1
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Gilliot PA, Gorochowski TE. Transfer learning for cross-context prediction of protein expression from 5'UTR sequence. Nucleic Acids Res 2024; 52:e58. [PMID: 38864396 PMCID: PMC11260469 DOI: 10.1093/nar/gkae491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 04/28/2024] [Accepted: 05/28/2024] [Indexed: 06/13/2024] Open
Abstract
Model-guided DNA sequence design can accelerate the reprogramming of living cells. It allows us to engineer more complex biological systems by removing the need to physically assemble and test each potential design. While mechanistic models of gene expression have seen some success in supporting this goal, data-centric, deep learning-based approaches often provide more accurate predictions. This accuracy, however, comes at a cost - a lack of generalization across genetic and experimental contexts that has limited their wider use outside the context in which they were trained. Here, we address this issue by demonstrating how a simple transfer learning procedure can effectively tune a pre-trained deep learning model to predict protein translation rate from 5' untranslated region (5'UTR) sequence for diverse contexts in Escherichia coli using a small number of new measurements. This allows for important model features learnt from expensive massively parallel reporter assays to be easily transferred to new settings. By releasing our trained deep learning model and complementary calibration procedure, this study acts as a starting point for continually refined model-based sequence design that builds on previous knowledge and future experimental efforts.
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Affiliation(s)
- Pierre-Aurélien Gilliot
- School of Biological Sciences, University of Bristol, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Thomas E Gorochowski
- School of Biological Sciences, University of Bristol, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
- BrisEngBio, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, UK
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2
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Bose R, Saleem I, Mustoe AM. Causes, functions, and therapeutic possibilities of RNA secondary structure ensembles and alternative states. Cell Chem Biol 2024; 31:17-35. [PMID: 38199037 PMCID: PMC10842484 DOI: 10.1016/j.chembiol.2023.12.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/21/2023] [Accepted: 12/12/2023] [Indexed: 01/12/2024]
Abstract
RNA secondary structure plays essential roles in encoding RNA regulatory fate and function. Most RNAs populate ensembles of alternatively paired states and are continually unfolded and refolded by cellular processes. Measuring these structural ensembles and their contributions to cellular function has traditionally posed major challenges, but new methods and conceptual frameworks are beginning to fill this void. In this review, we provide a mechanism- and function-centric compendium of the roles of RNA secondary structural ensembles and minority states in regulating the RNA life cycle, from transcription to degradation. We further explore how dysregulation of RNA structural ensembles contributes to human disease and discuss the potential of drugging alternative RNA states to therapeutically modulate RNA activity. The emerging paradigm of RNA structural ensembles as central to RNA function provides a foundation for a deeper understanding of RNA biology and new therapeutic possibilities.
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Affiliation(s)
- Ritwika Bose
- Therapeutic Innovation Center (THINC), Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - Irfana Saleem
- Therapeutic Innovation Center (THINC), Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - Anthony M Mustoe
- Therapeutic Innovation Center (THINC), Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
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3
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Zanin O, Eastham M, Winczura K, Ashe M, Martinez-Nunez RT, Hebenstreit D, Grzechnik P. Ceg1 depletion reveals mechanisms governing degradation of non-capped RNAs in Saccharomyces cerevisiae. Commun Biol 2023; 6:1112. [PMID: 37919390 PMCID: PMC10622555 DOI: 10.1038/s42003-023-05495-6] [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: 01/20/2023] [Accepted: 10/20/2023] [Indexed: 11/04/2023] Open
Abstract
Most functional eukaryotic mRNAs contain a 5' 7-methylguanosine (m7G) cap. Although capping is essential for many biological processes including mRNA processing, export and translation, the fate of uncapped transcripts has not been studied extensively. Here, we employed fast nuclear depletion of the capping enzymes in Saccharomyces cerevisiae to uncover the turnover of the transcripts that failed to be capped. We show that although the degradation of cap-deficient mRNA is dominant, the levels of hundreds of non-capped mRNAs increase upon depletion of the capping enzymes. Overall, the abundance of non-capped mRNAs is inversely correlated to the expression levels, altogether resembling the effects observed in cells lacking the cytoplasmic 5'-3' exonuclease Xrn1 and indicating differential degradation fates of non-capped mRNAs. The inactivation of the nuclear 5'-3' exonuclease Rat1 does not rescue the non-capped mRNA levels indicating that Rat1 is not involved in their degradation and consequently, the lack of the capping does not affect the distribution of RNA Polymerase II on the chromatin. Our data indicate that the cap presence is essential to initiate the Xrn1-dependent degradation of mRNAs underpinning the role of 5' cap in the Xrn1-dependent buffering of the cellular mRNA levels.
