1
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Huston NC, Tsao LH, Brackney DE, Pyle AM. The West Nile virus genome harbors essential riboregulatory elements with conserved and host-specific functional roles. Proc Natl Acad Sci U S A 2024; 121:e2312080121. [PMID: 38985757 DOI: 10.1073/pnas.2312080121] [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: 07/16/2023] [Accepted: 05/25/2024] [Indexed: 07/12/2024] Open
Abstract
West Nile virus (WNV) is an arthropod-borne, positive-sense RNA virus that poses an increasing global threat due to warming climates and lack of effective therapeutics. Like other enzootic viruses, little is known about how host context affects the structure of the full-length RNA genome. Here, we report a complete secondary structure of the entire WNV genome within infected mammalian and arthropod cell lines. Our analysis affords structural insights into multiple, conserved aspects of flaviviral biology. We show that the WNV genome folds with minimal host dependence, and we prioritize well-folded regions for functional validation using structural homology between hosts as a guide. Using structure-disrupting, antisense locked nucleic acids, we then demonstrate that the WNV genome contains riboregulatory structures with conserved and host-specific functional roles. These results reveal promising RNA drug targets within flaviviral genomes, and they highlight the therapeutic potential of ASO-LNAs as both WNV-specific and pan-flaviviral therapeutic agents.
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Affiliation(s)
- Nicholas C Huston
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511
| | - Lucille H Tsao
- Department of Chemistry, Yale University, New Haven, CT 06511
| | - Doug E Brackney
- Department of Entomology, Connecticut Agricultural Experimental Station, New Haven, CT 06511
| | - Anna Marie Pyle
- Department of Chemistry, Yale University, New Haven, CT 06511
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511
- HHMI, Chevy Chase, MD 20815
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2
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Bampali M, Kouvela A, Kesesidis N, Kassela K, Dovrolis N, Karakasiliotis I. West Nile Virus Subgenomic RNAs Modulate Gene Expression in a Neuronal Cell Line. Viruses 2024; 16:812. [PMID: 38793693 PMCID: PMC11125720 DOI: 10.3390/v16050812] [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: 02/19/2024] [Revised: 04/24/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024] Open
Abstract
Subgenomic flaviviral RNAs (sfRNAs) are small non-coding products of the incomplete degradation of viral genomic RNA. They accumulate during flaviviral infection and have been associated with many functional roles inside the host cell. Studies so far have demonstrated that sfRNA plays a crucial role in determining West Nile virus (WNV) pathogenicity. However, its modulatory role on neuronal homeostasis has not been studied in depth. In this study, we investigated the mechanism of sfRNA biosynthesis and its importance for WNV replication in neuronal cells. We found that sfRNA1 is functionally redundant for both replication and translation of WNV. However, the concurrent absence of sfRNA1 and sfRNA2 species is detrimental for the survival of the virus. Differential expression analysis on RNA-seq data from WT and ΔsfRNA replicon cell lines revealed transcriptional changes induced by sfRNA and identified a number of putative targets. Overall, it was shown that sfRNA contributes to the viral evasion by suppressing the interferon-mediated antiviral response. An additional differential expression analysis among replicon and control Neuro2A cells also clarified the transcriptional changes that support WNV replication in neuronal cells. Increased levels of translation and oxidative phosphorylation, post-translational modification processes, and activated DNA repair pathways were observed in replicon cell lines, while developmental processes such as axonal growth were deficient.
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Affiliation(s)
| | | | | | | | | | - Ioannis Karakasiliotis
- Laboratory of Biology, Department of Medicine, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (M.B.); (A.K.); (N.K.); (K.K.); (N.D.)
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3
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Wang LL, Cheng Q, Newton ND, Wolfinger MT, Morgan MS, Slonchak A, Khromykh AA, Cheng TY, Parry RH. Xinyang flavivirus, from Haemaphysalis flava ticks in Henan Province, China, defines a basal, likely tick-only Orthoflavivirus clade. J Gen Virol 2024; 105:001991. [PMID: 38809251 PMCID: PMC11165663 DOI: 10.1099/jgv.0.001991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Accepted: 05/08/2024] [Indexed: 05/30/2024] Open
Abstract
Tick-borne orthoflaviviruses (TBFs) are classified into three conventional groups based on genetics and ecology: mammalian, seabird and probable-TBF group. Recently, a fourth basal group has been identified in Rhipicephalus ticks from Africa: Mpulungu flavivirus (MPFV) in Zambia and Ngoye virus (NGOV) in Senegal. Despite attempts, isolating these viruses in vertebrate and invertebrate cell lines or intracerebral injection of newborn mice with virus-containing homogenates has remained unsuccessful. In this study, we report the discovery of Xinyang flavivirus (XiFV) in Haemaphysalis flava ticks from Xìnyáng, Henan Province, China. Phylogenetic analysis shows that XiFV was most closely related to MPFV and NGOV, marking the first identification of this tick orthoflavivirus group in Asia. We developed a reverse transcriptase quantitative PCR assay to screen wild-collected ticks and egg clutches, with absolute infection rates of 20.75 % in adult females and 15.19 % in egg clutches, suggesting that XiFV could be potentially spread through transovarial transmission. To examine potential host range, dinucleotide composition analyses revealed that XiFV, MPFV and NGOV share a closer composition to classical insect-specific orthoflaviviruses than to vertebrate-infecting TBFs, suggesting that XiFV could be a tick-only orthoflavivirus. Additionally, both XiFV and MPFV lack a furin cleavage site in the prM protein, unlike other TBFs, suggesting these viruses might exist towards a biased immature particle state. To examine this, chimeric Binjari virus with XIFV-prME (bXiFV) was generated, purified and analysed by SDS-PAGE and negative-stain transmission electron microscopy, suggesting prototypical orthoflavivirus size (~50 nm) and bias towards uncleaved prM. In silico structural analyses of the 3'-untranslated regions show that XiFV forms up to five pseudo-knot-containing stem-loops and a prototypical orthoflavivirus dumbbell element, suggesting the potential for multiple exoribonuclease-resistant RNA structures.
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Affiliation(s)
- Lan-Lan Wang
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan Province, PR China
| | - Qia Cheng
- Children’s Medical Center, Hunan Provincial People’s Hospital, Changsha, PR China
| | - Natalee D. Newton
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - 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
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
- RNA Forecast e.U., Vienna, Austria
| | - Mahali S. Morgan
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Andrii Slonchak
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Alexander A. Khromykh
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
- GVN Center of Excellence, Australian Infectious Diseases Research Centre, Brisbane, QLD, Australia
| | - Tian-Yin Cheng
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan Province, PR China
| | - Rhys H. Parry
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
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4
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Nemes K, Gil JF, Liebe S, Mansi M, Poimenopoulou E, Lennefors BL, Varrelmann M, Savenkov EI. Intermolecular base-pairing interactions, a unique topology and exoribonuclease-resistant noncoding RNAs drive formation of viral chimeric RNAs in plants. THE NEW PHYTOLOGIST 2024; 241:861-877. [PMID: 37897070 DOI: 10.1111/nph.19346] [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: 05/04/2023] [Accepted: 10/02/2023] [Indexed: 10/29/2023]
Abstract
In plants, exoribonuclease-resistant RNAs (xrRNAs) are produced by many viruses. Whereas xrRNAs contribute to the pathogenicity of these viruses, the role of xrRNAs in the virus infectious cycle remains elusive. Here, we show that xrRNAs produced by a benyvirus (a multipartite RNA virus with four genomic segments) in plants are involved in the formation of monocistronic coat protein (CP)-encoding chimeric RNAs. Naturally occurring chimeric RNAs, we discovered, are composed of 5'-end of RNA 2 and 3'-end of either RNA 3 or RNA 4 bearing conservative exoribonuclease-resistant 'coremin' region. Using computational tools and site-directed mutagenesis, we show that de novo formation of chimeric RNAs requires intermolecular base-pairing interaction between 'coremin' and 3'-proximal part of the CP gene of RNA 2 as well as a stem-loop structure immediately adjacent to the CP gene. Moreover, knockdown of the expression of the XRN4 gene, encoding 5'→3' exoribonuclease, inhibits biogenesis of both xrRNAs and chimeric RNAs. Our findings suggest a novel mechanism involving a unique tropology of the intermolecular base-pairing complex between xrRNAs and RNA2 to promote formation of chimeric RNAs in plants. XrRNAs, essential for chimeric RNA biogenesis, are generated through the action of cytoplasmic Xrn 4 5'→3' exoribonuclease conserved in all plant species.
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Affiliation(s)
- Katalin Nemes
- Department of Plant Biology, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences (SLU), Uppsala, 75007, Sweden
| | - Jose F Gil
- Department of Plant Biology, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences (SLU), Uppsala, 75007, Sweden
- VEDAS Corporación de Investigación e Innovación (VEDAS CII), Medellín, 050024, Colombia
| | - Sebastian Liebe
- Department of Phytopathology, Institute of Sugar Beet Research, Göttingen, 37079, Germany
| | - Mansi Mansi
- Department of Plant Biology, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences (SLU), Uppsala, 75007, Sweden
| | - Efstratia Poimenopoulou
- Department of Plant Biology, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences (SLU), Uppsala, 75007, Sweden
| | | | - Mark Varrelmann
- Department of Phytopathology, Institute of Sugar Beet Research, Göttingen, 37079, Germany
| | - Eugene I Savenkov
- Department of Plant Biology, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences (SLU), Uppsala, 75007, Sweden
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5
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Parry RH, Slonchak A, Campbell LJ, Newton ND, Debat HJ, Gifford RJ, Khromykh AA. A novel tamanavirus ( Flaviviridae) of the European common frog ( Rana temporaria) from the UK. J Gen Virol 2023; 104:001927. [PMID: 38059479 PMCID: PMC10770923 DOI: 10.1099/jgv.0.001927] [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: 07/07/2023] [Accepted: 11/19/2023] [Indexed: 12/08/2023] Open
Abstract
Flavivirids are small, enveloped, positive-sense RNA viruses from the family Flaviviridae with genomes of ~9-13 kb. Metatranscriptomic analyses of metazoan organisms have revealed a diversity of flavivirus-like or flavivirid viral sequences in fish and marine invertebrate groups. However, no flavivirus-like virus has been identified in amphibians. To remedy this, we investigated the virome of the European common frog (Rana temporaria) in the UK, utilizing high-throughput sequencing at six catch locations. De novo assembly revealed a coding-complete virus contig of a novel flavivirid ~11.2 kb in length. The virus encodes a single ORF of 3456 aa and 5' and 3' untranslated regions (UTRs) of 227 and 666 nt, respectively. We named this virus Rana tamanavirus (RaTV), as BLASTp analysis of the polyprotein showed the closest relationships to Tamana bat virus (TABV) and Cyclopterus lumpus virus from Pteronotus parnellii and Cyclopterus lumpus, respectively. Phylogenetic analysis of the RaTV polyprotein compared to Flavivirus and Flavivirus-like members indicated that RaTV was sufficiently divergent and basal to the vertebrate Tamanavirus clade. In addition to the Mitcham strain, partial but divergent RaTV, sharing 95.64-97.39 % pairwise nucleotide identity, were also obtained from the Poole and Deal samples, indicating that RaTV is widespread in UK frog samples. Bioinformatic analyses of predicted secondary structures in the 3'UTR of RaTV showed the presence of an exoribonuclease-resistant RNA (xrRNA) structure standard in flaviviruses and TABV. To examine this biochemically, we conducted an in vitro Xrn1 digestion assay showing that RaTV probably forms a functional Xrn1-resistant xrRNA.
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Affiliation(s)
- Rhys H. Parry
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Andrii Slonchak
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre (AIDRC), Brisbane, QLD, Australia
| | - Lewis J. Campbell
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
- Institute of Zoology, Zoological Society of London, London, UK
- Environment and Sustainability Institute, University of Exeter, Penryn, UK
| | - Natalee D. Newton
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre (AIDRC), Brisbane, QLD, Australia
| | - Humberto J. Debat
- Instituto de Patología Vegetal, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnología Agropecuaria (IPAVE-CIAP-INTA), Córdoba X5020ICA, Argentina
- Unidad de Fitopatología y Modelización Agrícola (UFYMA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Córdoba X5020ICA, Argentina
| | | | - Alexander A. Khromykh
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre (AIDRC), Brisbane, QLD, Australia
- AIDRC Global Virus Network Centre of Excellence, Brisbane, QLD, Australia
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6
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Liu Y, Guan W, Liu H. Subgenomic Flaviviral RNAs of Dengue Viruses. Viruses 2023; 15:2306. [PMID: 38140548 PMCID: PMC10747610 DOI: 10.3390/v15122306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 11/15/2023] [Accepted: 11/22/2023] [Indexed: 12/24/2023] Open
Abstract
Subgenomic flaviviral RNAs (sfRNAs) are produced during flavivirus infections in both arthropod and vertebrate cells. They are undegraded products originating from the viral 3' untranslated region (3' UTR), a result of the action of the host 5'-3' exoribonuclease, Xrn1, when it encounters specific RNA structures known as Xrn1-resistant RNAs (xrRNAs) within the viral 3' UTR. Dengue viruses generate three to four distinct species of sfRNAs through the presence of two xrRNAs and two dumbbell structures (DBs). The tertiary structures of xrRNAs have been characterized to form a ringlike structure around the 5' end of the viral RNA, effectively inhibiting the activity of Xrn1. The most important role of DENV sfRNAs is to inhibit host antiviral responses by interacting with viral and host proteins, thereby influencing viral pathogenicity, replicative fitness, epidemiological fitness, and transmission. In this review, we aimed to summarize the biogenesis, structures, and functions of DENV sfRNAs, exploring their implications for viral interference.
