viral genomes. However, understanding RNA dimerization has been hampered by the lack of systematic in vivo detection methods. Here, we show that CLASH, PARIS, and other RNA proximity ligation methods detect RNA homodimers transcriptome-wide as "overlapping" chimeric reads that contain more than one copy of the same sequence. Analyzing published proximity ligation data sets, we show that RNA:RNA homodimers mediated by direct base-pairing are rare across the human transcriptome, but highly enriched in specific transcripts, including U8 snoRNA, U2 snRNA, and a subset of tRNAs. Mutations in the homodimerization domain of U8 snoRNA impede dimerization in vitro and disrupt zebrafish development in vivo, suggesting an evolutionarily conserved role of this domain. Analysis of virus-infected cells reveals homodimerization of SARS-CoV-2 and Zika genomes, mediated by specific palindromic sequences located within protein-coding regions of N gene in SARS-CoV-2 and NS2A gene in Zika. We speculate that regions of viral genomes involved in homodimerization may constitute effective targets for antiviral therapies.
Collapse
Affiliation(s)
- Marta M. Gabryelska
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh, EH4 2XU, United Kingdom;,Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, Bedford Park, South Australia 5042, Australia
| | - Andrew P. Badrock
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, United Kingdom
| | - Jian You Lau
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh, EH4 2XU, United Kingdom
| | - Raymond T. O'Keefe
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, School of Biological Sciences, University of Manchester, Manchester, M13 9PL, United Kingdom
| | - Yanick J. Crow
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, United Kingdom
| | - Grzegorz Kudla
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh, EH4 2XU, United Kingdom
| |
Collapse
|
35
|
Gosavi D, Wower I, Beckmann IK, Hofacker IL, Wower J, Wolfinger MT, Sztuba-Solinska J. Insights into the secondary and tertiary structure of the Bovine Viral Diarrhea Virus Internal Ribosome Entry Site. RNA Biol 2022; 19:496-506. [PMID: 35380920 PMCID: PMC8986297 DOI: 10.1080/15476286.2022.2058818] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
The internal ribosome entry site (IRES) RNA of bovine viral diarrhoea virus (BVDV), an economically significant Pestivirus, is required for the cap-independent translation of viral genomic RNA. Thus, it is essential for viral replication and pathogenesis. We applied a combination of high-throughput biochemical RNA structure probing (SHAPE-MaP) and in silico modelling approaches to gain insight into the secondary and tertiary structures of BVDV IRES RNA. Our study demonstrated that BVDV IRES RNA in solution forms a modular architecture composed of three distinct structural domains (I-III). Two regions within domain III are represented in tertiary interactions to form an H-type pseudoknot. Computational modelling of the pseudoknot motif provided a fine-grained picture of the tertiary structure and local arrangement of helices in the BVDV IRES. Furthermore, comparative genomics and consensus structure predictions revealed that the pseudoknot is evolutionarily conserved among many Pestivirus species. These studies provide detailed insight into the structural arrangement of BVDV IRES RNA H-type pseudoknot and encompassing motifs that likely contribute to the optimal functionality of viral cap-independent translation element.
Collapse
Affiliation(s)
- Devadatta Gosavi
- Department of Biological Sciences, Auburn University, 120 W. Samford Ave, Rouse Life Sciences Building, Auburn, AL, United States
| | - Iwona Wower
- Department of Animal and Dairy Sciences, Auburn University, Auburn, AL, United States
| | - Irene K Beckmann
- Department of Theoretical Chemistry, University of Vienna, Vienna, Austria
| | - Ivo L Hofacker
- Department of Theoretical Chemistry, University of Vienna, Vienna, Austria.,Research Group Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria
| | - Jacek Wower
- Department of Animal and Dairy Sciences, Auburn University, Auburn, AL, United States
| | - 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
| | - Joanna Sztuba-Solinska
- Department of Biological Sciences, Auburn University, 120 W. Samford Ave, Rouse Life Sciences Building, Auburn, AL, United States.,Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| |
Collapse
|
36
|
Morandi E, van Hemert MJ, Incarnato D. SHAPE-guided RNA structure homology search and motif discovery. Nat Commun 2022; 13:1722. [PMID: 35361788 PMCID: PMC8971488 DOI: 10.1038/s41467-022-29398-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 03/11/2022] [Indexed: 01/13/2023] Open
Abstract
The rapidly growing popularity of RNA structure probing methods is leading to increasingly large amounts of available RNA structure information. This demands the development of efficient tools for the identification of RNAs sharing regions of structural similarity by direct comparison of their reactivity profiles, hence enabling the discovery of conserved structural features. We here introduce SHAPEwarp, a largely sequence-agnostic SHAPE-guided algorithm for the identification of structurally-similar regions in RNA molecules. Analysis of Dengue, Zika and coronavirus genomes recapitulates known regulatory RNA structures and identifies novel highly-conserved structural elements. This work represents a preliminary step towards the model-free search and identification of shared and conserved RNA structural features within transcriptomes.