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Affiliation(s)
- Onofrio Zanin
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
- School of Immunology & Microbial Sciences, King's College London, Guy's Campus, London, SE1 9RT, UK
| | - Matthew Eastham
- Division of Molecular and Cellular Function, School of Biological Sciences, University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Kinga Winczura
- Division of Molecular and Cellular Function, School of Biological Sciences, University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Mark Ashe
- Division of Molecular and Cellular Function, School of Biological Sciences, University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Rocio T Martinez-Nunez
- School of Immunology & Microbial Sciences, King's College London, Guy's Campus, London, SE1 9RT, UK
| | | | - Pawel Grzechnik
- Division of Molecular and Cellular Function, School of Biological Sciences, University of Manchester, Oxford Road, Manchester, M13 9PT, UK.
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4
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Perroud PF, Guyon-Debast A, Casacuberta JM, Paul W, Pichon JP, Comeau D, Nogué F. Improved prime editing allows for routine predictable gene editing in Physcomitrium patens. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:6176-6187. [PMID: 37243510 PMCID: PMC10575697 DOI: 10.1093/jxb/erad189] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 05/25/2023] [Indexed: 05/29/2023]
Abstract
Efficient and precise gene editing is the gold standard of any reverse genetic study. The recently developed prime editing approach, a modified CRISPR/Cas9 [clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein] editing method, has reached the precision goal but its editing rate can be improved. We present an improved methodology that allows for routine prime editing in the model plant Physcomitrium patens, whilst exploring potential new prime editing improvements. Using a standardized protoplast transfection procedure, multiple prime editing guide RNA (pegRNA) structural and prime editor variants were evaluated targeting the APT reporter gene through direct plant selection. Together, enhancements of expression of the prime editor, modifications of the 3' extension of the pegRNA, and the addition of synonymous mutation in the reverse transcriptase template sequence of the pegRNA dramatically improve the editing rate without affecting the quality of the edits. Furthermore, we show that prime editing is amenable to edit a gene of interest through indirect selection, as demonstrated by the generation of a Ppdek10 mutant. Additionally, we determine that a plant retrotransposon reverse transcriptase enables prime editing. Finally, we show for the first time the possibility of performing prime editing with two independently coded peptides.
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Affiliation(s)
- Pierre-François Perroud
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
| | - Anouchka Guyon-Debast
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
| | - Josep M Casacuberta
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Bellaterra, 08193 Barcelona, Spain
| | - Wyatt Paul
- Limagrain Europe, Centre de Recherche de Chappes, 63720 Chappes, France
| | | | - David Comeau
- Limagrain Europe, Centre de Recherche de Chappes, 63720 Chappes, France
| | - Fabien Nogué
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
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5
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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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6
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Solodushko V, Fouty B. Terminal hairpins improve protein expression in IRES-initiated mRNA in the absence of a cap and polyadenylated tail. Gene Ther 2023; 30:620-627. [PMID: 36828937 PMCID: PMC9951143 DOI: 10.1038/s41434-023-00391-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 01/31/2023] [Accepted: 02/08/2023] [Indexed: 02/26/2023]
Abstract
Synthesizing mRNA in vitro is a standard and simple procedure. Adding the 5' cap and 3' polyadenylated (poly(A)) tail to make this mRNA functional for use as a vaccine or therapy increases the time and cost of production and usually decreases the yield, however. We designed mRNA that lacked a cap and poly(A) tail but included an internal ribosomal entry site (IRES) to initiate protein translation. To protect the 5' and 3' ends of mRNA from exonucleases, we added stable terminal hairpins. When compared against typical mRNA (i.e., mRNA that contained a cap and poly(A) tail but lacked hairpins), expression of the delivered reporter protein in HEK293 cells was similar. Using a triple instead of a single hairpin at each end increased protein expression even more. This method has the potential to simplify the production and reduce the cost of synthesizing exogenous mRNA for use as biologics or vaccines.