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Affiliation(s)
- Yi Liu
- Hubei Jiangxia Laboratory, Wuhan 430200, China
| | - Wuxiang Guan
- Hubei Jiangxia Laboratory, Wuhan 430200, China
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430207, China
| | - Haibin Liu
- Hubei Jiangxia Laboratory, Wuhan 430200, China
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430207, China
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7
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Tomecki R, Drazkowska K, Kobylecki K, Tudek A. SKI complex: A multifaceted cytoplasmic RNA exosome cofactor in mRNA metabolism with links to disease, developmental processes, and antiviral responses. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1795. [PMID: 37384835 DOI: 10.1002/wrna.1795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/26/2023] [Accepted: 05/01/2023] [Indexed: 07/01/2023]
Abstract
RNA stability and quality control are integral parts of gene expression regulation. A key factor shaping eukaryotic transcriptomes, mainly via 3'-5' exoribonucleolytic trimming or degradation of diverse transcripts in nuclear and cytoplasmic compartments, is the RNA exosome. Precise exosome targeting to various RNA molecules requires strict collaboration with specialized auxiliary factors, which facilitate interactions with its substrates. The predominant class of cytoplasmic RNA targeted by the exosome are protein-coding transcripts, which are carefully scrutinized for errors during translation. Normal, functional mRNAs are turned over following protein synthesis by the exosome or by Xrn1 5'-3'-exonuclease, acting in concert with Dcp1/2 decapping complex. In turn, aberrant transcripts are eliminated by dedicated surveillance pathways, triggered whenever ribosome translocation is impaired. Cytoplasmic 3'-5' mRNA decay and surveillance are dependent on the tight cooperation between the exosome and its evolutionary conserved co-factor-the SKI (superkiller) complex (SKIc). Here, we summarize recent findings from structural, biochemical, and functional studies of SKIc roles in controlling cytoplasmic RNA metabolism, including links to various cellular processes. Mechanism of SKIc action is illuminated by presentation of its spatial structure and details of its interactions with exosome and ribosome. Furthermore, contribution of SKIc and exosome to various mRNA decay pathways, usually converging on recycling of ribosomal subunits, is delineated. A crucial physiological role of SKIc is emphasized by describing association between its dysfunction and devastating human disease-a trichohepatoenteric syndrome (THES). Eventually, we discuss SKIc functions in the regulation of antiviral defense systems, cell signaling and developmental transitions, emerging from interdisciplinary investigations. This article is categorized under: RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms RNA Turnover and Surveillance > Regulation of RNA Stability RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes.
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Affiliation(s)
- Rafal Tomecki
- Laboratory of RNA Processing and Decay, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Karolina Drazkowska
- Laboratory of Epitranscriptomics, Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | - Kamil Kobylecki
- Laboratory of RNA Processing and Decay, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Agnieszka Tudek
- Laboratory of RNA Processing and Decay, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
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8
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Dilweg IW, Peer J, Olsthoorn RCL. Xrn1-resistant RNA motifs are disseminated throughout the RNA virome and are able to block scanning ribosomes. Sci Rep 2023; 13:15987. [PMID: 37749116 PMCID: PMC10520033 DOI: 10.1038/s41598-023-43001-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 09/18/2023] [Indexed: 09/27/2023] Open
Abstract
RNAs that are able to prevent degradation by the 5'-3' exoribonuclease Xrn1 have emerged as crucial structures during infection by an increasing number of RNA viruses. Several plant viruses employ the so-called coremin motif, an Xrn1-resistant RNA that is usually located in 3' untranslated regions. Investigation of its structural and sequence requirements has led to its identification in plant virus families beyond those in which the coremin motif was initially discovered. In this study, we identified coremin-like motifs that deviate from the original in the number of nucleotides present in the loop region of the 5' proximal hairpin. They are present in a number of viral families that previously did not have an Xrn1-resistant RNA identified yet, including the double-stranded RNA virus families Hypoviridae and Chrysoviridae. Through systematic mutational analysis, we demonstrated that a coremin motif carrying a 6-nucleotide loop in the 5' proximal hairpin generally requires a YGNNAD consensus for stalling Xrn1, similar to the previously determined YGAD consensus required for Xrn1 resistance of the original coremin motif. Furthermore, we determined the minimal requirements for the 3' proximal hairpin. Since some putative coremin motifs were found in intergenic regions or coding sequences, we demonstrated their capacity for inhibiting translation through an in vitro ribosomal scanning inhibition assay. Consequently, this study provides a further expansion on the number of viral families with known Xrn1-resistant elements, while adding a novel, potentially regulatory function for this structure.
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Affiliation(s)
- Ivar W Dilweg
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333CC, Leiden, The Netherlands
| | - Jasper Peer
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333CC, Leiden, The Netherlands
| | - René C L Olsthoorn
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333CC, Leiden, The Netherlands.
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9
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Booth BJ, Nourreddine S, Katrekar D, Savva Y, Bose D, Long TJ, Huss DJ, Mali P. RNA editing: Expanding the potential of RNA therapeutics. Mol Ther 2023; 31:1533-1549. [PMID: 36620962 PMCID: PMC9824937 DOI: 10.1016/j.ymthe.2023.01.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 12/06/2022] [Accepted: 01/04/2023] [Indexed: 01/09/2023] Open
Abstract
RNA therapeutics have had a tremendous impact on medicine, recently exemplified by the rapid development and deployment of mRNA vaccines to combat the COVID-19 pandemic. In addition, RNA-targeting drugs have been developed for diseases with significant unmet medical needs through selective mRNA knockdown or modulation of pre-mRNA splicing. Recently, RNA editing, particularly antisense RNA-guided adenosine deaminase acting on RNA (ADAR)-based programmable A-to-I editing, has emerged as a powerful tool to manipulate RNA to enable correction of disease-causing mutations and modulate gene expression and protein function. Beyond correcting pathogenic mutations, the technology is particularly well suited for therapeutic applications that require a transient pharmacodynamic effect, such as the treatment of acute pain, obesity, viral infection, and inflammation, where it would be undesirable to introduce permanent alterations to the genome. Furthermore, transient modulation of protein function, such as altering the active sites of enzymes or the interface of protein-protein interactions, opens the door to therapeutic avenues ranging from regenerative medicine to oncology. These emerging RNA-editing-based toolsets are poised to broadly impact biotechnology and therapeutic applications. Here, we review the emerging field of therapeutic RNA editing, highlight recent laboratory advancements, and discuss the key challenges on the path to clinical development.
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Affiliation(s)
| | - Sami Nourreddine
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | | | | | | | | | | | - Prashant Mali
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
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10
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White LK, Strugar SM, MacFadden A, Hesselberth JR. Nanopore sequencing of internal 2'-PO 4 modifications installed by RNA repair. RNA (NEW YORK, N.Y.) 2023; 29:847-861. [PMID: 36854608 PMCID: PMC10187680 DOI: 10.1261/rna.079290.122] [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: 06/04/2022] [Accepted: 02/09/2023] [Indexed: 05/18/2023]
Abstract
Ligation by plant and fungal RNA ligases yields an internal 2'-phosphate group on each RNA ligation product. In budding yeast, this covalent mark occurs at the splice junction of two targets of ligation: intron-containing tRNAs and the messenger RNA HAC1 The repertoire of RNA molecules repaired by RNA ligation has not been explored due to a lack of unbiased approaches for identifying RNA ligation products. Here, we define several unique signals produced by 2'-phosphorylated RNAs during nanopore sequencing. A 2'-phosphate at the splice junction of HAC1 mRNA inhibits 5' → 3' degradation, enabling detection of decay intermediates in yeast RNA repair mutants by nanopore sequencing. During direct RNA sequencing, intact 2'-phosphorylated RNAs on HAC1 and tRNAs produce diagnostic changes in nanopore current properties and base calling features, including stalls produced as the modified RNA translocates through the nanopore motor protein. These approaches enable directed studies to identify novel RNA repair events in other contexts.
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Affiliation(s)
- Laura K White
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Saylor M Strugar
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Andrea MacFadden
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Jay R Hesselberth
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
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11
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Isolation and Genetic Characterization of Japanese Encephalitis Virus Two Decades after Its Elimination in Singapore. Viruses 2022; 14:v14122662. [PMID: 36560666 PMCID: PMC9786948 DOI: 10.3390/v14122662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/23/2022] [Accepted: 11/24/2022] [Indexed: 11/30/2022] Open
Abstract
Japanese encephalitis virus (JEV) is an important arbovirus in Asia that can cause serious neurological disease. JEV is transmitted by mosquitoes in an enzootic cycle involving porcine and avian reservoirs, in which humans are accidental, dead-end hosts. JEV is currently not endemic in Singapore, after pig farming was abolished in 1992; the last known human case was reported in 2005. However, due to its location along the East-Asian Australasian Flyway (EAAF), Singapore is vulnerable to JEV re-introduction from the endemic regions. Serological and genetic evidence in the last decade suggests JEV's presence in the local fauna. In the present study, we report the genetic characterization and the first isolation of JEV from 3214 mosquito pools consisting of 41,843 Culex mosquitoes, which were trapped from April 2014 to May 2021. The findings demonstrated the presence of genotype I of JEV (n = 10), in contrast to the previous reports of the presence of genotype II of JEV in Singapore. The genetic analyses also suggested that JEV has entered Singapore on several occasions and has potentially established an enzootic cycle in the local fauna. These observations have important implications in the risk assessment and the control of Japanese encephalitis in non-endemic countries, such as Singapore, that are at risk for JEV transmission.
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12
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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.
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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
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13
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Kutschera LS, Wolfinger MT. Evolutionary traits of Tick-borne encephalitis virus: Pervasive non-coding RNA structure conservation and molecular epidemiology. Virus Evol 2022; 8:veac051. [PMID: 35822110 PMCID: PMC9272599 DOI: 10.1093/ve/veac051] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 04/14/2022] [Accepted: 06/09/2022] [Indexed: 12/17/2022] Open
Abstract
Tick-borne encephalitis virus (TBEV) is the aetiological agent of tick-borne
encephalitis, an infectious disease of the central nervous system that is often associated
with severe sequelae in humans. While TBEV is typically classified into three subtypes,
recent evidence suggests a more varied range of TBEV subtypes and lineages that differ
substantially in the architecture of their 3ʹ untranslated region (3ʹUTR). Building on
comparative genomic approaches and thermodynamic modelling, we characterize the TBEV UTR
structureome diversity and propose a unified picture of pervasive non-coding RNA structure
conservation. Moreover, we provide an updated phylogeny of TBEV, building on more than 220
publicly available complete genomes, and investigate the molecular epidemiology and
phylodynamics with Nextstrain, a web-based visualization framework for real-time pathogen
evolution.
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Affiliation(s)
- Lena S Kutschera
- Department of Theoretical Chemistry, University of Vienna, Währinger Straße 17, Vienna 1090, Austria
| | - Michael T Wolfinger
- Department of Theoretical Chemistry, University of Vienna, Währinger Straße 17, Vienna 1090, Austria
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14
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Wan H, Adams RL, Lindenbach BD, Pyle AM. The In Vivo and In Vitro Architecture of the Hepatitis C Virus RNA Genome Uncovers Functional RNA Secondary and Tertiary Structures. J Virol 2022; 96:e0194621. [PMID: 35353000 PMCID: PMC9044954 DOI: 10.1128/jvi.01946-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 02/24/2022] [Indexed: 01/21/2023] Open
Abstract
Hepatitis C virus (HCV) is a positive-strand RNA virus that remains one of the main contributors to chronic liver disease worldwide. Studies over the last 30 years have demonstrated that HCV contains a highly structured RNA genome and many of these structures play essential roles in the HCV life cycle. Despite the importance of riboregulation in this virus, most of the HCV RNA genome remains functionally unstudied. Here, we report a complete secondary structure map of the HCV RNA genome in vivo, which was studied in parallel with the secondary structure of the same RNA obtained in vitro. Our results show that HCV is folded extensively in the cellular context. By performing comprehensive structural analyses on both in vivo data and in vitro data, we identify compact and conserved secondary and tertiary structures throughout the genome. Genetic and evolutionary functional analyses demonstrate that many of these elements play important roles in the virus life cycle. In addition to providing a comprehensive map of RNA structures and riboregulatory elements in HCV, this work provides a resource for future studies aimed at identifying therapeutic targets and conducting further mechanistic studies on this important human pathogen. IMPORTANCE HCV has one of the most highly structured RNA genomes studied to date, and it is a valuable model system for studying the role of RNA structure in protein-coding genes. While previous studies have identified individual cases of regulatory RNA structures within the HCV genome, the full-length structure of the HCV genome has not been determined in vivo. Here, we present the complete secondary structure map of HCV determined both in cells and from corresponding transcripts generated in vitro. In addition to providing a comprehensive atlas of functional secondary structural elements throughout the genomic RNA, we identified a novel set of tertiary interactions and demonstrated their functional importance. In terms of broader implications, the pipeline developed in this study can be applied to other long RNAs, such as long noncoding RNAs. In addition, the RNA structural motifs characterized in this study broaden the repertoire of known riboregulatory elements.