Collapse
Affiliation(s)
- Edoardo Morandi
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Groningen, The Netherlands
| | - Martijn J van Hemert
- Department of Medical Microbiology, Molecular Virology Laboratory, Leiden University Medical Center, Leiden, The Netherlands
| | - Danny Incarnato
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Groningen, The Netherlands.
| |
Collapse
|
37
|
Wang S, Chan KWK, Tan MJA, Flory C, Luo D, Lescar J, Forwood JK, Vasudevan SG. A conserved arginine in NS5 binds genomic 3' stem-loop RNA for primer-independent initiation of flavivirus RNA replication. RNA (NEW YORK, N.Y.) 2022; 28:177-193. [PMID: 34759006 PMCID: PMC8906541 DOI: 10.1261/rna.078949.121] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 10/15/2021] [Indexed: 06/13/2023]
Abstract
The commitment to replicate the RNA genome of flaviviruses without a primer involves RNA-protein interactions that have been shown to include the recognition of the stem-loop A (SLA) in the 5' untranslated region (UTR) by the nonstructural protein NS5. We show that DENV2 NS5 arginine 888, located within the carboxy-terminal 18 residues, is completely conserved in all flaviviruses and interacts specifically with the top-loop of 3'SL in the 3'UTR which contains the pentanucleotide 5'-CACAG-3' previously shown to be critical for flavivirus RNA replication. We present virological and biochemical data showing the importance of this Arg 888 in virus viability and de novo initiation of RNA polymerase activity in vitro. Based on our binding studies, we hypothesize that ternary complex formation of NS5 with 3'SL, followed by dimerization, leads to the formation of the de novo initiation complex that could be regulated by the reversible zipping and unzipping of cis-acting RNA elements.
Collapse
Affiliation(s)
- Sai Wang
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 169857 Singapore
| | - Kitti Wing Ki Chan
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 169857 Singapore
| | - Min Jie Alvin Tan
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 169857 Singapore
| | - Charlotte Flory
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 169857 Singapore
| | - Dahai Luo
- Lee Kong Chian School of Medicine, Nanyang Technological University, 636921 Singapore
| | - Julian Lescar
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
| | - Jade K Forwood
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, New South Wales 2650, Australia
| | - Subhash G Vasudevan
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 169857 Singapore
- Department of Microbiology and Immunology, National University of Singapore, 117545 Singapore
- Institute for Glycomics, Griffith University, Gold Coast Campus, QLD 4222, Australia
| |
Collapse
|
38
|
Bernardo-Menezes LC, Agrelli A, Oliveira ASLED, Moura RRD, Crovella S, Brandão LAC. An overview of Zika virus genotypes and their infectivity. Rev Soc Bras Med Trop 2022; 55:e02632022. [PMID: 36197380 PMCID: PMC9536801 DOI: 10.1590/0037-8682-0263-2022] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 08/31/2022] [Indexed: 11/22/2022] Open
Abstract
Zika virus (ZIKV) is an enveloped, single-stranded RNA arbovirus belonging to the
genus Flavivirus. It was first isolated from a sentinel monkey
in Uganda in 1947. More recently, ZIKV has undergone rapid geographic expansion
and has been responsible for outbreaks in Southeast Asia, the Pacific Islands,
and America. In this review, we have highlighted the influence of viral genetic
variants on ZIKV pathogenesis. Two major ZIKV genotypes (African and Asian) have
been identified. The Asian genotype is subdivided into Southwest Asia, Pacific
Island, and American strains, and is responsible for most outbreaks.