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Affiliation(s)
- Victor Solodushko
- Department of Pharmacology, University of South Alabama School of Medicine, Mobile, AL, 36688, USA.
- The Center for Lung Biology, University of South Alabama School of Medicine, Mobile, AL, 36688, USA.
| | - Brian Fouty
- Department of Pharmacology, University of South Alabama School of Medicine, Mobile, AL, 36688, USA.
- The Center for Lung Biology, University of South Alabama School of Medicine, Mobile, AL, 36688, USA.
- Department of Internal Medicine, University of South Alabama School of Medicine, Mobile, AL, 36688, USA.
- The Division of Pulmonary and Critical Care Medicine, University of South Alabama School of Medicine, Mobile, AL, 36688, USA.
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7
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Li Q, Ding Y, Zhang Y. Capture the in vivo intact RNA structurome by CAP-STRUCTURE-seq. Methods Enzymol 2023; 691:127-152. [PMID: 37914443 DOI: 10.1016/bs.mie.2023.05.008] [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: 11/03/2023]
Abstract
RNA decay serves as a crucial mechanism for maintaining cellular homeostasis and regulating gene expression. Large-scale analyses indicate that altered rates of decay contribute significantly to changes in mRNA levels, with up to half of these changes attributed to decay. The regulation of RNA decay is, at least in part, through structured RNA elements, especially in the non-coding regions of the mRNAs. The development of next-generation sequencing, and in vivo chemical probing techniques has allowed for unprecedented understanding of RNA folding in vivo and genome-wide. To explore the RNA structure elements that are responsible for RNA cleavage, we need to capture the RNA structure before cleavage. In this method, we introduce a new experimental procedure called CAP-STRUCTURE-seq, a modified STRUCTURE-Seq approach combining with the enrichment of in intact mRNAs by the use of terminator exonuclease treatment (5'-Phosphate-Dependent Exonuclease) that digests RNA containing 5-monophosphate ends. This approach is designed to investigate the RNA structure for these intact RNAs, providing a means to study the impact of RNA structure on RNA decay in greater detail. This method can provide insights into the function of RNA structure in RNA decay and help advance our understanding of biological processes.
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Affiliation(s)
- Qianqian Li
- Guangdong Provincial Key Laboratory of Applied Botany & Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, P.R. China; Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Yiliang Ding
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, United Kingdom.
| | - Yueying Zhang
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, United Kingdom.