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Affiliation(s)
- Han Wan
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, USA
| | - Rebecca L. Adams
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| | - Brett D. Lindenbach
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Anna Marie Pyle
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, USA
- Department of Chemistry, Yale University, New Haven, Connecticut, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
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15
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Enhancement of prime editing via xrRNA motif-joined pegRNA. Nat Commun 2022; 13:1856. [PMID: 35387980 PMCID: PMC8986804 DOI: 10.1038/s41467-022-29507-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 03/21/2022] [Indexed: 11/09/2022] Open
Abstract
The prime editors (PEs) have shown great promise for precise genome modification. However, their suboptimal efficiencies present a significant technical challenge. Here, by appending a viral exoribonuclease-resistant RNA motif (xrRNA) to the 3'-extended portion of pegRNAs for their increased resistance against degradation, we develop an upgraded PE platform (xrPE) with substantially enhanced editing efficiencies in multiple cell lines. A pan-target average enhancement of up to 3.1-, 4.5- and 2.5-fold in given cell types is observed for base conversions, small deletions, and small insertions, respectively. Additionally, xrPE exhibits comparable edit:indel ratios and similarly minimal off-target editing as the canonical PE3. Of note, parallel comparison of xrPE to the most recently developed epegRNA-based PE system shows their largely equivalent editing performances. Our study establishes a highly adaptable platform of improved PE that shall have broad implications.
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16
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Structural analysis of 3'UTRs in insect flaviviruses reveals novel determinants of sfRNA biogenesis and provides new insights into flavivirus evolution. Nat Commun 2022; 13:1279. [PMID: 35277507 PMCID: PMC8917146 DOI: 10.1038/s41467-022-28977-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 02/14/2022] [Indexed: 11/13/2022] Open
Abstract
Subgenomic flaviviral RNAs (sfRNAs) are virus-derived noncoding RNAs produced by pathogenic mosquito-borne flaviviruses (MBF) to counteract the host antiviral response. To date, the ability of non-pathogenic flaviviruses to produce and utilise sfRNAs remains largely unexplored, and it is unclear what role XRN1 resistance plays in flavivirus evolution and host adaptation. Herein the production of sfRNAs by several insect-specific flaviviruses (ISFs) that replicate exclusively in mosquitoes is shown, and the secondary structures of their complete 3’UTRs are determined. The xrRNAs responsible for the biogenesis of ISF sfRNAs are also identified, and the role of these sfRNAs in virus replication is demonstrated. We demonstrate that 3’UTRs of all classical ISFs, except Anopheles spp-asscoaited viruses, and of the dual-host associated ISF Binjari virus contain duplicated xrRNAs. We also reveal novel structural elements in the 3’UTRs of dual host-associated and Anopheles-associated classical ISFs. Structure-based phylogenetic analysis demonstrates that xrRNAs identified in Anopheles spp-associated ISF are likely ancestral to xrRNAs of ISFs and MBFs. In addition, our data provide evidence that duplicated xrRNAs are selected in the evolution of flaviviruses to provide functional redundancy, which preserves the production of sfRNAs if one of the structures is disabled by mutations or misfolding. Subgenomic flaviviral RNAs (sfRNAs) are produced by pathogenic flaviviruses to counteract the host antiviral response. sfRNAs are products of incomplete degradation of viral RNA by the host exoribonuclease XRN1 which stalls on XRN1-resistant structural elements (xrRNAs) in the 3‟UTR. Here, Slonchak et al. identify xrRNAs for mosquito-specific flaviviruses, characterize their ability to stall XRN1 and produce sfRNAs, and apply structure-based phylogenetic analysis to provide evidence for evolutionary selection of these elements.
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17
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Truong DJJ, Armbrust N, Geilenkeuser J, Lederer EM, Santl TH, Beyer M, Ittermann S, Steinmaßl E, Dyka M, Raffl G, Phlairaharn T, Greisle T, Živanić M, Grosch M, Drukker M, Westmeyer GG. Intron-encoded cistronic transcripts for minimally invasive monitoring of coding and non-coding RNAs. Nat Cell Biol 2022; 24:1666-1676. [PMID: 36344775 PMCID: PMC9643161 DOI: 10.1038/s41556-022-00998-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 08/19/2022] [Indexed: 11/09/2022]
Abstract
Despite their fundamental role in assessing (patho)physiological cell states, conventional gene reporters can follow gene expression but leave scars on the proteins or substantially alter the mature messenger RNA. Multi-time-point measurements of non-coding RNAs are currently impossible without modifying their nucleotide sequence, which can alter their native function, half-life and localization. Thus, we developed the intron-encoded scarless programmable extranuclear cistronic transcript (INSPECT) as a minimally invasive transcriptional reporter embedded within an intron of a gene of interest. Post-transcriptional excision of INSPECT results in the mature endogenous RNA without sequence alterations and an additional engineered transcript that leaves the nucleus by hijacking the nuclear export machinery for subsequent translation into a reporter or effector protein. We showcase its use in monitoring interleukin-2 (IL2) after T cell activation and tracking the transcriptional dynamics of the long non-coding RNA (lncRNA) NEAT1 during CRISPR interference-mediated perturbation. INSPECT is a method for monitoring gene transcription without altering the mature lncRNA or messenger RNA of the target of interest.
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Affiliation(s)
- Dong-Jiunn Jeffery Truong
- grid.4567.00000 0004 0483 2525Institute for Synthetic Biomedicine, Helmholtz Zentrum München, Neuherberg, Germany ,grid.6936.a0000000123222966Department of Chemistry and TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Niklas Armbrust
- grid.4567.00000 0004 0483 2525Institute for Synthetic Biomedicine, Helmholtz Zentrum München, Neuherberg, Germany ,grid.6936.a0000000123222966Department of Chemistry and TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Julian Geilenkeuser
- grid.4567.00000 0004 0483 2525Institute for Synthetic Biomedicine, Helmholtz Zentrum München, Neuherberg, Germany ,grid.6936.a0000000123222966Department of Chemistry and TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Eva-Maria Lederer
- grid.4567.00000 0004 0483 2525Institute for Synthetic Biomedicine, Helmholtz Zentrum München, Neuherberg, Germany ,grid.6936.a0000000123222966Department of Chemistry and TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Tobias Heinrich Santl
- grid.4567.00000 0004 0483 2525Institute for Synthetic Biomedicine, Helmholtz Zentrum München, Neuherberg, Germany ,grid.6936.a0000000123222966Department of Chemistry and TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Maren Beyer
- grid.4567.00000 0004 0483 2525Institute for Synthetic Biomedicine, Helmholtz Zentrum München, Neuherberg, Germany ,grid.6936.a0000000123222966Department of Chemistry and TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Sebastian Ittermann
- grid.4567.00000 0004 0483 2525Institute of Stem Cell Research, Helmholtz Zentrum München, Neuherberg, Germany
| | - Emily Steinmaßl
- grid.4567.00000 0004 0483 2525Institute for Synthetic Biomedicine, Helmholtz Zentrum München, Neuherberg, Germany ,grid.6936.a0000000123222966Department of Chemistry and TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Mariya Dyka
- grid.4567.00000 0004 0483 2525Institute for Synthetic Biomedicine, Helmholtz Zentrum München, Neuherberg, Germany ,grid.6936.a0000000123222966Department of Chemistry and TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Gerald Raffl
- grid.4567.00000 0004 0483 2525Institute for Synthetic Biomedicine, Helmholtz Zentrum München, Neuherberg, Germany ,grid.6936.a0000000123222966Department of Chemistry and TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Teeradon Phlairaharn
- grid.4567.00000 0004 0483 2525Institute for Synthetic Biomedicine, Helmholtz Zentrum München, Neuherberg, Germany ,grid.6936.a0000000123222966Department of Chemistry and TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Tobias Greisle
- grid.4567.00000 0004 0483 2525Institute of Stem Cell Research, Helmholtz Zentrum München, Neuherberg, Germany
| | - Milica Živanić
- grid.4567.00000 0004 0483 2525Institute for Synthetic Biomedicine, Helmholtz Zentrum München, Neuherberg, Germany ,grid.6936.a0000000123222966Department of Chemistry and TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Markus Grosch
- grid.4567.00000 0004 0483 2525Institute of Stem Cell Research, Helmholtz Zentrum München, Neuherberg, Germany
| | - Micha Drukker
- grid.4567.00000 0004 0483 2525Institute of Stem Cell Research, Helmholtz Zentrum München, Neuherberg, Germany
| | - Gil Gregor Westmeyer
- grid.4567.00000 0004 0483 2525Institute for Synthetic Biomedicine, Helmholtz Zentrum München, Neuherberg, Germany ,grid.6936.a0000000123222966Department of Chemistry and TUM School of Medicine, Technical University of Munich, Munich, Germany
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18
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Effects of the noncoding subgenomic RNA of red clover necrotic mosaic virus in virus infection. J Virol 2021; 96:e0181521. [PMID: 34851690 PMCID: PMC8826918 DOI: 10.1128/jvi.01815-21] [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
In recent years, a new class of viral noncoding subgenomic RNA (ncsgRNA) has been identified. This RNA is generated as a stable degradation product via an exoribonuclease-resistant RNA (xrRNA) structure, which blocks the progression of 5′→3′ exoribonuclease on viral RNAs in infected cells. Here, we assess the effects of the ncsgRNA of red clover necrotic mosaic virus (RCNMV), called SR1f, in infected plants. We demonstrate the following: (i) the absence of SR1f reduces symptoms and decreases viral RNA accumulation in Nicotiana benthamiana and Arabidopsis thaliana plants; (ii) SR1f has an essential function other than suppression of RNA silencing; and (iii) the cytoplasmic exoribonuclease involved in mRNA turnover, XRN4, is not required for SR1f production or virus infection. A comparative transcriptomic analysis in N. benthamiana infected with wild-type RCNMV or an SR1f-deficient mutant RCNMV revealed that wild-type RCNMV infection, which produces SR1f and much higher levels of virus, has a greater and more significant impact on cellular gene expression than the SR1f-deficient mutant. Upregulated pathways include plant hormone signaling, plant-pathogen interaction, MAPK signaling, and several metabolic pathways, while photosynthesis-related genes were downregulated. We compare this to host genes known to participate in infection by other tombusvirids. Viral reads revealed a 10- to 100-fold ratio of positive to negative strand, and the abundance of reads of both strands mapping to the 3′ region of RCNMV RNA1 support the premature transcription termination mechanism of synthesis for the coding sgRNA. These results provide a framework for future studies of the interactions and functions of noncoding RNAs of plant viruses. IMPORTANCE Knowledge of how RNA viruses manipulate host and viral gene expression is crucial to our understanding of infection and disease. Unlike viral protein-host interactions, little is known about the control of gene expression by viral RNA. Here, we begin to address this question by investigating the noncoding subgenomic RNA (ncsgRNA) of red clover necrotic mosaic virus (RCNMV), called SR1f. Similar exoribonuclease-resistant RNAs of flaviviruses are well studied, but the roles of plant viral ncsgRNAs, and how they arise, are poorly understood. Surprisingly, we find the likely exonuclease candidate, XRN4, is not required to generate SR1f, and we assess the effects of SR1f on virus accumulation and symptom development. Finally, we compare the effects of infection by wild-type RCNMV versus an SR1f-deficient mutant on host gene expression in Nicotiana benthamiana, which reveals that ncsgRNAs such as SR1f are key players in virus-host interactions to facilitate productive infection.
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19
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Pseudoknot length modulates the folding, conformational dynamics, and robustness of Xrn1 resistance of flaviviral xrRNAs. Nat Commun 2021; 12:6417. [PMID: 34741027 PMCID: PMC8571300 DOI: 10.1038/s41467-021-26616-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 10/04/2021] [Indexed: 01/15/2023] Open
Abstract
To understand how RNA dynamics is regulated and connected to its function, we investigate the folding, conformational dynamics and robustness of Xrn1 resistance of a set of flaviviral xrRNAs using SAXS, smFRET and in vitro enzymatic assays. Flaviviral xrRNAs form discrete ring-like 3D structures, in which the length of a conserved long-range pseudoknot (PK2) ranges from 2 bp to 7 bp. We find that xrRNAs' folding, conformational dynamics and Xrn1 resistance are strongly correlated and highly Mg2+-dependent, furthermore, the Mg2+-dependence is modulated by PK2 length variations. xrRNAs with long PK2 require less Mg2+ to stabilize their folding, exhibit reduced conformational dynamics and strong Xrn1 resistance even at low Mg2+, and tolerate mutations at key tertiary motifs at high Mg2+, which generally are destructive to xrRNAs with short PK2. These results demonstrate an unusual regulatory mechanism of RNA dynamics providing insights into the functions and future biomedical applications of xrRNAs.
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20
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Harvey C, Klassa S, Finol E, Hall J, Hill AC. Chimeric Flaviviral RNA-siRNA Molecules Resist Degradation by The Exoribonuclease Xrn1 and Trigger Gene Silencing in Mammalian Cells. Chembiochem 2021; 22:3099-3106. [PMID: 34431199 PMCID: PMC8596575 DOI: 10.1002/cbic.202100434] [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: 08/19/2021] [Indexed: 11/11/2022]
Abstract
RNA is an emerging platform for drug delivery, but the susceptibility of RNA to nuclease degradation remains a major barrier to its implementation in vivo. Here, we engineered flaviviral Xrn1-resistant RNA (xrRNA) motifs to host small interfering RNA (siRNA) duplexes. The xrRNA-siRNA molecules self-assemble in vitro, resist degradation by the conserved eukaryotic 5' to 3' exoribonuclease Xrn1, and trigger gene silencing in 293T cells. The resistance of the molecules to Xrn1 does not translate to stability in blood serum. Nevertheless, our results demonstrate that flavivirus-derived xrRNA motifs can confer Xrn1 resistance on a model therapeutic payload and set the stage for further investigations into using the motifs as building blocks in RNA nanotechnology.
