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Li R, Sun K, Tuplin A, Harris M. A structural and functional analysis of opal stop codon translational readthrough during Chikungunya virus replication. J Gen Virol 2023; 104:10.1099/jgv.0.001909. [PMID: 37862073 PMCID: PMC7615711 DOI: 10.1099/jgv.0.001909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023] Open
Abstract
Chikungunya virus (CHIKV) is an alphavirus, transmitted by Aedes species mosquitoes. The CHIKV single-stranded positive-sense RNA genome contains two open reading frames, coding for the non-structural (nsP) and structural proteins of the virus. The non-structural polyprotein precursor is proteolytically cleaved to generate nsP1-4. Intriguingly, most isolates of CHIKV (and other alphaviruses) possess an opal stop codon close to the 3' end of the nsP3 coding sequence and translational readthrough is necessary to produce full-length nsP3 and the nsP4 RNA polymerase. Here we investigate the role of this stop codon by replacing the arginine codon with each of the three stop codons in the context of both a subgenomic replicon and infectious CHIKV. Both opal and amber stop codons were tolerated in mammalian cells, but the ochre was not. In mosquito cells all three stop codons were tolerated. Using SHAPE analysis we interrogated the structure of a putative stem loop 3' of the stop codon and used mutagenesis to probe the importance of a short base-paired region at the base of this structure. Our data reveal that this stem is not required for stop codon translational readthrough, and we conclude that other factors must facilitate this process to permit productive CHIKV replication.
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Affiliation(s)
- Raymond Li
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, West Yorkshire, LS2 9JT, UK
| | | | - Andrew Tuplin
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, West Yorkshire, LS2 9JT, UK
| | - Mark Harris
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, West Yorkshire, LS2 9JT, UK
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2
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Poulis P, Peske F, Rodnina MV. The many faces of ribosome translocation along the mRNA: reading frame maintenance, ribosome frameshifting and translational bypassing. Biol Chem 2023; 404:755-767. [PMID: 37077160 DOI: 10.1515/hsz-2023-0142] [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: 02/21/2023] [Accepted: 03/22/2023] [Indexed: 04/21/2023]
Abstract
In each round of translation elongation, the ribosome translocates along the mRNA by precisely one codon. Translocation is promoted by elongation factor G (EF-G) in bacteria (eEF2 in eukaryotes) and entails a number of precisely-timed large-scale structural rearrangements. As a rule, the movements of the ribosome, tRNAs, mRNA and EF-G are orchestrated to maintain the exact codon-wise step size. However, signals in the mRNA, as well as environmental cues, can change the timing and dynamics of the key rearrangements leading to recoding of the mRNA into production of trans-frame peptides from the same mRNA. In this review, we discuss recent advances on the mechanics of translocation and reading frame maintenance. Furthermore, we describe the mechanisms and biological relevance of non-canonical translocation pathways, such as hungry and programmed frameshifting and translational bypassing, and their link to disease and infection.
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Affiliation(s)
- Panagiotis Poulis
- Department of Physical Biochemistry, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077 Göttingen, Germany
| | - Frank Peske
- Department of Physical Biochemistry, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077 Göttingen, Germany
| | - Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077 Göttingen, Germany
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3
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Nath A, Kumar S, Gurav YK, Gangopadhayya A, Ghuge O, Sreelakshmi PR, Jadhav A, Rajan LS, Yadav K, Shinde K, Shil P, Sudeep A, Lole KS. Genomic Characterization of Mosquito Isolates of Chikungunya Virus (Outbreak Strains 2022) Using Next-Generation Sequencing. Vector Borne Zoonotic Dis 2023. [PMID: 37184895 DOI: 10.1089/vbz.2022.0100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023] Open
Abstract
Background: A massive outbreak of dengue-like illness was reported from Pune district of Maharashtra, India during May-June 2022. Isolation and characterization of the etiological agent at genomic level for possible mutations that led to higher transmissibility is the topic of the study. Methods: Entomological investigations were carried out by ICMR-National Institute of Virology (Pune, India); Aedes aegypti mosquitoes were collected and processed for virus detection by molecular techniques. Positive mosquito pools were processed for virus isolation in cell culture. Sanger sequencing and whole-genome sequencing (WGS) using Oxford Nanopore Technology platform were used for genomic characterization. Results: Reverse transcriptase RT-PCR and qRT-PCR analysis detected chikungunya virus (CHIKV) in mosquito samples. Six CHIKV isolates were obtained. WGS revealed four nonsynonymous mutations in the structural polyprotein region, and five in the nonstructural polyprotein encoding region when compared with Yawat-2000 and Shivane-2016 strains. Sixty-four nucleotide changes in the nonstructural polyprotein region and 35 in the structural polyprotein region were detected. One isolate had an exclusive amino acid change, T1123I, in the nsP2 (protease) region. Conclusion: Abundant Ae. aegypti breeding and detection of CHIKV RNA in mosquitoes confirmed it as a chikungunya outbreak. Novel mutations detected in the epidemic strain warrants investigations to address their role in disease severity, transmission, and fitness.