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8
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Rainey SM, Geoghegan V, Lefteri DA, Ant TH, Martinez J, McNamara CJ, Kamel W, de Laurent ZR, Castello A, Sinkins SP. Differences in proteome perturbations caused by the Wolbachia strain wAu suggest multiple mechanisms of Wolbachia-mediated antiviral activity. Sci Rep 2023; 13:11737. [PMID: 37474590 PMCID: PMC10359319 DOI: 10.1038/s41598-023-38127-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 07/03/2023] [Indexed: 07/22/2023] Open
Abstract
Some strains of the inherited bacterium Wolbachia have been shown to be effective at reducing the transmission of dengue virus (DENV) and other RNA viruses by Aedes aegypti in both laboratory and field settings and are being deployed for DENV control. The degree of virus inhibition varies between Wolbachia strains. Density and tissue tropism can contribute to these differences but there are also indications that this is not the only factor involved: for example, strains wAu and wAlbA are maintained at similar intracellular densities but only wAu produces strong DENV inhibition. We previously reported perturbations in lipid transport dynamics, including sequestration of cholesterol in lipid droplets, with strains wMel/wMelPop in Ae. aegypti. To further investigate the cellular basis underlying these differences, proteomic analysis of midguts was carried out on Ae. aegypti lines carrying strains wAu and wAlbA: with the hypothesis that differences in perturbations may underline Wolbachia-mediated antiviral activity. Surprisingly, wAu-carrying midguts not only showed distinct proteome perturbations when compared to non-Wolbachia carrying and wAlbA-carrying midguts but also wMel-carrying midguts. There are changes in RNA processing pathways and upregulation of a specific set of RNA-binding proteins in the wAu-carrying line, including genes with known antiviral activity. Lipid transport and metabolism proteome changes also differ between strains, and we show that strain wAu does not produce the same cholesterol sequestration phenotype as wMel. Moreover, in contrast to wMel, wAu antiviral activity was not rescued by cyclodextrin treatment. Together these results suggest that wAu could show unique features in its inhibition of arboviruses compared to previously characterized Wolbachia strains.
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Affiliation(s)
| | - Vincent Geoghegan
- MRC-University of Glasgow-Centre for Virus Research, Glasgow, UK
- The University of York, York, UK
| | | | - Thomas H Ant
- MRC-University of Glasgow-Centre for Virus Research, Glasgow, UK
| | - Julien Martinez
- MRC-University of Glasgow-Centre for Virus Research, Glasgow, UK
| | | | - Wael Kamel
- MRC-University of Glasgow-Centre for Virus Research, Glasgow, UK
| | | | - Alfredo Castello
- MRC-University of Glasgow-Centre for Virus Research, Glasgow, UK
| | - Steven P Sinkins
- MRC-University of Glasgow-Centre for Virus Research, Glasgow, UK.
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9
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Alternative cleavage and polyadenylation generates downstream uncapped RNA isoforms with translation potential. Mol Cell 2022; 82:3840-3855.e8. [PMID: 36270248 PMCID: PMC9636002 DOI: 10.1016/j.molcel.2022.09.036] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 06/13/2022] [Accepted: 09/26/2022] [Indexed: 11/06/2022]
Abstract
The use of alternative promoters, splicing, and cleavage and polyadenylation (APA) generates mRNA isoforms that expand the diversity and complexity of the transcriptome. Here, we uncovered thousands of previously undescribed 5' uncapped and polyadenylated transcripts (5' UPTs). We show that these transcripts resist exonucleases due to a highly structured RNA and N6-methyladenosine modification at their 5' termini. 5' UPTs appear downstream of APA sites within their host genes and are induced upon APA activation. Strong enrichment in polysomal RNA fractions indicates 5' UPT translational potential. Indeed, APA promotes downstream translation initiation, non-canonical protein output, and consistent changes to peptide presentation at the cell surface. Lastly, we demonstrate the biological importance of 5' UPTs using Bcl2, a prominent anti-apoptotic gene whose entire coding sequence is a 5' UPT generated from 5' UTR-embedded APA sites. Thus, APA is not only accountable for terminating transcripts, but also for generating downstream uncapped RNAs with translation potential and biological impact.
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10
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Bonilla SL, Sherlock ME, MacFadden A, Kieft JS. A viral RNA hijacks host machinery using dynamic conformational changes of a tRNA-like structure. Science 2021; 374:955-960. [PMID: 34793227 PMCID: PMC9033304 DOI: 10.1126/science.abe8526] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Viruses require multifunctional structured RNAs to hijack their host’s biochemistry, but their mechanisms can be obscured by the difficulty of solving conformationally dynamic RNA structures. Using cryo–electron microscopy (cryo-EM), we visualized the structure of the mysterious viral transfer RNA (tRNA)–like structure (TLS) from the brome mosaic virus, which affects replication, translation, and genome encapsidation. Structures in isolation and those bound to tyrosyl-tRNA synthetase (TyrRS) show that this ~55-kilodalton purported tRNA mimic undergoes large conformational rearrangements to bind TyrRS in a form that differs substantially from that of tRNA. Our study reveals how viral RNAs can use a combination of static and dynamic RNA structures to bind host machinery through highly noncanonical interactions, and we highlight the utility of cryo-EM for visualizing small, conformationally dynamic structured RNAs.