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Affiliation(s)
- Cressida Harvey
- Department of BiologyETH ZürichWolfgang-Pauli-Strasse 278093ZürichSwitzerland
| | - Sven Klassa
- Department of Chemistry and Applied BiosciencesInstitute of Pharmaceutical SciencesETH ZürichVladimir-Prelog-Weg 1-5/108093ZürichSwitzerland
| | - Esteban Finol
- Department of BiologyETH ZürichWolfgang-Pauli-Strasse 278093ZürichSwitzerland
| | - Jonathan Hall
- Department of Chemistry and Applied BiosciencesInstitute of Pharmaceutical SciencesETH ZürichVladimir-Prelog-Weg 1-5/108093ZürichSwitzerland
| | - Alyssa C. Hill
- Department of Chemistry and Applied BiosciencesInstitute of Pharmaceutical SciencesETH ZürichVladimir-Prelog-Weg 1-5/108093ZürichSwitzerland
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21
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Zhang S, Sun R, Perdoncini Carvalho C, Han J, Zheng L, Qu F. Replication-Dependent Biogenesis of Turnip Crinkle Virus Long Noncoding RNAs. J Virol 2021; 95:e0016921. [PMID: 34160262 PMCID: PMC8387050 DOI: 10.1128/jvi.00169-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 06/14/2021] [Indexed: 12/24/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) of virus origin accumulate in cells infected by many positive-strand (+) RNA viruses to bolster viral infectivity. Their biogenesis mostly utilizes exoribonucleases of host cells that degrade viral genomic or subgenomic RNAs in the 5'-to-3' direction until being stalled by well-defined RNA structures. Here, we report a viral lncRNA that is produced by a novel replication-dependent mechanism. This lncRNA corresponds to the last 283 nucleotides of the turnip crinkle virus (TCV) genome and hence is designated tiny TCV subgenomic RNA (ttsgR). ttsgR accumulated to high levels in TCV-infected Nicotiana benthamiana cells when the TCV-encoded RNA-dependent RNA polymerase (RdRp), also known as p88, was overexpressed. Both (+) and (-) strand forms of ttsgR were produced in a manner dependent on the RdRp functionality. Strikingly, templates as short as ttsgR itself were sufficient to program ttsgR amplification, as long as the TCV-encoded replication proteins p28 and p88 were provided in trans. Consistent with its replicational origin, ttsgR accumulation required a 5' terminal carmovirus consensus sequence (CCS), a sequence motif shared by genomic and subgenomic RNAs of many viruses phylogenetically related to TCV. More importantly, introducing a new CCS motif elsewhere in the TCV genome was alone sufficient to cause the emergence of another lncRNA. Finally, abolishing ttsgR by mutating its 5' CCS gave rise to a TCV mutant that failed to compete with wild-type TCV in Arabidopsis. Collectively, our results unveil a replication-dependent mechanism for the biogenesis of viral lncRNAs, thus suggesting that multiple mechanisms, individually or in combination, may be responsible for viral lncRNA production. IMPORTANCE Many positive-strand (+) RNA viruses produce long noncoding RNAs (lncRNAs) during the process of cellular infections and mobilize these lncRNAs to counteract antiviral defenses, as well as coordinate the translation of viral proteins. Most viral lncRNAs arise from 5'-to-3' degradation of longer viral RNAs being stalled at stable secondary structures. Here, we report a viral lncRNA that is produced by the replication machinery of turnip crinkle virus (TCV). This lncRNA, designated ttsgR, shares the terminal characteristics with TCV genomic and subgenomic RNAs and overaccumulates in the presence of moderately overexpressed TCV RNA-dependent RNA polymerase (RdRp). Furthermore, templates that are of similar sizes as ttsgR are readily replicated by TCV replication proteins (p28 and RdRp) provided from nonviral sources. In summary, this study establishes an approach for uncovering low abundance viral lncRNAs, and characterizes a replicating TCV lncRNA. Similar investigations on human-pathogenic (+) RNA viruses could yield novel therapeutic targets.
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Affiliation(s)
- Shaoyan Zhang
- Department of Plant Pathology, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, Ohio, USA
| | - Rong Sun
- Department of Plant Pathology, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, Ohio, USA
| | - Camila Perdoncini Carvalho
- Department of Plant Pathology, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, Ohio, USA
| | - Junping Han
- Department of Plant Pathology, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, Ohio, USA
| | - Limin Zheng
- Department of Plant Pathology, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, Ohio, USA
| | - Feng Qu
- Department of Plant Pathology, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, Ohio, USA
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22
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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.
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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
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23
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Mechanical strength of RNA knot in Zika virus protects against cellular defenses. Nat Chem Biol 2021; 17:975-981. [PMID: 34253909 DOI: 10.1038/s41589-021-00829-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 06/03/2021] [Indexed: 12/21/2022]
Abstract
Unusual knot-like structures recently discovered in viral exoribonuclease-resistant RNAs (xrRNAs) prevent digestion by host RNases to create subgenomic RNAs enhancing infection and pathogenicity. xrRNAs are proposed to prevent digestion through mechanical resistance to unfolding. However, their unfolding force has not been measured, and the factors determining RNase resistance are unclear. Furthermore, how these knots fold remains unknown. Unfolding a Zika virus xrRNA with optical tweezers revealed that it was the most mechanically stable RNA yet observed. The knot formed by threading the 5' end into a three-helix junction before pseudoknot interactions closed a ring around it. The pseudoknot and tertiary contacts stabilizing the threaded 5' end were both required to generate extreme force resistance, whereas removing a 5'-end contact produced a low-force knot lacking RNase resistance. These results indicate mechanical resistance plays a central functional role, with the fraction of molecules forming extremely high-force knots determining the RNase resistance level.
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24
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Zammit A, Helwerda L, Olsthoorn RCL, Verbeek FJ, Gultyaev AP. A database of flavivirus RNA structures with a search algorithm for pseudoknots and triple base interactions. Bioinformatics 2021; 37:956-962. [PMID: 32866223 PMCID: PMC8128465 DOI: 10.1093/bioinformatics/btaa759] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 08/19/2020] [Accepted: 08/24/2020] [Indexed: 12/13/2022] Open
Abstract
Motivation The Flavivirus genus includes several important pathogens, such as Zika, dengue and yellow fever virus. Flavivirus RNA genomes contain a number of functionally important structures in their 3′ untranslated regions (3′UTRs). Due to the diversity of sequences and topologies of these structures, their identification is often difficult. In contrast, predictions of such structures are important for understanding of flavivirus replication cycles and development of antiviral strategies. Results We have developed an algorithm for structured pattern search in RNA sequences, including secondary structures, pseudoknots and triple base interactions. Using the data on known conserved flavivirus 3′UTR structures, we constructed structural descriptors which covered the diversity of patterns in these motifs. The descriptors and the search algorithm were used for the construction of a database of flavivirus 3′UTR structures. Validating this approach, we identified a number of domains matching a general pattern of exoribonuclease Xrn1-resistant RNAs in the growing group of insect-specific flaviviruses. Availability and implementation The Leiden Flavivirus RNA Structure Database is available at https://rna.liacs.nl. The search algorithm is available at https://github.com/LeidenRNA/SRHS. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Alan Zammit
- Group Imaging & Bioinformatics, Leiden Institute of Advanced Computer Science (LIACS), Leiden University, 2300 RA Leiden, The Netherlands
| | - Leon Helwerda
- Group Imaging & Bioinformatics, Leiden Institute of Advanced Computer Science (LIACS), Leiden University, 2300 RA Leiden, The Netherlands
| | - René C L Olsthoorn
- Group Supramolecular & Biomaterials Chemistry, Leiden Institute of Chemistry, Leiden University, 2300 RA Leiden, The Netherlands
| | - Fons J Verbeek
- Group Imaging & Bioinformatics, Leiden Institute of Advanced Computer Science (LIACS), Leiden University, 2300 RA Leiden, The Netherlands
| | - Alexander P Gultyaev
- Group Imaging & Bioinformatics, Leiden Institute of Advanced Computer Science (LIACS), Leiden University, 2300 RA Leiden, The Netherlands.,Department of Viroscience, Erasmus Medical Center, Rotterdam, 3000 CA, The Netherlands
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25
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Hochrein LM, Li H, Pierce NA. High-Performance Allosteric Conditional Guide RNAs for Mammalian Cell-Selective Regulation of CRISPR/Cas. ACS Synth Biol 2021; 10:964-971. [PMID: 33930275 DOI: 10.1021/acssynbio.1c00037] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The activity of a conditional guide RNA (cgRNA) is dependent on the presence or absence of an RNA trigger, enabling cell-selective regulation of CRISPR/Cas function. cgRNAs are programmable at two levels, with the target-binding sequence controlling the target of Cas activity (edit, silence, or induce a gene of choice) and the trigger-binding sequence controlling the scope of Cas activity (subset of cells expressing the trigger RNA). Allosteric cgRNA mechanisms enable independent design of the target and trigger sequences, providing the flexibility to select the regulatory target and scope independently. Building on prior advances in dynamic RNA nanotechnology that demonstrated the cgRNA concept, here we set the goal of engineering high-performance allosteric cgRNA mechanisms for the mammalian setting, pursuing both ON → OFF logic (conditional inactivation by an RNA trigger) and OFF → ON logic (conditional activation by an RNA trigger). For each mechanism, libraries of orthogonal cgRNA/trigger pairs were designed using NUPACK. In HEK 293T cells expressing cgRNAs, triggers, and inducing dCas9: (1) a library of four ON → OFF "terminator switch" cgRNAs exhibit a median fold-change of ≈50×, a median fractional dynamic range of ≈20%, and a median crosstalk modulus of ≈9%; (2) a library of three OFF → ON "split-terminator switch" cgRNAs exhibit a median fold-change of ≈150×, a median fractional dynamic range of ≈50%, and a median crosstalk modulus of ≈4%. Further, we demonstrate that xrRNA elements that protect viral RNAs from degradation by exoribonucleases can dramatically enhance the performance of RNA synthetic biology. The high-performance allosteric cgRNAs demonstrated here for ON → OFF and OFF → ON logic in mammalian cells provide a foundation for pursuing applications of programmable cell-selective regulation.
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Affiliation(s)
- Lisa M Hochrein
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Heyun Li
- Division of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Niles A Pierce
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, California 91125, United States
- Division of Engineering & Applied Science, California Institute of Technology, Pasadena, California 91125, United States
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26
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Jansen S, Smlatic E, Copmans D, Debaveye S, Tangy F, Vidalain PO, Neyts J, Dallmeier K. Identification of host factors binding to dengue and Zika virus subgenomic RNA by efficient yeast three-hybrid screens of the human ORFeome. RNA Biol 2021; 18:732-744. [PMID: 33459164 PMCID: PMC8086697 DOI: 10.1080/15476286.2020.1868754] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 12/15/2020] [Accepted: 12/17/2020] [Indexed: 10/26/2022] Open
Abstract
Flaviviruses such as the dengue (DENV) and the Zika virus (ZIKV) are important human pathogens causing around 100 million symptomatic infections each year. During infection, small subgenomic flavivirus RNAs (sfRNAs) are formed inside the infected host cell as a result of incomplete degradation of the viral RNA genome by cellular exoribonuclease XRN1. Although the full extent of sfRNA functions is to be revealed, these non-coding RNAs are key virulence factors and their detrimental effects on multiple cellular processes seem to consistently involve molecular interactions with RNA-binding proteins (RBPs). Discovery of such sfRNA-binding host-factors has followed established biochemical pull-down approaches skewed towards highly abundant proteins hampering proteome-wide coverage. Yeast three-hybrid (Y3H) systems represent an attractive alternative approach. To facilitate proteome-wide screens for RBP, we revisited and improved existing RNA-Y3H methodology by (1) implementing full-length ORF libraries in combination with (2) efficient yeast mating to increase screening depth and sensitivity, and (3) stringent negative controls to eliminate over-representation of non-specific RNA-binders. These improvements were validated employing the well-characterized interaction between DDX6 (DEAD-box helicase 6) and sfRNA of DENV as paradigm. Our advanced Y3H system was used to screen for human proteins binding to DENV and ZIKV sfRNA, resulting in a list of 69 putative sfRNA-binders, including several previously reported as well as numerous novel RBP host factors. Our methodology requiring no sophisticated infrastructure or analytic pipeline may be employed for the discovery of meaningful RNA-protein interactions at large scale in other fields.
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Affiliation(s)
- Sander Jansen
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Enisa Smlatic
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Leuven, Belgium
- Division of Paediatric Infectious Diseases, Ludwig-Maximilians-University Munich, Dr. Von Hauner Children’s Hospital, Munich, Germany
| | - Daniëlle Copmans
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Leuven, Belgium
- KU Leuven Department of Pharmaceutical and Pharmacological Sciences, Laboratory for Molecular Biodiscovery, Leuven, Belgium
| | - Sarah Debaveye
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Frédéric Tangy
- Unité de Génomique Virale et Vaccination, Institut Pasteur, CNRS, Paris, France
| | - Pierre-Olivier Vidalain
- Unité de Génomique Virale et Vaccination, Institut Pasteur, CNRS, Paris, France
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm U1111, Université Claude Bernard Lyon 1, Lyon, France
| | - Johan Neyts
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Kai Dallmeier
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Leuven, Belgium
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27
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Dilweg IW, Bouabda A, Dalebout T, Gultyaev AP, Bredenbeek PJ, Olsthoorn RCL. Xrn1-resistant RNA structures are well-conserved within the genus flavivirus. RNA Biol 2021; 18:709-717. [PMID: 33064973 PMCID: PMC8078501 DOI: 10.1080/15476286.2020.1830238] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 09/24/2020] [Accepted: 09/25/2020] [Indexed: 12/18/2022] Open
Abstract
Subgenomic RNAs are produced by several RNA viruses through incomplete degradation of their genomic RNA by the exoribonuclease Xrn1, and have been shown to be essential for viral growth and pathogenicity. Within the flavivirus genus of the Flaviviridae family, two distinct classes of Xrn1-resistant RNA motifs have been proposed; one for mosquito-borne and insect-specific flaviviruses, and one for tick-borne flaviviruses and no-known-vector flaviviruses. We investigated tick-borne and no-known-vector flavivirus Xrn1-resistant RNA motifs through systematic in vitro mutational analysis and showed that both classes actually possess very similar structural configurations, including a double pseudoknot and a base-triple at identical, conserved locations. For the no-known-vector flavivirus Modoc virus, we show that in vivo generation of subgenomic flaviviral RNA was affected by mutations targeted at nucleotides involved in the structural features of flaviviral Xrn1-resistant RNA motifs that were defined in this work. Our results suggest that throughout the genus flavivirus Xrn1-resistant RNA motifs adopt the same topologically conserved structure.