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Affiliation(s)
- Amol Nath
- ICMR-National Institute of Virology, Pune, India
| | - Surendra Kumar
- Department of Medical Entomology, ICMR-National Institute of Virology, Pune, India
| | - Yogesh K Gurav
- Department of Dengue, ICMR-National Institute of Virology, Pune, India
| | | | - Onkar Ghuge
- ICMR-National Institute of Virology, Pune, India
| | | | - Abhijeet Jadhav
- Department of Medical Entomology, ICMR-National Institute of Virology, Pune, India
| | - Lekshmi S Rajan
- Department of Medical Entomology, ICMR-National Institute of Virology, Pune, India
| | | | - Krishna Shinde
- Department of Medical Entomology, ICMR-National Institute of Virology, Pune, India
| | - Pratip Shil
- Department of Bioinformatics, ICMR-National Institute of Virology, Pune, India
| | - Anakkathil Sudeep
- Department of Medical Entomology, ICMR-National Institute of Virology, Pune, India
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4
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Jürgenstein K, Tagel M, Ilves H, Leppik M, Kivisaar M, Remme J. Variance in translational fidelity of different bacterial species is affected by pseudouridines in the tRNA anticodon stem-loop. RNA Biol 2022; 19:1050-1058. [PMID: 36093925 PMCID: PMC9481147 DOI: 10.1080/15476286.2022.2121447] [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: 10/31/2022] Open
Abstract
Delicate variances in the translational machinery affect how efficiently different organisms approach protein synthesis. Determining the scale of this effect, however, requires knowledge on the differences of mistranslation levels. Here, we used a dual-luciferase reporter assay cloned into a broad host range plasmid to reveal the translational fidelity profiles of Pseudomonas putida, Pseudomonas aeruginosa and Escherichia coli. We observed that these profiles are surprisingly different, whereas species more prone to translational frameshifting are not necessarily more prone to stop codon readthrough. As tRNA modifications are among the factors that have been implicated to affect translation accuracy, we also show that translational fidelity is context-specifically influenced by pseudouridines in the anticodon stem-loop of tRNA, but the effect is not uniform between species.
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Affiliation(s)
- Karl Jürgenstein
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Mari Tagel
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Heili Ilves
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Margus Leppik
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Maia Kivisaar
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Jaanus Remme
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
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5
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Altered tRNA dynamics during translocation on slippery mRNA as determinant of spontaneous ribosome frameshifting. Nat Commun 2022; 13:4231. [PMID: 35869111 PMCID: PMC9307594 DOI: 10.1038/s41467-022-31852-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 07/06/2022] [Indexed: 11/08/2022] Open
Abstract
AbstractWhen reading consecutive mRNA codons, ribosomes move by exactly one triplet at a time to synthesize a correct protein. Some mRNA tracks, called slippery sequences, are prone to ribosomal frameshifting, because the same tRNA can read both 0- and –1-frame codon. Using smFRET we show that during EF-G-catalyzed translocation on slippery sequences a fraction of ribosomes spontaneously switches from rapid, accurate translation to a slow, frameshifting-prone translocation mode where the movements of peptidyl- and deacylated tRNA become uncoupled. While deacylated tRNA translocates rapidly, pept-tRNA continues to fluctuate between chimeric and posttranslocation states, which slows down the re-locking of the small ribosomal subunit head domain. After rapid release of deacylated tRNA, pept-tRNA gains unconstrained access to the –1-frame triplet, resulting in slippage followed by recruitment of the –1-frame aa-tRNA into the A site. Our data show how altered choreography of tRNA and ribosome movements reduces the translation fidelity of ribosomes translocating in a slow mode.