Non-synonymous mutations in ZIKV proteins C, prM, E, NS1, NS2A, NS2B, NS3, and
NS4B were found to have a higher prevalence and association with virulent
strains of the Asian genotype. Consequently, the Asian genotype appears to have
acquired higher cellular permissiveness, tissue persistence, and viral tropism
in human neural cells. Therefore, mutations in specific coding regions of the
Asian genotype may enhance ZIKV infectivity. Considering that mutations in the
genomes of emerging viruses may lead to new virulent variants in humans, there
is a potential for the re-emergence of new ZIKV cases in the future.
Collapse
|
39
|
Optimal flexibility of the linker region of Zika virus NS5 methyltransferase-polymerase is critical for virus replication. Antiviral Res 2021; 195:105194. [PMID: 34699863 DOI: 10.1016/j.antiviral.2021.105194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/20/2021] [Accepted: 10/21/2021] [Indexed: 11/20/2022]
Abstract
The flavivirus NS5 protein contains an N-terminal methyl-transferase (MTase) connected through a flexible linker with a C-terminal RNA-dependent RNA-polymerase (RdRp) domain, that work cooperatively to replicate and methylate the viral genome. In this study we probed the importance of an evolutionary-conserved hydrophobic residue (Val266) located at the start of the ten-residue interdomain linker of Zika virus (ZIKV) NS5. In flavivirus NS5 crystal structures, the start of the linker forms a 310 helix when NS5 adopts a compact conformation, but becomes disordered or extended in open conformations. Using reverse genetics system, we either introduced rigidity in the linker through mutation to a proline or flexibility through a glycine mutation at position 266. ZIKV NS5 Val 266 to Pro mutation was lethal for viral RNA replication while the Gly mutation was severely attenuated. Serial passaging of cell culture supernatant derived from C6/36 mosquito cells transfected with mutant ZIKV RNA showed that the attenuation can be rescued. Next generation deep sequencing revealed four single nucleotide polymorphisms that occur with an allele frequency >98%. The single non-synonymous NS5 mutation Glu419 to Lys is adjacent to RdRp motif G at the tip of the fingers subdomain, while the remaining three are synonymous variants at nucleotide positions 1403, 4403 and 6653 in the genome. Reverse engineering the changes into the ZIKV NS5/Val266Gly background followed by serial passaging revealed that residue 266 is under strong positive selection to revert back to Val. The interaction of the specific conformation of the NS5 linker with Val at position 266 and the RNA binding motif G region may present a potential strategy for allosteric antiviral drug development.
Collapse
|
40
|
Fairman CW, Lever AML, Kenyon JC. Evaluating RNA Structural Flexibility: Viruses Lead the Way. Viruses 2021; 13:v13112130. [PMID: 34834937 PMCID: PMC8624864 DOI: 10.3390/v13112130] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/12/2021] [Accepted: 10/18/2021] [Indexed: 12/11/2022] Open
Abstract
Our understanding of RNA structure has lagged behind that of proteins and most other biological polymers, largely because of its ability to adopt multiple, and often very different, functional conformations within a single molecule. Flexibility and multifunctionality appear to be its hallmarks. Conventional biochemical and biophysical techniques all have limitations in solving RNA structure and to address this in recent years we have seen the emergence of a wide diversity of techniques applied to RNA structural analysis and an accompanying appreciation of its ubiquity and versatility. Viral RNA is a particularly productive area to study in that this economy of function within a single molecule admirably suits the minimalist lifestyle of viruses. Here, we review the major techniques that are being used to elucidate RNA conformational flexibility and exemplify how the structure and function are, as in all biology, tightly linked.