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Affiliation(s)
- Steve L. Bonilla
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Madeline E. Sherlock
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Andrea MacFadden
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Jeffrey S. Kieft
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- RNA BioScience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO 10 80045, USA
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11
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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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12
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Barreiro K, Dwivedi OP, Valkonen S, Groop P, Tuomi T, Holthofer H, Rannikko A, Yliperttula M, Siljander P, Laitinen S, Serkkola E, af Hällström T, Forsblom C, Groop L, Puhka M. Urinary extracellular vesicles: Assessment of pre-analytical variables and development of a quality control with focus on transcriptomic biomarker research. J Extracell Vesicles 2021; 10:e12158. [PMID: 34651466 PMCID: PMC8517090 DOI: 10.1002/jev2.12158] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 09/06/2021] [Accepted: 09/24/2021] [Indexed: 12/13/2022] Open
Abstract
Urinary extracellular vesicles (uEV) are a topical source of non-invasive biomarkers for health and diseases of the urogenital system. However, several challenges have become evident in the standardization of uEV pipelines from collection of urine to biomarker analysis. Here, we studied the effect of pre-analytical variables and developed means of quality control for uEV isolates to be used in transcriptomic biomarker research. We included urine samples from healthy controls and individuals with type 1 or type 2 diabetes and normo-, micro- or macroalbuminuria and isolated uEV by ultracentrifugation. We studied the effect of storage temperature (-20°C vs. -80°C), time (up to 4 years) and storage format (urine or isolated uEV) on quality of uEV by nanoparticle tracking analysis, electron microscopy, Western blotting and qPCR. Urinary EV RNA was compared in terms of quantity, quality, and by mRNA or miRNA sequencing. To study the stability of miRNA levels in samples isolated by different methods, we created and tested a list of miRNAs commonly enriched in uEV isolates. uEV and their transcriptome were preserved in urine or as isolated uEV even after long-term storage at -80°C. However, storage at -20°C degraded particularly the GC-rich part of the transcriptome and EV protein markers. Transcriptome was preserved in RNA samples extracted with and without DNAse, but read distributions still showed some differences in e.g. intergenic and intronic reads. MiRNAs commonly enriched in uEV isolates were stable and concordant between different EV isolation methods. Analysis of never frozen uEV helped to identify surface characteristics of particles by EM. In addition to uEV, qPCR assays demonstrated that uEV isolates commonly contained polyoma viruses. Based on our results, we present recommendations how to store and handle uEV isolates for transcriptomics studies that may help to expedite standardization of the EV biomarker field.