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Khan YA, Loughran G, Steckelberg AL, Brown K, Kiniry SJ, Stewart H, Baranov PV, Kieft JS, Firth AE, Atkins JF. Evaluating ribosomal frameshifting in CCR5 mRNA decoding. Nature 2022; 604:E16-E23. [PMID: 35444316 PMCID: PMC9248028 DOI: 10.1038/s41586-022-04627-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 06/04/2021] [Indexed: 12/21/2022]
Affiliation(s)
- Yousuf A Khan
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, UK
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA
| | - Gary Loughran
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Anna-Lena Steckelberg
- Department of Biochemistry and Molecular Genetics, Denver School of Medicine, Aurora, CO, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Katherine Brown
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, UK
| | - Stephen J Kiniry
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Hazel Stewart
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, UK
| | - Pavel V Baranov
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Jeffrey S Kieft
- Department of Biochemistry and Molecular Genetics, Denver School of Medicine, Aurora, CO, USA.
| | - Andrew E Firth
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, UK.
| | - John F Atkins
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland.
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA.
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7
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Carmody PJ, Zimmer MH, Kuntz CP, Harrington HR, Duckworth K, Penn W, Mukhopadhyay S, Miller T, Schlebach J. Coordination of -1 programmed ribosomal frameshifting by transcript and nascent chain features revealed by deep mutational scanning. Nucleic Acids Res 2021; 49:12943-12954. [PMID: 34871407 PMCID: PMC8682741 DOI: 10.1093/nar/gkab1172] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 10/22/2021] [Accepted: 11/10/2021] [Indexed: 12/17/2022] Open
Abstract
Programmed ribosomal frameshifting (PRF) is a translational recoding mechanism that enables the synthesis of multiple polypeptides from a single transcript. During translation of the alphavirus structural polyprotein, the efficiency of -1PRF is coordinated by a 'slippery' sequence in the transcript, an adjacent RNA stem-loop, and a conformational transition in the nascent polypeptide chain. To characterize each of these effectors, we measured the effects of 4530 mutations on -1PRF by deep mutational scanning. While most mutations within the slip-site and stem-loop reduce the efficiency of -1PRF, the effects of mutations upstream of the slip-site are far more variable. We identify several regions where modifications of the amino acid sequence of the nascent polypeptide impact the efficiency of -1PRF. Molecular dynamics simulations of polyprotein biogenesis suggest the effects of these mutations primarily arise from their impacts on the mechanical forces that are generated by the translocon-mediated cotranslational folding of the nascent polypeptide chain. Finally, we provide evidence suggesting that the coupling between cotranslational folding and -1PRF depends on the translation kinetics upstream of the slip-site. These findings demonstrate how -1PRF is coordinated by features within both the transcript and nascent chain.
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Affiliation(s)
- Patrick J Carmody
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - Matthew H Zimmer
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Charles P Kuntz
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | | | - Kate E Duckworth
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - Wesley D Penn
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | | | - Thomas F Miller
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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8
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Abstract
Alphaviruses are positive-strand RNA viruses, typically transmitted by mosquitoes between vertebrate hosts. They encode four essential replication proteins, the non-structural proteins nsP1-4, which possess the enzymatic activities of RNA capping, RNA helicase, site-specific protease, ADP-ribosyl removal and RNA polymerase. Alphaviruses have been key models in the study of membrane-associated RNA replication, which is a conserved feature among the positive-strand RNA viruses of animals and plants. We review new structural and functional information on the nsPs and their interaction with host proteins and membranes, as well as with viral RNA sequences. The dodecameric ring structure of nsP1 is likely to be one of the evolutionary innovations that facilitated the success of the progenitors of current positive-strand RNA viruses.