Collapse
Affiliation(s)
| | - Andrew M. L. Lever
- Department of Medicine, Cambridge University, Level 5, Addenbrookes’ Hospital (Box 157), Cambridge CB2 0QQ, UK
- Correspondence: (A.M.L.L.); (J.C.K.); Tel.: +44-(0)-1223-747308 (A.M.L.L. & J.C.K.)
| | - Julia C. Kenyon
- Homerton College, University of Cambridge, Cambridge CB2 8PH, UK;
- Department of Medicine, Cambridge University, Level 5, Addenbrookes’ Hospital (Box 157), Cambridge CB2 0QQ, UK
- Correspondence: (A.M.L.L.); (J.C.K.); Tel.: +44-(0)-1223-747308 (A.M.L.L. & J.C.K.)
| |
Collapse
|
41
|
Zhang Y, Huang K, Xie D, Lau JY, Shen W, Li P, Wang D, Zou Z, Shi S, Ren H, Wang Y, Mao Y, Jin M, Kudla G, Zhao Z. In vivo structure and dynamics of the SARS-CoV-2 RNA genome. Nat Commun 2021; 12:5695. [PMID: 34584097 PMCID: PMC8478942 DOI: 10.1038/s41467-021-25999-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 09/10/2021] [Indexed: 02/08/2023] Open
Abstract
The dynamics of SARS-CoV-2 RNA structure and their functional relevance are largely unknown. Here we develop a simplified SPLASH assay and comprehensively map the in vivo RNA-RNA interactome of SARS-CoV-2 genome across viral life cycle. We report canonical and alternative structures including 5'-UTR and 3'-UTR, frameshifting element (FSE) pseudoknot and genome cyclization in both cells and virions. We provide direct evidence of interactions between Transcription Regulating Sequences, which facilitate discontinuous transcription. In addition, we reveal alternative short and long distance arches around FSE. More importantly, we find that within virions, while SARS-CoV-2 genome RNA undergoes intensive compaction, genome domains remain stable but with strengthened demarcation of local domains and weakened global cyclization. Taken together, our analysis reveals the structural basis for the regulation of replication, discontinuous transcription and translational frameshifting, the alternative conformations and the maintenance of global genome organization during the whole life cycle of SARS-CoV-2, which we anticipate will help develop better antiviral strategies.
Collapse
Affiliation(s)
- Yan Zhang
- Beijing institute of Biotechnology, Beijing, China
| | - Kun Huang
- Unit of Animal Infectious Diseases, National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Dejian Xie
- Wuhan Frasergen Bioinformatics Co., Ltd, Wuhan, China
| | - Jian You Lau
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Wenlong Shen
- Beijing institute of Biotechnology, Beijing, China
| | - Ping Li
- Beijing institute of Biotechnology, Beijing, China
| | - Dong Wang
- Department of Microbiology, University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong, China
| | - Zhong Zou
- Unit of Animal Infectious Diseases, National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shu Shi
- Beijing institute of Biotechnology, Beijing, China
| | | | | | - Youzhi Mao
- Wuhan Frasergen Bioinformatics Co., Ltd, Wuhan, China
| | - Meilin Jin
- Unit of Animal Infectious Diseases, National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Grzegorz Kudla
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh, EH4 2XU, UK.
| | - Zhihu Zhao
- Beijing institute of Biotechnology, Beijing, China.