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Affiliation(s)
- Karina Barreiro
- Institute for Molecular Medicine Finland FIMMUniversity of HelsinkiHelsinkiFinland
| | - Om Prakash Dwivedi
- Institute for Molecular Medicine Finland FIMMUniversity of HelsinkiHelsinkiFinland
| | - Sami Valkonen
- EV Group, Molecular and Integrative Biosciences Research ProgramFaculty of Biological and Environmental SciencesUniversity of HelsinkiHelsinkiFinland
- Research and DevelopmentFinnish Red Cross Blood ServiceHelsinkiFinland
- Drug Research ProgramDivision of Pharmaceutical BiosciencesFaculty of PharmacyUniversity of HelsinkiHelsinkiFinland
| | - Per‐Henrik Groop
- Folkhälsan Institute of GeneticsFolkhälsan Research CenterHelsinkiFinland
- Department of NephrologyUniversity of Helsinki and Helsinki University HospitalHelsinkiFinland
- Research Program for Clinical and Molecular MetabolismFaculty of MedicineUniversity of HelsinkiHelsinkiFinland
- Department of DiabetesCentral Clinical SchoolMonash UniversityMelbourneAustralia
| | - Tiinamaija Tuomi
- Institute for Molecular Medicine Finland FIMMUniversity of HelsinkiHelsinkiFinland
- Research Program for Clinical and Molecular MetabolismFaculty of MedicineUniversity of HelsinkiHelsinkiFinland
- Department of Clinical SciencesLund University Diabetes CenterMalmöSweden
- Skåne University HospitalLund UniversityMalmöSweden
- Abdominal Center, EndocrinologyUniversity of Helsinki and Helsinki University HospitalHelsinkiFinland
| | - Harry Holthofer
- Institute for Molecular Medicine Finland FIMMUniversity of HelsinkiHelsinkiFinland
- III Department of MedicineUniversity Medical Center Hamburg‐EppendorfHamburgGermany
| | - Antti Rannikko
- Department of UrologyUniversity of Helsinki and Helsinki University HospitalHelsinkiFinland
- Research Program in Systems OncologyFaculty of MedicineUniversity of HelsinkiHelsinkiFinland
| | - Marjo Yliperttula
- Drug Research ProgramDivision of Pharmaceutical BiosciencesFaculty of PharmacyUniversity of HelsinkiHelsinkiFinland
| | - Pia Siljander
- EV Group, Molecular and Integrative Biosciences Research ProgramFaculty of Biological and Environmental SciencesUniversity of HelsinkiHelsinkiFinland
- CURED, Drug Research ProgramDivision of Pharmaceutical BiosciencesFaculty of PharmacyUniversity of HelsinkiHelsinkiFinland
- EV‐coreFaculty of Biological and Environmental SciencesUniversity of HelsinkiHelsinkiFinland
| | - Saara Laitinen
- Research and DevelopmentFinnish Red Cross Blood ServiceHelsinkiFinland
| | | | | | - Carol Forsblom
- Institute for Molecular Medicine Finland FIMMUniversity of HelsinkiHelsinkiFinland
- Folkhälsan Institute of GeneticsFolkhälsan Research CenterHelsinkiFinland
- Department of NephrologyUniversity of Helsinki and Helsinki University HospitalHelsinkiFinland
- Research Program for Clinical and Molecular MetabolismFaculty of MedicineUniversity of HelsinkiHelsinkiFinland
| | - Leif Groop
- Institute for Molecular Medicine Finland FIMMUniversity of HelsinkiHelsinkiFinland
- Department of Clinical SciencesLund University Diabetes CenterMalmöSweden
- Skåne University HospitalLund UniversityMalmöSweden
| | - Maija Puhka
- Institute for Molecular Medicine Finland FIMMUniversity of HelsinkiHelsinkiFinland
- HiPrep and EV CoreInstitute for Molecular Medicine Finland FIMMUniversity of HelsinkiHelsinkiFinland
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13
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Miao S, Bhunia D, Devari S, Liang Y, Munyaradzi O, Rundell S, Bong D. Bifacial PNAs Destabilize MALAT1 by 3' A-Tail Displacement from the U-Rich Internal Loop. ACS Chem Biol 2021; 16:1600-1609. [PMID: 34382766 DOI: 10.1021/acschembio.1c00575] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
We report herein a new class of synthetic reagents for targeting the element for nuclear expression (ENE) in MALAT1, a long noncoding RNA upregulated in many cancers. The cis-acting ENE contains a U-rich internal loop (URIL) that forms an 11 base UAU-rich triplex stem with the truncated 3' oligo-A tail of MALAT1, protecting the terminus from exonuclease digestion and greatly extending transcript lifetime. Bifacial peptide nucleic acids (bPNAs) similarly bind URILs via base triple formation between two uracil bases and a synthetic base, melamine. We synthesized a set of low molecular weight bPNAs composed of α-linked peptide, isodipeptide, and diketopiperazine backbones and evaluated their ENE binding efficacy in vitro via oligo-A strand displacement and consequent exonuclease sensitivity. Degradation was greatly enhanced by bPNA treatment in the presence of exonucleases, with ENE half-life plunging to 6 min from >24 h. RNA digestion kinetics could clearly distinguish between bPNAs with similar URIL affinities, highlighting the utility of functional assays for evaluating synthetic RNA binders. In vitro activity was mirrored by a 50% knockdown of MALAT1 expression in pancreatic cancer (PANC-1) cells upon treatment with bPNAs, consistent with intracellular digestion triggered by a similar ENE A-tail displacement mechanism. Pulldown from PANC-1 total RNA with biotinylated bPNA enriched MALAT1 > 4000× , supportive of bPNA-URIL selectivity. Together, these experiments establish the feasibility of native transcript targeting by bPNA in both in vitro and intracellular contexts. Reagents such as bPNAs may be useful tools for the investigation of transcripts stabilized by cis-acting poly(A) binding RNA elements.