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Affiliation(s)
- Tero Ahola
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland
| | - Gerald McInerney
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Andres Merits
- Institute of Technology, University of Tartu, Tartu, Estonia.
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9
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Mahajan S, Choudhary S, Kumar P, Tomar S. Antiviral strategies targeting host factors and mechanisms obliging +ssRNA viral pathogens. Bioorg Med Chem 2021; 46:116356. [PMID: 34416512 PMCID: PMC8349405 DOI: 10.1016/j.bmc.2021.116356] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/30/2021] [Accepted: 07/31/2021] [Indexed: 12/21/2022]
Abstract
The ongoing COVID-19 pandemic, periodic recurrence of viral infections, and the emergence of challenging variants has created an urgent need of alternative therapeutic approaches to combat the spread of viral infections, failing to which may pose a greater risk to mankind in future. Resilience against antiviral drugs or fast evolutionary rate of viruses is stressing the scientific community to identify new therapeutic approaches for timely control of disease. Host metabolic pathways are exquisite reservoir of energy to viruses and contribute a diverse array of functions for successful replication and pathogenesis of virus. Targeting the host factors rather than viral enzymes to cease viral infection, has emerged as an alternative antiviral strategy. This approach offers advantage in terms of increased threshold to viral resistance and can provide broad-spectrum antiviral action against different viruses. The article here provides substantial review of literature illuminating the host factors and molecular mechanisms involved in innate/adaptive responses to viral infection, hijacking of signalling pathways by viruses and the intracellular metabolic pathways required for viral replication. Host-targeted drugs acting on the pathways usurped by viruses are also addressed in this study. Host-directed antiviral therapeutics might prove to be a rewarding approach in controlling the unprecedented spread of viral infection, however the probability of cellular side effects or cytotoxicity on host cell should not be ignored at the time of clinical investigations.
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Affiliation(s)
- Supreeti Mahajan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand 247667, India
| | - Shweta Choudhary
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand 247667, India
| | - Pravindra Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand 247667, India
| | - Shailly Tomar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand 247667, India.
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10
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LaPointe AT, Sokoloski KJ. De-Coding the Contributions of the Viral RNAs to Alphaviral Pathogenesis. Pathogens 2021; 10:pathogens10060771. [PMID: 34205345 PMCID: PMC8233893 DOI: 10.3390/pathogens10060771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 06/14/2021] [Accepted: 06/17/2021] [Indexed: 11/16/2022] Open
Abstract
Alphaviruses are positive-sense RNA arboviruses that are capable of causing severe disease in otherwise healthy individuals. There are many aspects of viral infection that determine pathogenesis and major efforts regarding the identification and characterization of virulence determinants have largely focused on the roles of the nonstructural and structural proteins. Nonetheless, the viral RNAs of the alphaviruses themselves play important roles in regard to virulence and pathogenesis. In particular, many sequences and secondary structures within the viral RNAs play an important part in the development of disease and may be considered important determinants of virulence. In this review article, we summarize the known RNA-based virulence traits and host:RNA interactions that influence alphaviral pathogenesis for each of the viral RNA species produced during infection. Overall, the viral RNAs produced during infection are important contributors to alphaviral pathogenesis and more research is needed to fully understand how each RNA species impacts the host response to infection as well as the development of disease.