| |
Collapse
|
42
|
Real-Hohn A, Blaas D. Rhinovirus Inhibitors: Including a New Target, the Viral RNA. Viruses 2021; 13:1784. [PMID: 34578365 PMCID: PMC8473194 DOI: 10.3390/v13091784] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 07/21/2021] [Accepted: 09/03/2021] [Indexed: 12/18/2022] Open
Abstract
Rhinoviruses (RVs) are the main cause of recurrent infections with rather mild symptoms characteristic of the common cold. Nevertheless, RVs give rise to enormous numbers of absences from work and school and may become life-threatening in particular settings. Vaccination is jeopardised by the large number of serotypes eliciting only poorly cross-neutralising antibodies. Conversely, antivirals developed over the years failed FDA approval because of a low efficacy and/or side effects. RV species A, B, and C are now included in the fifteen species of the genus Enteroviruses based upon the high similarity of their genome sequences. As a result of their comparably low pathogenicity, RVs have become a handy model for other, more dangerous members of this genus, e.g., poliovirus and enterovirus 71. We provide a short overview of viral proteins that are considered potential drug targets and their corresponding drug candidates. We briefly mention more recently identified cellular enzymes whose inhibition impacts on RVs and comment novel approaches to interfere with infection via aggregation, virus trapping, or preventing viral access to the cell receptor. Finally, we devote a large part of this article to adding the viral RNA genome to the list of potential drug targets by dwelling on its structure, folding, and the still debated way of its exit from the capsid. Finally, we discuss the recent finding that G-quadruplex stabilising compounds impact on RNA egress possibly via obfuscating the unravelling of stable secondary structural elements.
Collapse
Affiliation(s)
- Antonio Real-Hohn
- Center for Medical Biochemistry, Vienna Biocenter, Max Perutz Laboratories, Medical University of Vienna, Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria
| | - Dieter Blaas
- Center for Medical Biochemistry, Vienna Biocenter, Max Perutz Laboratories, Medical University of Vienna, Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria
| |
Collapse
|
43
|
Martin SE, Gan H, Toomer G, Sridhar N, Sztuba-Solinska J. The m 6A landscape of polyadenylated nuclear (PAN) RNA and its related methylome in the context of KSHV replication. RNA (NEW YORK, N.Y.) 2021; 27:1102-1125. [PMID: 34187903 PMCID: PMC8370742 DOI: 10.1261/rna.078777.121] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 06/25/2021] [Indexed: 05/10/2023]
Abstract
Polyadenylated nuclear (PAN) RNA is a long noncoding transcript involved in Kaposi's sarcoma-associated herpesvirus (KSHV) lytic reactivation and regulation of cellular and viral gene expression. We have previously shown that PAN RNA has dynamic secondary structure and protein binding profiles that can be influenced by epitranscriptomic modifications. N6-methyladenosine (m6A) is one of the most abundant chemical signatures found in viral RNA genomes and virus-encoded RNAs. Here, we combined antibody-independent next-generation mapping with direct RNA sequencing to address the epitranscriptomic status of PAN RNA in KSHV infected cells. We showed that PAN m6A status is dynamic, reaching the highest number of modifications at the late lytic stages of KSHV infection. Using a newly developed method, termed selenium-modified deoxythymidine triphosphate (SedTTP)-reverse transcription (RT) and ligation assisted PCR analysis of m6A (SLAP), we gained insight into the fraction of modification at identified sites. By applying comprehensive proteomic approaches, we identified writers and erasers that regulate the m6A status of PAN, and readers that can convey PAN m6A phenotypic effects. We verified the temporal and spatial subcellular availability of the methylome components for PAN modification by performing confocal microscopy analysis. Additionally, the RNA biochemical probing (SHAPE-MaP) outlined local and global structural alterations invoked by m6A in the context of full-length PAN RNA. This work represents the first comprehensive overview of the dynamic interplay that takes place between the cellular epitranscriptomic machinery and a specific viral RNA in the context of KSHV infected cells.