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Affiliation(s)
- Ivar W. Dilweg
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Assia Bouabda
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Tim Dalebout
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Alexander P. Gultyaev
- Leiden Institute of Advanced Computer Science, Leiden University, Leiden, The Netherlands
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Peter J. Bredenbeek
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - R. C. L. Olsthoorn
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
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28
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Dilweg IW, Savina A, Köthe S, Gultyaev AP, Bredenbeek PJ, Olsthoorn RCL. All genera of Flaviviridae host a conserved Xrn1-resistant RNA motif. RNA Biol 2021; 18:2321-2329. [PMID: 33858294 PMCID: PMC8632102 DOI: 10.1080/15476286.2021.1907044] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
After infection by flaviviruses like Zika and West Nile virus, eukaryotic hosts employ the well-conserved endoribonuclease Xrn1 to degrade the viral genomic RNA. Within the 3' untranslated regions, this enzyme encounters intricate Xrn1-resistant structures. This results in the accumulation of subgenomic flaviviral RNAs, an event that improves viral growth and aggravates viral pathogenicity. Xrn1-resistant RNAs have been established throughout the flaviviral genus, but not yet throughout the entire Flaviviridae family. In this work, we use previously determined characteristics of these structures to identify homologous sequences in many members of the genera pegivirus, hepacivirus and pestivirus. We used structural alignment and mutational analyses to establish that these sequences indeed represent Xrn1-resistant RNA and that they employ the general features of the flaviviral xrRNAs, consisting of a double pseudoknot formed by five base-paired regions stitched together by a crucial triple base interaction. Furthermore, we demonstrate that the pestivirus Bungowannah virus produces subgenomic RNA in vivo. Altogether, these results indicate that viruses make use of a universal Xrn1-resistant RNA throughout the Flaviviridae family.
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Affiliation(s)
- Ivar W Dilweg
- Leiden Institute of Chemistry, Leiden University, RA, Leiden, The Netherlands
| | - Anya Savina
- Leiden Institute of Chemistry, Leiden University, RA, Leiden, The Netherlands
| | - Susanne Köthe
- Friedrich-Loeffler-Institut, Institute of Diagnostic Virology, Greifswald, Germany
| | - Alexander P Gultyaev
- Leiden Institute of Advanced Computer Science, Leiden University, RA, Leiden, The Netherlands.,Department of Viroscience, Erasmus Medical Center, CA, Rotterdam, The Netherlands
| | - Peter J Bredenbeek
- Department of Medical Microbiology, Leiden University Medical Center, RC, Leiden, The Netherlands
| | - René C L Olsthoorn
- Leiden Institute of Chemistry, Leiden University, RA, Leiden, The Netherlands
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29
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Ramos-Lorente S, Romero-López C, Berzal-Herranz A. Information Encoded by the Flavivirus Genomes beyond the Nucleotide Sequence. Int J Mol Sci 2021; 22:3738. [PMID: 33916729 PMCID: PMC8038387 DOI: 10.3390/ijms22073738] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 03/30/2021] [Accepted: 03/31/2021] [Indexed: 02/05/2023] Open
Abstract
The genus Flavivirus comprises numerous, small, single positive-stranded RNA viruses, many of which are important human pathogens. To store all the information required for their successful propagation, flaviviruses use discrete structural genomic RNA elements to code for functional information by the establishment of dynamic networks of long-range RNA-RNA interactions that promote specific folding. These structural elements behave as true cis-acting, non-coding RNAs (ncRNAs) and have essential regulatory roles in the viral cycle. These include the control of the formation of subgenomic RNAs, known as sfRNAs, via the prevention of the complete degradation of the RNA genome. These sfRNAs are important in ensuring viral fitness. This work summarizes our current knowledge of the functions performed by the genome conformations and the role of RNA-RNA interactions in these functions. It also reviews the role of RNA structure in the production of sfRNAs across the genus Flavivirus, and their existence in related viruses.
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Affiliation(s)
| | - Cristina Romero-López
- Instituto de Parasitología y Biomedicina López-Neyra (IPBLN-CSIC), Av. Conocimiento 17, Armilla, 18016 Granada, Spain;
| | - Alfredo Berzal-Herranz
- Instituto de Parasitología y Biomedicina López-Neyra (IPBLN-CSIC), Av. Conocimiento 17, Armilla, 18016 Granada, Spain;
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30
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Harima H, Orba Y, Torii S, Qiu Y, Kajihara M, Eto Y, Matsuta N, Hang'ombe BM, Eshita Y, Uemura K, Matsuno K, Sasaki M, Yoshii K, Nakao R, Hall WW, Takada A, Abe T, Wolfinger MT, Simuunza M, Sawa H. An African tick flavivirus forming an independent clade exhibits unique exoribonuclease-resistant RNA structures in the genomic 3'-untranslated region. Sci Rep 2021; 11:4883. [PMID: 33649491 PMCID: PMC7921595 DOI: 10.1038/s41598-021-84365-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 02/15/2021] [Indexed: 12/16/2022] Open
Abstract
Tick-borne flaviviruses (TBFVs) infect mammalian hosts through tick bites and can cause various serious illnesses, such as encephalitis and hemorrhagic fevers, both in humans and animals. Despite their importance to public health, there is limited epidemiological information on TBFV infection in Africa. Herein, we report that a novel flavivirus, Mpulungu flavivirus (MPFV), was discovered in a Rhipicephalus muhsamae tick in Zambia. MPFV was found to be genetically related to Ngoye virus detected in ticks in Senegal, and these viruses formed a unique lineage in the genus Flavivirus. Analyses of dinucleotide contents of flaviviruses indicated that MPFV was similar to those of other TBFVs with a typical vertebrate genome signature, suggesting that MPFV may infect vertebrate hosts. Bioinformatic analyses of the secondary structures in the 3′-untranslated regions (UTRs) revealed that MPFV exhibited unique exoribonuclease-resistant RNA (xrRNA) structures. Utilizing biochemical approaches, we clarified that two xrRNA structures of MPFV in the 3′-UTR could prevent exoribonuclease activity. In summary, our findings provide new information regarding the geographical distribution of TBFV and xrRNA structures in the 3′-UTR of flaviviruses.
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Affiliation(s)
- Hayato Harima
- Hokudai Center for Zoonosis Control in Zambia, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Yasuko Orba
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan.,International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Shiho Torii
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Yongjin Qiu
- Hokudai Center for Zoonosis Control in Zambia, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Masahiro Kajihara
- Division of Global Epidemiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Yoshiki Eto
- Division of Global Epidemiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Naoya Matsuta
- Department of Electrical and Information Engineering, Graduate School of Science and Technology, Niigata University, Niigata, Japan
| | - Bernard M Hang'ombe
- Department of Para-Clinical Studies, School of Veterinary Medicine, The University of Zambia, Lusaka, Zambia.,Africa Center of Excellence for Infectious Diseases of Humans and Animals, The University of Zambia, Lusaka, Zambia
| | - Yuki Eshita
- Hokudai Center for Zoonosis Control in Zambia, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Kentaro Uemura
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan.,Drug Discovery and Disease Research Laboratory, Shionogi & Co., Ltd., Osaka, Japan
| | - Keita Matsuno
- International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan.,Unit of Risk Analysis and Management, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Michihito Sasaki
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Kentaro Yoshii
- Laboratory of Public Health, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan.,National Research Center for the Control and Prevention of Infectious Diseases (CCPID), Nagasaki University, Nagasaki, Japan
| | - Ryo Nakao
- Laboratory of Parasitology, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - William W Hall
- International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan.,National Virus Reference Laboratory, School of Medicine, University College Dublin, Dublin, Ireland.,Centre for Research in Infectious Diseases, School of Medicine, University College Dublin, Dublin, Ireland.,Global Virus Network, Baltimore, MD, USA
| | - Ayato Takada
- International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan.,Division of Global Epidemiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan.,Africa Center of Excellence for Infectious Diseases of Humans and Animals, The University of Zambia, Lusaka, Zambia.,Department of Disease Control, School of Veterinary Medicine, The University of Zambia, Lusaka, Zambia
| | - Takashi Abe
- Department of Electrical and Information Engineering, Graduate School of Science and Technology, Niigata University, Niigata, Japan
| | - Michael T Wolfinger
- Department of Theoretical Chemistry, University of Vienna, Vienna, Austria.,Research Group Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria
| | - Martin Simuunza
- Africa Center of Excellence for Infectious Diseases of Humans and Animals, The University of Zambia, Lusaka, Zambia.,Department of Disease Control, School of Veterinary Medicine, The University of Zambia, Lusaka, Zambia
| | - Hirofumi Sawa
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan. .,International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan. .,Africa Center of Excellence for Infectious Diseases of Humans and Animals, The University of Zambia, Lusaka, Zambia. .,Global Virus Network, Baltimore, MD, USA. .,Department of Disease Control, School of Veterinary Medicine, The University of Zambia, Lusaka, Zambia.
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31
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Becchi M, Chiarantoni P, Suma A, Micheletti C. RNA Pore Translocation with Static and Periodic Forces: Effect of Secondary and Tertiary Elements on Process Activation and Duration. J Phys Chem B 2021; 125:1098-1106. [PMID: 33497228 PMCID: PMC7875513 DOI: 10.1021/acs.jpcb.0c09966] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 01/19/2021] [Indexed: 11/28/2022]
Abstract
We use MD simulations to study the pore translocation properties of a pseudoknotted viral RNA. We consider the 71-nucleotide-long xrRNA from the Zika virus and establish how it responds when driven through a narrow pore by static or periodic forces applied to either of the two termini. Unlike the case of fluctuating homopolymers, the onset of translocation is significantly delayed with respect to the application of static driving forces. Because of the peculiar xrRNA architecture, activation times can differ by orders of magnitude at the two ends. Instead, translocation duration is much smaller than activation times and occurs on time scales comparable at the two ends. Periodic forces amplify significantly the differences at the two ends, for both activation times and translocation duration. Finally, we use a waiting-times analysis to examine the systematic slowing downs in xrRNA translocations and associate them to the hindrance of specific secondary and tertiary elements of xrRNA. The findings provide a useful reference to interpret and design future theoretical and experimental studies of RNA translocation.
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Affiliation(s)
- Matteo Becchi
- Physics
Area, Scuola Internazionale Superiore di
Studi Avanzati (SISSA), Via Bonomea 265, 34136 Trieste, Italy
| | - Pietro Chiarantoni
- Physics
Area, Scuola Internazionale Superiore di
Studi Avanzati (SISSA), Via Bonomea 265, 34136 Trieste, Italy
| | - Antonio Suma
- Dipartimento
di Fisica, Università di Bari and
Sezione INFN di Bari, via Amendola 173, 70126 Bari, Italy
| | - Cristian Micheletti
- Physics
Area, Scuola Internazionale Superiore di
Studi Avanzati (SISSA), Via Bonomea 265, 34136 Trieste, Italy
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32
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Jones RA, Steckelberg AL, Vicens Q, Szucs MJ, Akiyama BM, Kieft JS. Different tertiary interactions create the same important 3D features in a distinct flavivirus xrRNA. RNA (NEW YORK, N.Y.) 2021; 27:54-65. [PMID: 33004436 PMCID: PMC7749634 DOI: 10.1261/rna.077065.120] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 09/27/2020] [Indexed: 05/12/2023]
Abstract
During infection by a flavivirus (FV), cells accumulate noncoding subgenomic flavivirus RNAs (sfRNAs) that interfere with several antiviral pathways. These sfRNAs are formed by structured RNA elements in the 3' untranslated region (UTR) of the viral genomic RNA, which block the progression of host cell exoribonucleases that have targeted the viral RNA. Previous work on these exoribonuclease-resistant RNAs (xrRNAs) from mosquito-borne FVs revealed a specific three-dimensional fold with a unique topology in which a ring-like structure protectively encircles the 5' end of the xrRNA. Conserved nucleotides make specific tertiary interactions that support this fold. Examination of more divergent FVs reveals differences in their 3' UTR sequences, raising the question of whether they contain xrRNAs and if so, how they fold. To answer this, we demonstrated the presence of an authentic xrRNA in the 3' UTR of the Tamana bat virus (TABV) and solved its structure by X-ray crystallography. The structure reveals conserved features from previously characterized xrRNAs, but in the TABV version these features are created through a novel set of tertiary interactions not previously seen in xrRNAs. This includes two important A-C interactions, four distinct backbone kinks, several ordered Mg2+ ions, and a C+-G-C base triple. The discovery that the same overall architecture can be achieved by very different sequences and interactions in distantly related flaviviruses provides insight into the diversity of this type of RNA and will inform searches for undiscovered xrRNAs in viruses and beyond.