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Affiliation(s)
- Autumn T. LaPointe
- Department of Microbiology and Immunology, School of Medicine, University of Louisville, Louisville, KT 40202, USA;
| | - Kevin J. Sokoloski
- Center for Predictive Medicine and Emerging Infectious Diseases, University of Louisville, Louisville, KT 40202, USA
- Correspondence:
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11
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Madden EA, Plante KS, Morrison CR, Kutchko KM, Sanders W, Long KM, Taft-Benz S, Cruz Cisneros MC, White AM, Sarkar S, Reynolds G, Vincent HA, Laederach A, Moorman NJ, Heise MT. Using SHAPE-MaP To Model RNA Secondary Structure and Identify 3'UTR Variation in Chikungunya Virus. J Virol 2020; 94:e00701-20. [PMID: 32999019 PMCID: PMC7925192 DOI: 10.1128/jvi.00701-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 09/17/2020] [Indexed: 01/04/2023] Open
Abstract
Chikungunya virus (CHIKV) is a mosquito-borne alphavirus associated with debilitating arthralgia in humans. RNA secondary structure in the viral genome plays an important role in the lifecycle of alphaviruses; however, the specific role of RNA structure in regulating CHIKV replication is poorly understood. Our previous studies found little conservation in RNA secondary structure between alphaviruses, and this structural divergence creates unique functional structures in specific alphavirus genomes. Therefore, to understand the impact of RNA structure on CHIKV biology, we used SHAPE-MaP to inform the modeling of RNA secondary structure throughout the genome of a CHIKV isolate from the 2013 Caribbean outbreak. We then analyzed regions of the genome with high levels of structural specificity to identify potentially functional RNA secondary structures and identified 23 regions within the CHIKV genome with higher than average structural stability, including four previously identified, functionally important CHIKV RNA structures. We also analyzed the RNA flexibility and secondary structures of multiple 3'UTR variants of CHIKV that are known to affect virus replication in mosquito cells. This analysis found several novel RNA structures within these 3'UTR variants. A duplication in the 3'UTR that enhances viral replication in mosquito cells led to an overall increase in the amount of unstructured RNA in the 3'UTR. This analysis demonstrates that the CHIKV genome contains a number of unique, specific RNA secondary structures and provides a strategy for testing these secondary structures for functional importance in CHIKV replication and pathogenesis.IMPORTANCE Chikungunya virus (CHIKV) is a mosquito-borne RNA virus that causes febrile illness and debilitating arthralgia in humans. CHIKV causes explosive outbreaks but there are no approved therapies to treat or prevent CHIKV infection. The CHIKV genome contains functional RNA secondary structures that are essential for proper virus replication. Since RNA secondary structures have only been defined for a small portion of the CHIKV genome, we used a chemical probing method to define the RNA secondary structures of CHIKV genomic RNA. We identified 23 highly specific structured regions of the genome, and confirmed the functional importance of one structure using mutagenesis. Furthermore, we defined the RNA secondary structure of three CHIKV 3'UTR variants that differ in their ability to replicate in mosquito cells. Our study highlights the complexity of the CHIKV genome and describes new systems for designing compensatory mutations to test the functional relevance of viral RNA secondary structures.
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Affiliation(s)
- Emily A Madden
- Department of Microbiology and Immunology, UNC-Chapel Hill, Chapel Hill, North Carolina, USA
| | - Kenneth S Plante
- Department of Genetics, UNC-Chapel Hill, Chapel Hill, North Carolina, USA
| | - Clayton R Morrison
- Department of Genetics, UNC-Chapel Hill, Chapel Hill, North Carolina, USA
| | - Katrina M Kutchko
- Biology Department, UNC-Chapel Hill, Chapel Hill, North Carolina, USA
- Curriculum in Bioinformatics and Computational Biology, UNC-Chapel Hill, Chapel Hill, North Carolina, USA
| | - Wes Sanders
- Department of Microbiology and Immunology, UNC-Chapel Hill, Chapel Hill, North Carolina, USA
| | - Kristin M Long
- Department of Genetics, UNC-Chapel Hill, Chapel Hill, North Carolina, USA
| | - Sharon Taft-Benz
- Department of Genetics, UNC-Chapel Hill, Chapel Hill, North Carolina, USA
| | | | | | - Sanjay Sarkar
- Department of Genetics, UNC-Chapel Hill, Chapel Hill, North Carolina, USA
| | - Grace Reynolds
- Department of Genetics, UNC-Chapel Hill, Chapel Hill, North Carolina, USA
| | - Heather A Vincent
- Department of Microbiology and Immunology, UNC-Chapel Hill, Chapel Hill, North Carolina, USA
| | - Alain Laederach
- Biology Department, UNC-Chapel Hill, Chapel Hill, North Carolina, USA
| | - Nathanial J Moorman
- Department of Microbiology and Immunology, UNC-Chapel Hill, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, UNC-Chapel Hill, Chapel Hill, North Carolina, USA
| | - Mark T Heise
- Department of Microbiology and Immunology, UNC-Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Genetics, UNC-Chapel Hill, Chapel Hill, North Carolina, USA