Collapse
MESH Headings
- Adenosine/analogs & derivatives
- Adenosine/genetics
- Adenosine/metabolism
- Alpha-Ketoglutarate-Dependent Dioxygenase FTO/genetics
- Alpha-Ketoglutarate-Dependent Dioxygenase FTO/metabolism
- Base Pairing
- Base Sequence
- Cell Line, Tumor
- Endonucleases/genetics
- Endonucleases/metabolism
- Epigenesis, Genetic
- Herpesvirus 8, Human/genetics
- Herpesvirus 8, Human/metabolism
- Heterogeneous-Nuclear Ribonucleoprotein Group C/genetics
- Heterogeneous-Nuclear Ribonucleoprotein Group C/metabolism
- Host-Pathogen Interactions/genetics
- Humans
- Lymphocytes/metabolism
- Lymphocytes/virology
- Methylation
- Methyltransferases/genetics
- Methyltransferases/metabolism
- Nucleic Acid Conformation
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Nuclear/genetics
- RNA, Nuclear/metabolism
- RNA-Binding Proteins/genetics
- RNA-Binding Proteins/metabolism
- Reverse Transcription
- Sequence Analysis, RNA
- Transcriptome
Collapse
Affiliation(s)
| | - Huachen Gan
- Department of Biological Sciences, Auburn University, Auburn, Alabama 36849, USA
| | - Gabriela Toomer
- Department of Biological Sciences, Auburn University, Auburn, Alabama 36849, USA
| | - Nikitha Sridhar
- Department of Biological Sciences, Auburn University, Auburn, Alabama 36849, USA
| | | |
Collapse
|
44
|
Comprehensive mapping of SARS-CoV-2 interactions in vivo reveals functional virus-host interactions. Nat Commun 2021; 12:5113. [PMID: 34433821 PMCID: PMC8387478 DOI: 10.1038/s41467-021-25357-1] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 07/27/2021] [Indexed: 02/07/2023] Open
Abstract
SARS-CoV-2 is a major threat to global health. Here, we investigate the RNA structure and RNA-RNA interactions of wildtype (WT) and a mutant (Δ382) SARS-CoV-2 in cells using Illumina and Nanopore platforms. We identify twelve potentially functional structural elements within the SARS-CoV-2 genome, observe that subgenomic RNAs can form different structures, and that WT and Δ382 virus genomes fold differently. Proximity ligation sequencing identify hundreds of RNA-RNA interactions within the virus genome and between the virus and host RNAs. SARS-CoV-2 genome binds strongly to mitochondrial and small nucleolar RNAs and is extensively 2'-O-methylated. 2'-O-methylation sites are enriched in viral untranslated regions, associated with increased virus pair-wise interactions, and are decreased in host mRNAs upon virus infection, suggesting that the virus sequesters methylation machinery from host RNAs towards its genome. These studies deepen our understanding of the molecular and cellular basis of SARS-CoV-2 pathogenicity and provide a platform for targeted therapy.
Collapse
|
45
|
Vicens Q, Kieft JS. Shared properties and singularities of exoribonuclease-resistant RNAs in viruses. Comput Struct Biotechnol J 2021; 19:4373-4380. [PMID: 34471487 PMCID: PMC8374639 DOI: 10.1016/j.csbj.2021.07.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 07/21/2021] [Accepted: 07/23/2021] [Indexed: 11/29/2022] Open
Abstract
What viral RNA genomes lack in size, they make up for in intricacy. Elaborate RNA structures embedded in viral genomes can hijack essential cellular mechanisms aiding virus propagation. Exoribonuclease-resistant RNAs (xrRNAs) are an emerging class of viral elements, which resist degradation by host cellular exoribonucleases to produce viral RNAs with diverse roles during infection. Detailed three-dimensional structural studies of xrRNAs from flaviviruses and a subset of plant viruses led to a mechanistic model in which xrRNAs block enzymatic digestion using a ring-like structure that encircles the 5' end of the resistant structure. In this mini-review, we describe the state of our understanding of the phylogenetic distribution of xrRNAs, their structures, and their conformational dynamics. Because xrRNAs have now been found in several major superfamilies of RNA viruses, they may represent a more widely used strategy than currently appreciated. Could xrRNAs represent a 'molecular clock' that would help us understand virus evolution and pathogenicity? The more we study xrRNAs in viruses, the closer we get to finding xrRNAs within cellular RNAs.