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MESH Headings
- 3' Untranslated Regions
- Animals
- Base Pairing
- Base Sequence
- Cations, Divalent
- Crystallography, X-Ray
- Encephalitis Virus, Murray Valley/genetics
- Encephalitis Virus, Murray Valley/metabolism
- Encephalitis Virus, Murray Valley/ultrastructure
- Exoribonucleases/chemistry
- Exoribonucleases/metabolism
- Flaviviridae/genetics
- Flaviviridae/metabolism
- Flaviviridae/ultrastructure
- Host-Pathogen Interactions/genetics
- Magnesium/chemistry
- Magnesium/metabolism
- RNA Folding
- RNA, Untranslated/chemistry
- RNA, Untranslated/genetics
- RNA, Untranslated/metabolism
- RNA, Viral/chemistry
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Viruses, Unclassified/genetics
- Viruses, Unclassified/metabolism
- Viruses, Unclassified/ultrastructure
- Zika Virus/genetics
- Zika Virus/metabolism
- Zika Virus/ultrastructure
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Affiliation(s)
- Rachel A Jones
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, Colorado 80045, USA
| | - Anna-Lena Steckelberg
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, Colorado 80045, USA
| | - Quentin Vicens
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, Colorado 80045, USA
| | - Matthew J Szucs
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, Colorado 80045, USA
| | - Benjamin M Akiyama
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, Colorado 80045, USA
| | - Jeffrey S Kieft
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, Colorado 80045, USA
- RNA BioScience Initiative, University of Colorado Denver School of Medicine, Aurora, Colorado 80045, USA
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33
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Steckelberg AL, Vicens Q, Costantino DA, Nix JC, Kieft JS. The crystal structure of a Polerovirus exoribonuclease-resistant RNA shows how diverse sequences are integrated into a conserved fold. RNA (NEW YORK, N.Y.) 2020; 26:1767-1776. [PMID: 32848042 PMCID: PMC7668246 DOI: 10.1261/rna.076224.120] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 08/19/2020] [Indexed: 05/31/2023]
Abstract
Exoribonuclease-resistant RNAs (xrRNAs) are discrete elements that block the progression of 5' to 3' exoribonucleases using specifically folded RNA structures. A recently discovered class of xrRNA is widespread in several genera of plant-infecting viruses, within both noncoding and protein-coding subgenomic RNAs. The structure of one such xrRNA from a dianthovirus revealed three-dimensional details of the resistant fold but did not answer all questions regarding the conservation and diversity of this xrRNA class. Here, we present the crystal structure of a representative polerovirus xrRNA that contains sequence elements that diverge from the previously solved structure. This new structure rationalizes previously unexplained sequence conservation patterns and shows interactions not present in the first structure. Together, the structures of these xrRNAs from dianthovirus and polerovirus genera support the idea that these plant virus xrRNAs fold through a defined pathway that includes a programmed intermediate conformation. This work deepens our knowledge of the structure-function relationship of xrRNAs and shows how evolution can craft similar RNA folds from divergent sequences.
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Affiliation(s)
- Anna-Lena Steckelberg
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, Colorado 80045, USA
| | - Quentin Vicens
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, Colorado 80045, USA
| | - David A Costantino
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, Colorado 80045, USA
| | - Jay C Nix
- Molecular Biology Consortium, Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Jeffrey S Kieft
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, Colorado 80045, USA
- RNA BioScience Initiative, University of Colorado Denver School of Medicine, Aurora, Colorado 80045, USA
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34
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Steckelberg AL, Vicens Q, Costantino DA, Nix JC, Kieft JS. The crystal structure of a Polerovirus exoribonuclease-resistant RNA shows how diverse sequences are integrated into a conserved fold. RNA (NEW YORK, N.Y.) 2020; 26:1767-1776. [PMID: 32848042 DOI: 10.1101/2020.04.30.070631] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 08/19/2020] [Indexed: 05/26/2023]
Abstract
Exoribonuclease-resistant RNAs (xrRNAs) are discrete elements that block the progression of 5' to 3' exoribonucleases using specifically folded RNA structures. A recently discovered class of xrRNA is widespread in several genera of plant-infecting viruses, within both noncoding and protein-coding subgenomic RNAs. The structure of one such xrRNA from a dianthovirus revealed three-dimensional details of the resistant fold but did not answer all questions regarding the conservation and diversity of this xrRNA class. Here, we present the crystal structure of a representative polerovirus xrRNA that contains sequence elements that diverge from the previously solved structure. This new structure rationalizes previously unexplained sequence conservation patterns and shows interactions not present in the first structure. Together, the structures of these xrRNAs from dianthovirus and polerovirus genera support the idea that these plant virus xrRNAs fold through a defined pathway that includes a programmed intermediate conformation. This work deepens our knowledge of the structure-function relationship of xrRNAs and shows how evolution can craft similar RNA folds from divergent sequences.
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Affiliation(s)
- Anna-Lena Steckelberg
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, Colorado 80045, USA
| | - Quentin Vicens
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, Colorado 80045, USA
| | - David A Costantino
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, Colorado 80045, USA
| | - Jay C Nix
- Molecular Biology Consortium, Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Jeffrey S Kieft
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, Colorado 80045, USA
- RNA BioScience Initiative, University of Colorado Denver School of Medicine, Aurora, Colorado 80045, USA
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35
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Niu X, Liu Q, Xu Z, Chen Z, Xu L, Xu L, Li J, Fang X. Molecular mechanisms underlying the extreme mechanical anisotropy of the flaviviral exoribonuclease-resistant RNAs (xrRNAs). Nat Commun 2020; 11:5496. [PMID: 33127896 PMCID: PMC7603331 DOI: 10.1038/s41467-020-19260-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 10/07/2020] [Indexed: 02/06/2023] Open
Abstract
Mechanical anisotropy is an essential property for many biomolecules to assume their structures, functions and applications, however, the mechanisms for their direction-dependent mechanical responses remain elusive. Herein, by using a single-molecule nanopore sensing technique, we explore the mechanisms of directional mechanical stability of the xrRNA1 RNA from ZIKA virus (ZIKV), which forms a complex ring-like architecture. We reveal extreme mechanical anisotropy in ZIKV xrRNA1 which highly depends on Mg2+ and the key tertiary interactions. The absence of Mg2+ and disruption of the key tertiary interactions strongly affect the structural integrity and attenuate mechanical anisotropy. The significance of ring structures in RNA mechanical anisotropy is further supported by steered molecular dynamics simulations in combination with force distribution analysis. We anticipate the ring structures can be used as key elements to build RNA-based nanostructures with controllable mechanical anisotropy for biomaterial and biomedical applications.
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Affiliation(s)
- Xiaolin Niu
- Beijing Advanced Innovation Center for Structfural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Qiuhan Liu
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Zhonghe Xu
- Beijing Advanced Innovation Center for Structfural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Zhifeng Chen
- Beijing Advanced Innovation Center for Structfural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Linghui Xu
- Beijing Advanced Innovation Center for Structfural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Lilei Xu
- Beijing Advanced Innovation Center for Structfural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Jinghong Li
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing, 100084, China.
| | - Xianyang Fang
- Beijing Advanced Innovation Center for Structfural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
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36
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Berrio A, Gartner V, Wray GA. Positive selection within the genomes of SARS-CoV-2 and other Coronaviruses independent of impact on protein function. PeerJ 2020; 8:e10234. [PMID: 33088633 PMCID: PMC7571416 DOI: 10.7717/peerj.10234] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 10/04/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND The emergence of a novel coronavirus (SARS-CoV-2) associated with severe acute respiratory disease (COVID-19) has prompted efforts to understand the genetic basis for its unique characteristics and its jump from non-primate hosts to humans. Tests for positive selection can identify apparently nonrandom patterns of mutation accumulation within genomes, highlighting regions where molecular function may have changed during the origin of a species. Several recent studies of the SARS-CoV-2 genome have identified signals of conservation and positive selection within the gene encoding Spike protein based on the ratio of synonymous to nonsynonymous substitution. Such tests cannot, however, detect changes in the function of RNA molecules. METHODS Here we apply a test for branch-specific oversubstitution of mutations within narrow windows of the genome without reference to the genetic code. RESULTS We recapitulate the finding that the gene encoding Spike protein has been a target of both purifying and positive selection. In addition, we find other likely targets of positive selection within the genome of SARS-CoV-2, specifically within the genes encoding Nsp4 and Nsp16. Homology-directed modeling indicates no change in either Nsp4 or Nsp16 protein structure relative to the most recent common ancestor. These SARS-CoV-2-specific mutations may affect molecular processes mediated by the positive or negative RNA molecules, including transcription, translation, RNA stability, and evasion of the host innate immune system. Our results highlight the importance of considering mutations in viral genomes not only from the perspective of their impact on protein structure, but also how they may impact other molecular processes critical to the viral life cycle.
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Affiliation(s)
| | - Valerie Gartner
- Department of Biology, Duke University, Durham, NC, USA
- University Program in Genetics and Genomics, Duke University, Durham, NC, USA
| | - Gregory A. Wray
- Department of Biology, Duke University, Durham, NC, USA
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
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37
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Szucs MJ, Nichols PJ, Jones RA, Vicens Q, Kieft JS. A New Subclass of Exoribonuclease-Resistant RNA Found in Multiple Genera of Flaviviridae. mBio 2020; 11:mBio.02352-20. [PMID: 32994331 DOI: 10.1101/2020.06.26.172668] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023] Open
Abstract
Viruses have developed innovative strategies to exploit the cellular machinery and overcome the antiviral defenses of the host, often using specifically structured RNA elements. Examples are found in the Flavivirus genus (in the family Flaviviridae), where during flaviviral infection, pathogenic subgenomic flaviviral RNAs (sfRNAs) accumulate in the cell. These sfRNAs are formed when a host cell 5' to 3' exoribonuclease degrades the viral genomic RNA but is blocked by an exoribonuclease-resistant RNA structure (xrRNA) located in the viral genome's 3' untranslated region (UTR). Although known to exist in several Flaviviridae genera, the full distribution and diversity of xrRNAs in this family were unknown. Using the recently solved high-resolution structure of an xrRNA from the divergent flavivirus Tamana bat virus (TABV) as a reference, we used bioinformatic searches to identify xrRNAs in the remaining three genera of Flaviviridae: Pegivirus, Pestivirus, and Hepacivirus We biochemically and structurally characterized several examples, determining that they are genuine xrRNAs with a conserved fold. These new xrRNAs look superficially similar to the previously described xrRNAs but possess structural differences making them distinct from previous classes of xrRNAs. Overall, we have identified the presence of xrRNA in all four genera of Flaviviridae, but not in all species. Our findings thus require adjustments of previous xrRNA classification schemes and expand the previously known distribution of xrRNA in Flaviviridae.IMPORTANCE The members of the Flaviviridae comprise one of the largest families of positive-sense single-stranded RNA (+ssRNA) and are divided into the Flavivirus, Pestivirus, Pegivirus, and Hepacivirus genera. The genus Flavivirus contains many medically relevant viruses such as Zika virus, dengue virus, and Powassan virus. In these, a part of the RNA of the virus twists up into a distinct three-dimensional shape called an exoribonuclease-resistant RNA (xrRNA) that blocks the ability of the cell to "chew up" the viral RNA. Hence, part of the RNA of the virus remains intact, and this protected part is important for viral infection. These xrRNAs were known to occur in flaviviruses, but whether they existed in the other members of the family was not known. In this study, we identified a new subclass of xrRNA found not only in flaviviruses but also in the remaining three genera. The fact that these structured viral RNAs exist throughout the Flaviviridae family suggests they are important parts of the infection strategy of diverse pathogens, which could lead to new avenues of research.
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Affiliation(s)
- Matthew J Szucs
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, Colorado, USA
| | - Parker J Nichols
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, Colorado, USA
| | - Rachel A Jones
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, Colorado, USA
| | - Quentin Vicens
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, Colorado, USA
| | - Jeffrey S Kieft
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, Colorado, USA
- RNA BioScience Initiative, University of Colorado Denver School of Medicine, Aurora, Colorado, USA
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38
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Abstract
The members of the Flaviviridae comprise one of the largest families of positive-sense single-stranded RNA (+ssRNA) and are divided into the Flavivirus, Pestivirus, Pegivirus, and Hepacivirus genera. The genus Flavivirus contains many medically relevant viruses such as Zika virus, dengue virus, and Powassan virus. In these, a part of the RNA of the virus twists up into a distinct three-dimensional shape called an exoribonuclease-resistant RNA (xrRNA) that blocks the ability of the cell to “chew up” the viral RNA. Hence, part of the RNA of the virus remains intact, and this protected part is important for viral infection. These xrRNAs were known to occur in flaviviruses, but whether they existed in the other members of the family was not known. In this study, we identified a new subclass of xrRNA found not only in flaviviruses but also in the remaining three genera. The fact that these structured viral RNAs exist throughout the Flaviviridae family suggests they are important parts of the infection strategy of diverse pathogens, which could lead to new avenues of research. Viruses have developed innovative strategies to exploit the cellular machinery and overcome the antiviral defenses of the host, often using specifically structured RNA elements. Examples are found in the Flavivirus genus (in the family Flaviviridae), where during flaviviral infection, pathogenic subgenomic flaviviral RNAs (sfRNAs) accumulate in the cell. These sfRNAs are formed when a host cell 5′ to 3′ exoribonuclease degrades the viral genomic RNA but is blocked by an exoribonuclease-resistant RNA structure (xrRNA) located in the viral genome’s 3′ untranslated region (UTR). Although known to exist in several Flaviviridae genera, the full distribution and diversity of xrRNAs in this family were unknown. Using the recently solved high-resolution structure of an xrRNA from the divergent flavivirus Tamana bat virus (TABV) as a reference, we used bioinformatic searches to identify xrRNAs in the remaining three genera of Flaviviridae: Pegivirus, Pestivirus, and Hepacivirus. We biochemically and structurally characterized several examples, determining that they are genuine xrRNAs with a conserved fold. These new xrRNAs look superficially similar to the previously described xrRNAs but possess structural differences making them distinct from previous classes of xrRNAs. Overall, we have identified the presence of xrRNA in all four genera of Flaviviridae, but not in all species. Our findings thus require adjustments of previous xrRNA classification schemes and expand the previously known distribution of xrRNA in Flaviviridae.