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12
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Abstract
DEAD box RNA helicases regulate diverse facets of RNA biology. Proteins of this family carry out essential cellular functions, and emerging literature is revealing additional roles in immune defense. Using RNA interference screening, we identified an evolutionarily conserved antiviral role for the helicase DDX56 against the alphavirus Sindbis virus (SINV), a mosquito-transmitted pathogen that infects humans. Depletion of DDX56 enhanced infection in Drosophila and human cells. Furthermore, we found that DDX56 also controls the emerging alphavirus chikungunya virus (CHIKV) through an interferon-independent mechanism. Using cross-linking immunoprecipitation (CLIP-Seq), we identified a predicted stem-loop on the viral genomic RNA bound by DDX56. Mechanistically, we found that DDX56 levels increase in the cytoplasm during CHIKV infection. In the cytoplasm, DDX56 impacts the earliest step in the viral replication cycle by binding and destabilizing the incoming viral genomic RNA, thereby attenuating infection. Thus, DDX56 is a conserved antiviral RNA binding protein that controls alphavirus infection.IMPORTANCE Arthropod-borne viruses are diverse pathogens and include the emerging virus chikungunya virus, which is associated with human disease. Through genetic screening, we found that the conserved RNA binding protein DDX56 is antiviral against chikungunya virus in insects and humans. DDX56 relocalizes from the nucleus to the cytoplasm, where it binds to a stem-loop in the viral genome and destabilizes incoming genomes. Thus, DDX56 is an evolutionarily conserved antiviral factor that controls alphavirus infection.
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Two Examples of RNA Aptamers with Antiviral Activity. Are Aptamers the Wished Antiviral Drugs? Pharmaceuticals (Basel) 2020; 13:ph13080157. [PMID: 32707768 PMCID: PMC7463695 DOI: 10.3390/ph13080157] [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: 06/09/2020] [Revised: 07/03/2020] [Accepted: 07/20/2020] [Indexed: 02/06/2023] Open
Abstract
The current Covid-19 pandemic has pointed out some major deficiencies of the even most advanced societies to fight against viral RNA infections. Once more, it has been demonstrated that there is a lack of efficient drugs to control RNA viruses. Aptamers are efficient ligands of a great variety of molecules including proteins and nucleic acids. Their specificity and mechanism of action make them very promising molecules for interfering with the function encoded in viral RNA genomes. RNA viruses store essential information in conserved structural genomic RNA elements that promote important steps for the consecution of the infective cycle. This work describes two well documented examples of RNA aptamers with antiviral activity against highly conserved structural domains of the HIV-1 and HCV RNA genome, respectively, performed in our laboratory. They are two good examples that illustrate the potential of the aptamers to fill the therapeutic gaps in the fight against RNA viruses.
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14
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Harrington HR, Zimmer MH, Chamness LM, Nash V, Penn WD, Miller TF, Mukhopadhyay S, Schlebach JP. Cotranslational folding stimulates programmed ribosomal frameshifting in the alphavirus structural polyprotein. J Biol Chem 2020; 295:6798-6808. [PMID: 32169904 DOI: 10.1074/jbc.ra120.012706] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 03/04/2020] [Indexed: 11/06/2022] Open
Abstract
Viruses maximize their genetic coding capacity through a variety of biochemical mechanisms, including programmed ribosomal frameshifting (PRF), which facilitates the production of multiple proteins from a single mRNA transcript. PRF is typically stimulated by structural elements within the mRNA that generate mechanical tension between the transcript and ribosome. However, in this work, we show that the forces generated by the cotranslational folding of the nascent polypeptide chain can also enhance PRF. Using an array of biochemical, cellular, and computational techniques, we first demonstrate that the Sindbis virus structural polyprotein forms two competing topological isomers during its biosynthesis at the ribosome-translocon complex. We then show that the formation of one of these topological isomers is linked to PRF. Coarse-grained molecular dynamics simulations reveal that the translocon-mediated membrane integration of a transmembrane domain upstream from the ribosomal slip site generates a force on the nascent polypeptide chain that scales with observed frameshifting. Together, our results indicate that cotranslational folding of this viral protein generates a tension that stimulates PRF. To our knowledge, this constitutes the first example in which the conformational state of the nascent polypeptide chain has been linked to PRF. These findings raise the possibility that, in addition to RNA-mediated translational recoding, a variety of cotranslational folding or binding events may also stimulate PRF.