Collapse
Affiliation(s)
- Quentin Vicens
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, CO 80045, USA
- RNA BioScience Initiative, University of Colorado Denver School of Medicine, Aurora, CO 80045, USA
| | - Jeffrey S. Kieft
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, CO 80045, USA
- RNA BioScience Initiative, University of Colorado Denver School of Medicine, Aurora, CO 80045, USA
| |
Collapse
|
46
|
Wang XW, Liu CX, Chen LL, Zhang QC. RNA structure probing uncovers RNA structure-dependent biological functions. Nat Chem Biol 2021; 17:755-766. [PMID: 34172967 DOI: 10.1038/s41589-021-00805-7] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 04/23/2021] [Indexed: 01/22/2023]
Abstract
RNA molecules fold into complex structures that enable their diverse functions in cells. Recent revolutionary innovations in transcriptome-wide RNA structural probing of living cells have ushered in a new era in understanding RNA functions. Here, we summarize the latest technological advances for probing RNA secondary structures and discuss striking discoveries that have linked RNA regulation and biological processes through interrogation of RNA structures. In particular, we highlight how different long noncoding RNAs form into distinct secondary structures that determine their modes of interactions with protein partners to realize their unique functions. These dynamic structures mediate RNA regulatory functions through altering interactions with proteins and other RNAs. We also outline current methodological hurdles and speculate about future directions for development of the next generation of RNA structure-probing technologies of higher sensitivity and resolution, which could then be applied in increasingly physiologically relevant studies.
Collapse
Affiliation(s)
- Xi-Wen Wang
- 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, China.,Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Chu-Xiao Liu
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of the Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Ling-Ling Chen
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of the Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China. .,School of Life Science and Technology, ShanghaiTech University, Shanghai, China. .,School of Life Sciences, Hangzhou Institute for Advanced Study, University of the Chinese Academy of Sciences, Hangzhou, 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, China. .,Tsinghua-Peking Center for Life Sciences, Beijing, China.
| |
Collapse
|
47
|
Cao C, Cai Z, Xiao X, Rao J, Chen J, Hu N, Yang M, Xing X, Wang Y, Li M, Zhou B, Wang X, Wang J, Xue Y. The architecture of the SARS-CoV-2 RNA genome inside virion. Nat Commun 2021; 12:3917. [PMID: 34168138 PMCID: PMC8225788 DOI: 10.1038/s41467-021-22785-x] [Citation(s) in RCA: 105] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 03/30/2021] [Indexed: 02/08/2023] Open
Abstract
SARS-CoV-2 carries the largest single-stranded RNA genome and is the causal pathogen of the ongoing COVID-19 pandemic. How the SARS-CoV-2 RNA genome is folded in the virion remains unknown. To fill the knowledge gap and facilitate structure-based drug development, we develop a virion RNA in situ conformation sequencing technology, named vRIC-seq, for probing viral RNA genome structure unbiasedly. Using vRIC-seq data, we reconstruct the tertiary structure of the SARS-CoV-2 genome and reveal a surprisingly "unentangled globule" conformation. We uncover many long-range duplexes and higher-order junctions, both of which are under purifying selections and contribute to the sequential package of the SARS-CoV-2 genome. Unexpectedly, the D614G and the other two accompanying mutations may remodel duplexes into more stable forms. Lastly, the structure-guided design of potent small interfering RNAs can obliterate the SARS-CoV-2 in Vero cells. Overall, our work provides a framework for studying the genome structure, function, and dynamics of emerging deadly RNA viruses.
Collapse
Affiliation(s)
- Changchang Cao
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Zhaokui Cai
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xia Xiao
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jian Rao
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Juan Chen
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Naijing Hu
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Minnan Yang
- CAS Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Xiaorui Xing
- CAS Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yongle Wang
- CAS Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Manman Li
- School of Life Sciences, Henan Normal University, Xinxiang, China
| | - Bing Zhou
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
| | - Xiangxi Wang
- CAS Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Jianwei Wang
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Yuanchao Xue
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
| |
Collapse
|
48
|
Kabir MA, Zilouchian H, Younas MA, Asghar W. Dengue Detection: Advances in Diagnostic Tools from Conventional Technology to Point of Care. BIOSENSORS 2021; 11:206. [PMID: 34201849 PMCID: PMC8301808 DOI: 10.3390/bios11070206] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 06/05/2021] [Accepted: 06/15/2021] [Indexed: 06/02/2023]
Abstract
The dengue virus (DENV) is a vector-borne flavivirus that infects around 390 million individuals each year with 2.5 billion being in danger. Having access to testing is paramount in preventing future infections and receiving adequate treatment. Currently, there are numerous conventional methods for DENV testing, such as NS1 based antigen testing, IgM/IgG antibody testing, and Polymerase Chain Reaction (PCR). In addition, novel methods are emerging that can cut both cost and time. Such methods can be effective in rural and low-income areas throughout the world. In this paper, we discuss the structural evolution of the virus followed by a comprehensive review of current dengue detection strategies and methods that are being developed or commercialized. We also discuss the state of art biosensing technologies, evaluated their performance and outline strategies to address challenges posed by the disease. Further, we outline future guidelines for the improved usage of diagnostic tools during recurrence or future outbreaks of DENV.