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39
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Discoveries of Exoribonuclease-Resistant Structures of Insect-Specific Flaviviruses Isolated in Zambia. Viruses 2020; 12:v12091017. [PMID: 32933075 PMCID: PMC7551683 DOI: 10.3390/v12091017] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 09/08/2020] [Accepted: 09/08/2020] [Indexed: 12/13/2022] Open
Abstract
To monitor the arthropod-borne virus transmission in mosquitoes, we have attempted both to detect and isolate viruses from 3304 wild-caught female mosquitoes in the Livingstone (Southern Province) and Mongu (Western Province) regions in Zambia in 2017. A pan-flavivirus RT-PCR assay was performed to identify flavivirus genomes in total RNA extracted from mosquito lysates, followed by virus isolation and full genome sequence analysis using next-generation sequencing and rapid amplification of cDNA ends. We isolated a newly identified Barkedji virus (BJV Zambia) (10,899 nt) and a novel flavivirus, tentatively termed Barkedji-like virus (BJLV) (10,885 nt) from Culex spp. mosquitoes which shared 96% and 75% nucleotide identity with BJV which has been isolated in Israel, respectively. These viruses could replicate in C6/36 cells but not in mammalian and avian cell lines. In parallel, a comparative genomics screening was conducted to study evolutionary traits of the 5'- and 3'-untranslated regions (UTRs) of isolated viruses. Bioinformatic analyses of the secondary structures in the UTRs of both viruses revealed that the 5'-UTRs exhibit canonical stem-loop structures, while the 3'-UTRs contain structural homologs to exoribonuclease-resistant RNAs (xrRNAs), SL-III, dumbbell, and terminal stem-loop (3'SL) structures. The function of predicted xrRNA structures to stop RNA degradation by Xrn1 exoribonuclease was further proved by the in vitro Xrn1 resistance assay.
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40
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Liu Y, Zhang Y, Wang M, Cheng A, Yang Q, Wu Y, Jia R, Liu M, Zhu D, Chen S, Zhang S, Zhao X, Huang J, Mao S, Ou X, Gao Q, Wang Y, Xu Z, Chen Z, Zhu L, Luo Q, Liu Y, Yu Y, Zhang L, Tian B, Pan L, Chen X. Structures and Functions of the 3' Untranslated Regions of Positive-Sense Single-Stranded RNA Viruses Infecting Humans and Animals. Front Cell Infect Microbiol 2020; 10:453. [PMID: 32974223 PMCID: PMC7481400 DOI: 10.3389/fcimb.2020.00453] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 07/23/2020] [Indexed: 12/20/2022] Open
Abstract
The 3′ untranslated region (3′ UTR) of positive-sense single-stranded RNA [ssRNA(+)] viruses is highly structured. Multiple elements in the region interact with other nucleotides and proteins of viral and cellular origin to regulate various aspects of the virus life cycle such as replication, translation, and the host-cell response. This review attempts to summarize the primary and higher order structures identified in the 3′UTR of ssRNA(+) viruses and their functional roles.
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Affiliation(s)
- Yuanzhi Liu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yu Zhang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Mingshu Wang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Anchun Cheng
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Qiao Yang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Ying Wu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Renyong Jia
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Mafeng Liu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Dekang Zhu
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Shun Chen
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Shaqiu Zhang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - XinXin Zhao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Juan Huang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Sai Mao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xumin Ou
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Qun Gao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yin Wang
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Zhiwen Xu
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Zhengli Chen
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Ling Zhu
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Qihui Luo
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Yunya Liu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yanling Yu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Ling Zhang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Bin Tian
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Leichang Pan
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xiaoyue Chen
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
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41
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Ng CS, Kasumba DM, Fujita T, Luo H. Spatio-temporal characterization of the antiviral activity of the XRN1-DCP1/2 aggregation against cytoplasmic RNA viruses to prevent cell death. Cell Death Differ 2020; 27:2363-2382. [PMID: 32034313 PMCID: PMC7370233 DOI: 10.1038/s41418-020-0509-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 01/23/2020] [Accepted: 01/28/2020] [Indexed: 12/25/2022] Open
Abstract
Host nucleases are implicated in antiviral response through the processing of pathogen-derived nucleic acids. Among many host RNases, decapping enzymes DCP1 and 2, and 5'→3' exonuclease XRN1, which are components of the RNA decay machinery, have been extensively studied in prokaryotes, plants, and invertebrates but less so in mammalian systems. As a result, the implication of XRN1 and DCPs in viral replication, in particular, the spatio-temporal dynamics during RNA viral infections remains elusive. Here, we highlight that XRN1 and DCPs play a critical role in limiting several groups of RNA viral infections. This antiviral activity was not obvious in wild-type cells but clearly observed in type I interferon (IFN-I)-deficient cells. Mechanistically, infection with RNA viruses induced the enrichment of XRN1 and DCPs in viral replication complexes (vRCs), hence forming distinct cytoplasmic aggregates. These aggregates served as sites for direct interaction between XRN1, DCP1/2, and viral ribonucleoprotein that contains viral RNA (vRNA). Although these XRN1-DCP1/2-vRC-containing foci resemble antiviral stress granules (SGs) or P-body (PB), they did not colocalize with known SG markers and did not correlate with critical PB functions. Furthermore, the presence of 5' mono- and 5' triphosphate structures on vRNA was not required for the formation of XRN1-DCP1/2-vRC-containing foci. On the other hand, single-, double-stranded, and higher-ordered vRNA species play a role but are not deterministic for efficient formation of XRN1-DCP1/2 foci and consequent antiviral activity in a manner proportional to RNA length. These results highlight the mechanism behind the antiviral function of XRN1-DCP1/2 in RNA viral infections independent of IFN-I response, protein kinase R and PB function.
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Affiliation(s)
- Chen Seng Ng
- Centre for Heart Lung Innovation, St. Paul's Hospital, University of British Columbia, Vancouver, BC, Canada.
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.
| | - Dacquin M Kasumba
- Centre de Recherche du Centre Hospitalier de I'Université de Montréal, Université de Montréal, Montréal, QC, Canada
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Takashi Fujita
- Laboratory of Molecular Genetics, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
- Laboratory of Molecular and Cellular Immunology, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Honglin Luo
- Centre for Heart Lung Innovation, St. Paul's Hospital, University of British Columbia, Vancouver, BC, Canada.
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.
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42
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Suma A, Coronel L, Bussi G, Micheletti C. Directional translocation resistance of Zika xrRNA. Nat Commun 2020; 11:3749. [PMID: 32719310 PMCID: PMC7385498 DOI: 10.1038/s41467-020-17508-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 06/29/2020] [Indexed: 12/14/2022] Open
Abstract
xrRNAs from flaviviruses survive in host cells because of their exceptional dichotomic response to the unfolding action of different enzymes. They can be unwound, and hence copied, by replicases, and yet can resist degradation by exonucleases. How the same stretch of xrRNA can encode such diverse responses is an open question. Here, by using atomistic models and translocation simulations, we uncover an elaborate and directional mechanism for how stress propagates when the two xrRNA ends, [Formula: see text] and [Formula: see text], are driven through a pore. Pulling the [Formula: see text] end, as done by replicases, elicits a progressive unfolding; pulling the [Formula: see text] end, as done by exonucleases, triggers a counterintuitive molecular tightening. Thus, in what appears to be a remarkable instance of intra-molecular tensegrity, the very pulling of the [Formula: see text] end is what boosts resistance to translocation and consequently to degradation. The uncovered mechanistic principle might be co-opted to design molecular meta-materials.
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Affiliation(s)
- Antonio Suma
- Dipartimento di Fisica, Università di Bari and INFN Sezione di Bari, via Amendola 173, 70126, Bari, Italy
- Institute for Computational Molecular Science (ICMS), Temple University, 19122, Philadelphia, PA, Italy
| | - Lucia Coronel
- Physics Area, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265, 34136, Trieste, Italy
| | - Giovanni Bussi
- Physics Area, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265, 34136, Trieste, Italy
| | - Cristian Micheletti
- Physics Area, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265, 34136, Trieste, Italy.
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43
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Filomatori CV, Merwaiss F, Bardossy ES, Alvarez DE. Impact of alphavirus 3'UTR plasticity on mosquito transmission. Semin Cell Dev Biol 2020; 111:148-155. [PMID: 32665176 DOI: 10.1016/j.semcdb.2020.07.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 07/04/2020] [Accepted: 07/07/2020] [Indexed: 12/21/2022]
Abstract
Alphaviruses such as chikungunya and western equine encephalitis viruses are important human pathogens transmitted by mosquitoes that have recently caused large epidemic and epizootic outbreaks. The epidemic potential of alphaviruses is often related to enhanced mosquito transmission. Tissue barriers and antiviral responses impose bottlenecks to viral populations in mosquitoes. Substitutions in the envelope proteins and the presence of repeated sequence elements (RSEs) in the 3'UTR of epidemic viruses were proposed to be specifically associated to efficient replication in mosquito vectors. Here, we discuss the molecular mechanisms that originated RSEs, the evolutionary forces that shape the 3'UTR of alphaviruses, and the significance of RSEs for mosquito transmission. Finally, the presence of RSEs in the 3'UTR of viral genomes appears as evolutionary trait associated to mosquito adaptation and emerges as a common feature among viruses from the alphavirus and flavivirus genera.
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Affiliation(s)
- Claudia V Filomatori
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín-CONICET, Argentina
| | - Fernando Merwaiss
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín-CONICET, Argentina
| | - Eugenia S Bardossy
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín-CONICET, Argentina
| | - Diego E Alvarez
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín-CONICET, Argentina.
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44
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Huston NC, Wan H, de Cesaris Araujo Tavares R, Wilen C, Pyle AM. Comprehensive in-vivo secondary structure of the SARS-CoV-2 genome reveals novel regulatory motifs and mechanisms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.07.10.197079. [PMID: 32676598 PMCID: PMC7359520 DOI: 10.1101/2020.07.10.197079] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
SARS-CoV-2 is the positive-sense RNA virus that causes COVID-19, a disease that has triggered a major human health and economic crisis. The genome of SARS-CoV-2 is unique among viral RNAs in its vast potential to form stable RNA structures and yet, as much as 97% of its 30 kilobases have not been structurally explored in the context of a viral infection. Our limited knowledge of SARS-CoV-2 genomic architecture is a fundamental limitation to both our mechanistic understanding of coronavirus life cycle and the development of COVID-19 RNA-based therapeutics. Here, we apply a novel long amplicon strategy to determine for the first time the secondary structure of the SARS-CoV-2 RNA genome probed in infected cells. In addition to the conserved structural motifs at the viral termini, we report new structural features like a conformationally flexible programmed ribosomal frameshifting pseudoknot, and a host of novel RNA structures, each of which highlights the importance of studying viral structures in their native genomic context. Our in-depth structural analysis reveals extensive networks of well-folded RNA structures throughout Orf1ab and reveals new aspects of SARS-CoV-2 genome architecture that distinguish it from other single-stranded, positive-sense RNA viruses. Evolutionary analysis of RNA structures in SARS-CoV-2 shows that several features of its genomic structure are conserved across beta coronaviruses and we pinpoint individual regions of well-folded RNA structure that merit downstream functional analysis. The native, complete secondary structure of SAR-CoV-2 presented here is a roadmap that will facilitate focused studies on mechanisms of replication, translation and packaging, and guide the identification of new RNA drug targets against COVID-19.
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Affiliation(s)
- Nicholas C. Huston
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Han Wan
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, USA
| | | | - Craig Wilen
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Anna Marie Pyle
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, USA
- Department of Chemistry, Yale University, New Haven, CT, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
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45
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VADR: validation and annotation of virus sequence submissions to GenBank. BMC Bioinformatics 2020; 21:211. [PMID: 32448124 PMCID: PMC7245624 DOI: 10.1186/s12859-020-3537-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 05/05/2020] [Indexed: 12/18/2022] Open
Abstract
Background GenBank contains over 3 million viral sequences. The National Center for Biotechnology Information (NCBI) previously made available a tool for validating and annotating influenza virus sequences that is used to check submissions to GenBank. Before this project, there was no analogous tool in use for non-influenza viral sequence submissions. Results We developed a system called VADR (Viral Annotation DefineR) that validates and annotates viral sequences in GenBank submissions. The annotation system is based on the analysis of the input nucleotide sequence using models built from curated RefSeqs. Hidden Markov models are used to classify sequences by determining the RefSeq they are most similar to, and feature annotation from the RefSeq is mapped based on a nucleotide alignment of the full sequence to a covariance model. Predicted proteins encoded by the sequence are validated with nucleotide-to-protein alignments using BLAST. The system identifies 43 types of “alerts” that (unlike the previous BLAST-based system) provide deterministic and rigorous feedback to researchers who submit sequences with unexpected characteristics. VADR has been integrated into GenBank’s submission processing pipeline allowing for viral submissions passing all tests to be accepted and annotated automatically, without the need for any human (GenBank indexer) intervention. Unlike the previous submission-checking system, VADR is freely available (https://github.com/nawrockie/vadr) for local installation and use. VADR has been used for Norovirus submissions since May 2018 and for Dengue virus submissions since January 2019. Since March 2020, VADR has also been used to check SARS-CoV-2 sequence submissions. Other viruses with high numbers of submissions will be added incrementally. Conclusion VADR improves the speed with which non-flu virus submissions to GenBank can be checked and improves the content and quality of the GenBank annotations. The availability and portability of the software allow researchers to run the GenBank checks prior to submitting their viral sequences, and thereby gain confidence that their submissions will be accepted immediately without the need to correspond with GenBank staff. Reciprocally, the adoption of VADR frees GenBank staff to spend more time on services other than checking routine viral sequence submissions.