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Affiliation(s)
| | - Matthew H Zimmer
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125
| | - Laura M Chamness
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405
| | - Veronica Nash
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405
| | - Wesley D Penn
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405
| | - Thomas F Miller
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125
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Werner SL, Banda BK, Burnsides CL, Stuber AJ. Zoonosis: Update on Existing and Emerging Vector-Borne Illnesses in the USA. CURRENT EMERGENCY AND HOSPITAL MEDICINE REPORTS 2019; 7:91-106. [PMID: 32288973 PMCID: PMC7102350 DOI: 10.1007/s40138-019-00189-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
PURPOSE OF REVIEW This review describes mosquito- and tick-borne diseases found in the Western Hemisphere. It focuses on emerging diseases and recent geographic shifts in the presence of disease vectors. RECENT FINDINGS Mosquito and tick vectors have become more widespread as environmental conditions have become more favorable. Zika recently has emerged as a concern for fetal anomalies. West Nile Virus has become widespread. Lyme disease and other tick-borne diseases are more prevalent in areas previously inhospitable to these ticks. SUMMARY Healthcare providers must consider the possibility of mosquito- and tick-borne diseases in broader geographic areas and council patients traveling to endemic areas on precautions against these diseases. Treatment for suspected cases of serious tick-borne illnesses should not be delayed pending culture results.
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Affiliation(s)
- Sandra Lee Werner
- MetroHealth/Cleveland Clinic/CWRU Emergency Medicine Residency Program, Department of Emergency Medicine, MetroHealth Medical Center, 2500 MetroHealth Drive, Cleveland, OH 44109 USA
| | - Bhanu Kirthi Banda
- MetroHealth/Cleveland Clinic/CWRU Emergency Medicine Residency Program, Department of Emergency Medicine, MetroHealth Medical Center, 2500 MetroHealth Drive, Cleveland, OH 44109 USA
| | - Christopher Lee Burnsides
- MetroHealth/Cleveland Clinic/CWRU Emergency Medicine Residency Program, Department of Emergency Medicine, MetroHealth Medical Center, 2500 MetroHealth Drive, Cleveland, OH 44109 USA
| | - Alexander James Stuber
- MetroHealth/Cleveland Clinic/CWRU Emergency Medicine Residency Program, Department of Emergency Medicine, MetroHealth Medical Center, 2500 MetroHealth Drive, Cleveland, OH 44109 USA
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Domains of the TF protein important in regulating its own palmitoylation. Virology 2019; 531:31-39. [PMID: 30852269 DOI: 10.1016/j.virol.2019.02.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 02/21/2019] [Accepted: 02/22/2019] [Indexed: 11/23/2022]
Abstract
Sindbis virus particles contain the viral proteins capsid, E1 and E2, and low levels of a small membrane protein called TF. TF is produced during a (-1) programmed ribosomal frameshifting event during the translation of the structural polyprotein. TF from Sindbis virus-infected cells is present in two palmitoylated states, basal and maximal; unpalmitoylated TF is not detectable. Mutagenesis studies demonstrated that without palmitoylation, TF is not incorporated into released virions, suggesting palmitoylation of TF is a regulated step in virus assembly. In this work, we identified Domains within the TF protein that regulate its palmitoylation state. Mutations and insertions in Domain III, a region proposed to be in the cytoplasmic loop of TF, increase levels of unpalmitoylated TF found during an infection but still unpalmitoylated TF was not incorporated into virions. Mutations in Domain IV, the TF unique region, are likely to impact the balance between basal and maximal palmitoylation.
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