Collapse
Affiliation(s)
- Md Alamgir Kabir
- Asghar-Lab, Micro and Nanotechnology in Medicine, College of Engineering and Computer Science, Boca Raton, FL 33431, USA; (M.A.K.); (H.Z.)
- Department of Computer & Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - Hussein Zilouchian
- Asghar-Lab, Micro and Nanotechnology in Medicine, College of Engineering and Computer Science, Boca Raton, FL 33431, USA; (M.A.K.); (H.Z.)
- College of Medicine, University of Central Florida, Orlando, FL 32827, USA
| | | | - Waseem Asghar
- Asghar-Lab, Micro and Nanotechnology in Medicine, College of Engineering and Computer Science, Boca Raton, FL 33431, USA; (M.A.K.); (H.Z.)
- Department of Computer & Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL 33431, USA
- Department of Biological Sciences (Courtesy Appointment), Florida Atlantic University, Boca Raton, FL 33431, USA
| |
Collapse
|
49
|
Andrews RJ, O’Leary CA, Tompkins VS, Peterson JM, Haniff H, Williams C, Disney MD, Moss WN. A map of the SARS-CoV-2 RNA structurome. NAR Genom Bioinform 2021; 3:lqab043. [PMID: 34046592 PMCID: PMC8140738 DOI: 10.1093/nargab/lqab043] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 04/06/2021] [Accepted: 04/28/2021] [Indexed: 12/11/2022] Open
Abstract
SARS-CoV-2 has exploded throughout the human population. To facilitate efforts to gain insights into SARS-CoV-2 biology and to target the virus therapeutically, it is essential to have a roadmap of likely functional regions embedded in its RNA genome. In this report, we used a bioinformatics approach, ScanFold, to deduce the local RNA structural landscape of the SARS-CoV-2 genome with the highest likelihood of being functional. We recapitulate previously-known elements of RNA structure and provide a model for the folding of an essential frameshift signal. Our results find that SARS-CoV-2 is greatly enriched in unusually stable and likely evolutionarily ordered RNA structure, which provides a large reservoir of potential drug targets for RNA-binding small molecules. Results are enhanced via the re-analyses of publicly-available genome-wide biochemical structure probing datasets that are broadly in agreement with our models. Additionally, ScanFold was updated to incorporate experimental data as constraints in the analysis to facilitate comparisons between ScanFold and other RNA modelling approaches. Ultimately, ScanFold was able to identify eight highly structured/conserved motifs in SARS-CoV-2 that agree with experimental data, without explicitly using these data. All results are made available via a public database (the RNAStructuromeDB: https://structurome.bb.iastate.edu/sars-cov-2) and model comparisons are readily viewable at https://structurome.bb.iastate.edu/sars-cov-2-global-model-comparisons.
Collapse
Affiliation(s)
- Ryan J Andrews
- Roy J. Carver Department of Biophysics, Biochemistry and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Collin A O’Leary
- Roy J. Carver Department of Biophysics, Biochemistry and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Van S Tompkins
- Roy J. Carver Department of Biophysics, Biochemistry and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Jake M Peterson
- Roy J. Carver Department of Biophysics, Biochemistry and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Hafeez S Haniff
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | | | - Matthew D Disney
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Walter N Moss
- Roy J. Carver Department of Biophysics, Biochemistry and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| |
Collapse
|
50
|
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.
Collapse
|