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46
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Syenina A, Vijaykrishna D, Gan ES, Tan HC, Choy MM, Siriphanitchakorn T, Cheng C, Vasudevan SG, Ooi EE. Positive epistasis between viral polymerase and the 3' untranslated region of its genome reveals the epidemiologic fitness of dengue virus. Proc Natl Acad Sci U S A 2020; 117:11038-11047. [PMID: 32366663 PMCID: PMC7245076 DOI: 10.1073/pnas.1919287117] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Dengue virus (DENV) is a global health threat, causing repeated epidemics throughout the tropical world. While low herd immunity levels to any one of the four antigenic types of DENV predispose populations to outbreaks, viral genetic determinants that confer greater fitness for epidemic spread is an important but poorly understood contributor of dengue outbreaks. Here we report that positive epistasis between the coding and noncoding regions of the viral genome combined to elicit an epidemiologic fitness phenotype associated with the 1994 DENV2 outbreak in Puerto Rico. We found that five amino acid substitutions in the NS5 protein reduced viral genomic RNA (gRNA) replication rate to achieve a more favorable and relatively more abundant subgenomic flavivirus RNA (sfRNA), a byproduct of host 5'-3' exoribonuclease activity. The resulting increase in sfRNA relative to gRNA levels not only inhibited type I interferon (IFN) expression in infected cells through a previously described mechanism, but also enabled sfRNA to compete with gRNA for packaging into infectious particles. We suggest that delivery of sfRNA to new susceptible cells to inhibit type I IFN induction before gRNA replication and without the need for further de novo sfRNA synthesis could form a "preemptive strike" strategy against DENV.
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Affiliation(s)
- Ayesa Syenina
- Program in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, 169857 Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, 117549 Singapore
| | - Dhanasekaran Vijaykrishna
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Esther Shuyi Gan
- Program in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, 169857 Singapore
| | - Hwee Cheng Tan
- Program in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, 169857 Singapore
| | - Milly M Choy
- Program in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, 169857 Singapore
| | - Tanamas Siriphanitchakorn
- Program in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, 169857 Singapore
- Department of Biological Sciences, National University of Singapore, 117558 Singapore
| | - Colin Cheng
- Program in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, 169857 Singapore
| | - Subhash G Vasudevan
- Program in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, 169857 Singapore
| | - Eng Eong Ooi
- Program in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, 169857 Singapore;
- Saw Swee Hock School of Public Health, National University of Singapore, 117549 Singapore
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 119228 Singapore
- SingHealth Duke-National University of Singapore Global Health Institute, 169857 Singapore
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47
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Slonchak A, Hugo LE, Freney ME, Hall-Mendelin S, Amarilla AA, Torres FJ, Setoh YX, Peng NYG, Sng JDJ, Hall RA, van den Hurk AF, Devine GJ, Khromykh AA. Zika virus noncoding RNA suppresses apoptosis and is required for virus transmission by mosquitoes. Nat Commun 2020; 11:2205. [PMID: 32371874 PMCID: PMC7200751 DOI: 10.1038/s41467-020-16086-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 04/12/2020] [Indexed: 12/27/2022] Open
Abstract
Flaviviruses, including Zika virus (ZIKV), utilise host mRNA degradation machinery to produce subgenomic flaviviral RNA (sfRNA). In mammalian hosts, this noncoding RNA facilitates replication and pathogenesis of flaviviruses by inhibiting IFN-signalling, whereas the function of sfRNA in mosquitoes remains largely elusive. Herein, we conduct a series of in vitro and in vivo experiments to define the role of ZIKV sfRNA in infected Aedes aegypti employing viruses deficient in production of sfRNA. We show that sfRNA-deficient viruses have reduced ability to disseminate and reach saliva, thus implicating the role for sfRNA in productive infection and transmission. We also demonstrate that production of sfRNA alters the expression of mosquito genes related to cell death pathways, and prevents apoptosis in mosquito tissues. Inhibition of apoptosis restored replication and transmission of sfRNA-deficient mutants. Hence, we propose anti-apoptotic activity of sfRNA as the mechanism defining its role in ZIKV transmission. The function on subgenomic flaviviral RNA (sfRNA) in the mosquito vector is not well understood. Here, Slonchak et al. show that sfRNA affects virus-induced apoptosis and dissemination of ZIKV in Aedes aegypti mosquitoes, suggesting a role of sfRNA in Zika virus replication and transmission.
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Affiliation(s)
- Andrii Slonchak
- The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Leon E Hugo
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Morgan E Freney
- The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Sonja Hall-Mendelin
- Public Health Virology, Forensic and Scientific Services, Department of Health, Queensland Government, Brisbane, QLD, 4108, Australia
| | | | | | - Yin Xiang Setoh
- The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Nias Y G Peng
- The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Julian D J Sng
- The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Roy A Hall
- The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Andrew F van den Hurk
- Public Health Virology, Forensic and Scientific Services, Department of Health, Queensland Government, Brisbane, QLD, 4108, Australia
| | - Gregor J Devine
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
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48
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Diosa-Toro M, Prasanth KR, Bradrick SS, Garcia Blanco MA. Role of RNA-binding proteins during the late stages of Flavivirus replication cycle. Virol J 2020; 17:60. [PMID: 32334603 PMCID: PMC7183730 DOI: 10.1186/s12985-020-01329-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 04/11/2020] [Indexed: 12/21/2022] Open
Abstract
The genus Flavivirus encompasses several worldwide-distributed arthropod-borne viruses including, dengue virus, Japanese encephalitis virus, West Nile virus, yellow fever virus, Zika virus, and tick-borne encephalitis virus. Infection with these viruses manifest with symptoms ranging from febrile illness to life- threatening hypotensive shock and encephalitis. Therefore, flaviviruses pose a great risk to public health. Currently, preventive measures are falling short to control epidemics and there are no antivirals against any Flavivirus.Flaviviruses carry a single stranded positive-sense RNA genome that plays multiple roles in infected cells: it is translated into viral proteins, used as template for genome replication, it is the precursor of the subgenomic flaviviral RNA and it is assembled into new virions. Furthermore, viral RNA genomes are also packaged into extracellular vesicles, e.g. exosomes, which represent an alternate mode of virus dissemination.Because RNA molecules are at the center of Flavivirus replication cycle, viral and host RNA-binding proteins (RBPs) are critical determinants of infection. Numerous studies have revealed the function of RBPs during Flavivirus infection, particularly at the level of RNA translation and replication. These proteins, however, are also critical participants at the late stages of the replication cycle. Here we revise the function of host RBPs and the viral proteins capsid, NS2A and NS3, during the packaging of viral RNA and the assembly of new virus particles. Furthermore, we go through the evidence pointing towards the importance of host RBPs in mediating cellular RNA export with the idea that the biogenesis of exosomes harboring Flavivirus RNA would follow an analogous pathway.
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Affiliation(s)
- Mayra Diosa-Toro
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore.
| | - K Reddisiva Prasanth
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Shelton S Bradrick
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
- Global Health, Surveillance & Diagnostics Group, MRIGlobal, Kansas City, MO, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
| | - Mariano A Garcia Blanco
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore.
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA.
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA.
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49
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Lemmens I, Jansen S, de Rouck S, de Smet AS, Defever D, Neyts J, Dallmeier K, Tavernier J. The Development of RNA-KISS, a Mammalian Three-Hybrid Method to Detect RNA-Protein Interactions in Living Mammalian Cells. J Proteome Res 2020; 19:2529-2538. [PMID: 32216351 DOI: 10.1021/acs.jproteome.0c00068] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
RNA-protein interactions are essential for the regulation of mRNA and noncoding RNA functions and are implicated in many diseases, such as cancer and neurodegenerative disorders. A method that can detect RNA-protein interactions in living mammalian cells on a proteome-wide scale will be an important asset to identify and study these interactions. Here we show that a combination of the mammalian two-hybrid protein-protein detection method KISS (kinase substrate sensor) and the yeast RNA three-hybrid method, utilizing the specific interaction between the MS2 RNA and MS2 coat protein, is capable of detecting RNA-protein interactions in living mammalian cells. For conceptional proof we used the subgenomic flavivirus RNA (sfRNA) of the dengue virus (DENV), a highly structured noncoding RNA derived from the DENV genome known to target host cell proteins involved in innate immunity and antiviral defense, as bait. Using RNA-KISS, we could confirm the previously established interaction between the RNA-binding domain of DDX6 and the DENV sfRNA. Finally, we performed a human proteome-wide screen for DENV sfRNA-binding host factors, identifying several known flavivirus host factors such as DDX6 and PACT, further validating the RNA-KISS method as a robust and high-throughput cell-based RNA-protein interaction screening tool.
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Affiliation(s)
- Irma Lemmens
- Cytokine Receptor Laboratory, Faculty of Medicine and Health Sciences, Department of Biomolecular Medicine, Ghent University, B-9000 Ghent, Belgium.,Center for Medical Biotechnology, VIB, B-9000 Ghent, Belgium
| | - Sander Jansen
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, B-3000 Leuven, Belgium
| | - Steffi de Rouck
- Cytokine Receptor Laboratory, Faculty of Medicine and Health Sciences, Department of Biomolecular Medicine, Ghent University, B-9000 Ghent, Belgium.,Center for Medical Biotechnology, VIB, B-9000 Ghent, Belgium
| | - Anne-Sophie de Smet
- Cytokine Receptor Laboratory, Faculty of Medicine and Health Sciences, Department of Biomolecular Medicine, Ghent University, B-9000 Ghent, Belgium.,Center for Medical Biotechnology, VIB, B-9000 Ghent, Belgium
| | - Dieter Defever
- Cytokine Receptor Laboratory, Faculty of Medicine and Health Sciences, Department of Biomolecular Medicine, Ghent University, B-9000 Ghent, Belgium.,Center for Medical Biotechnology, VIB, B-9000 Ghent, Belgium
| | - Johan Neyts
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, B-3000 Leuven, Belgium
| | - Kai Dallmeier
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, B-3000 Leuven, Belgium
| | - Jan Tavernier
- Cytokine Receptor Laboratory, Faculty of Medicine and Health Sciences, Department of Biomolecular Medicine, Ghent University, B-9000 Ghent, Belgium.,Center for Medical Biotechnology, VIB, B-9000 Ghent, Belgium.,Orionis Biosciences, B-9052 Ghent, Belgium
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50
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Zeng M, Duan Y, Zhang W, Wang M, Jia R, Zhu D, Liu M, Zhao X, Yang Q, Wu Y, Zhang S, Liu Y, Zhang L, Yu Y, Chen S, Cheng A. Universal RNA Secondary Structure Insight Into Mosquito-Borne Flavivirus (MBFV) cis-Acting RNA Biology. Front Microbiol 2020; 11:473. [PMID: 32292394 PMCID: PMC7118588 DOI: 10.3389/fmicb.2020.00473] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 03/04/2020] [Indexed: 12/22/2022] Open
Abstract
Mosquito-borne flaviviruses (MBFVs) spread between vertebrate (mammals and birds) and invertebrate (mosquitoes) hosts. The cis-acting RNAs of MBFV share common evolutionary origins and contain frequent alterations, which control the balance of linear and circular genome conformations and allow effective replication. Importantly, multiple cis-acting RNAs interact with trans-acting regulatory RNA-binding proteins (RBPs) and affect the MBFV lifecycle process, including viral replicase binding, viral RNA translation-cyclisation-synthesis and nucleocapsid assembly. Considering that extensive structural probing analyses have been performed on MBFV cis-acting RNAs, herein the homologous RNA structures are online folded and consensus structures are constructed by sort. The specific traits and underlying biology of MBFV cis-acting RNA are illuminated accordingly in a review of RNA structure. These findings deepen our understanding of MBFV cis-acting RNA biology and serve as a resource for designing therapeutics in targeting protein-viral RNA interaction or viral RNA secondary structures.
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Affiliation(s)
- Miao Zeng
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yanping Duan
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Wei Zhang
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Mingshu Wang
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Institute of Preventive Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Renyong Jia
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Institute of Preventive Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Dekang Zhu
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Institute of Preventive Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Mafeng Liu
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Institute of Preventive Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Xinxin Zhao
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Institute of Preventive Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Qiao Yang
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Institute of Preventive Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Ying Wu
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Institute of Preventive Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Shaqiu Zhang
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Institute of Preventive Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Yunya Liu
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Ling Zhang
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yangling Yu
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Shun Chen
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Institute of Preventive Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Anchun Cheng
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Institute of Preventive Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
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