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Affiliation(s)
- Shiqin Miao
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Debmalya Bhunia
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Shekaraiah Devari
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Yufeng Liang
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Oliver Munyaradzi
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Sarah Rundell
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Dennis Bong
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
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14
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Akiyama BM, Graham ME, O′Donoghue Z, Beckham J, Kieft J. Three-dimensional structure of a flavivirus dumbbell RNA reveals molecular details of an RNA regulator of replication. Nucleic Acids Res 2021; 49:7122-7138. [PMID: 34133732 PMCID: PMC8266583 DOI: 10.1093/nar/gkab462] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 05/07/2021] [Accepted: 05/17/2021] [Indexed: 11/14/2022] Open
Abstract
Mosquito-borne flaviviruses (MBFVs) including dengue, West Nile, yellow fever, and Zika viruses have an RNA genome encoding one open reading frame flanked by 5' and 3' untranslated regions (UTRs). The 3' UTRs of MBFVs contain regions of high sequence conservation in structured RNA elements known as dumbbells (DBs). DBs regulate translation and replication of the viral RNA genome, functions proposed to depend on the formation of an RNA pseudoknot. To understand how DB structure provides this function, we solved the x-ray crystal structure of the Donggang virus DB to 2.1Å resolution and used structural modeling to reveal the details of its three-dimensional fold. The structure confirmed the predicted pseudoknot and molecular modeling revealed how conserved sequences form a four-way junction that appears to stabilize the pseudoknot. Single-molecule FRET suggests that the DB pseudoknot is a stable element that can regulate the switch between translation and replication during the viral lifecycle by modulating long-range RNA conformational changes.
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Affiliation(s)
- Benjamin M Akiyama
- Department of Biochemistry and Molecular Genetics, Aurora, CO 80045, USA
| | - Monica E Graham
- Department of Immunology and Microbiology, Aurora, CO 80045, USA
| | - Zoe O′Donoghue
- Department of Immunology and Microbiology, Aurora, CO 80045, USA
| | - J David Beckham
- Department of Immunology and Microbiology, Aurora, CO 80045, USA
- Department of Medicine Division of Infectious Diseases, Aurora, CO 80045, USA
| | - Jeffrey S Kieft
- Department of Biochemistry and Molecular Genetics, Aurora, CO 80045, USA
- RNA BioScience Initiative, University of Colorado Denver School of Medicine, Aurora, CO 80045, USA
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15
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Dolan PT, Taguwa S, Rangel MA, Acevedo A, Hagai T, Andino R, Frydman J. Principles of dengue virus evolvability derived from genotype-fitness maps in human and mosquito cells. eLife 2021; 10:e61921. [PMID: 33491648 PMCID: PMC7880689 DOI: 10.7554/elife.61921] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Accepted: 01/24/2021] [Indexed: 01/11/2023] Open
Abstract
Dengue virus (DENV) cycles between mosquito and mammalian hosts. To examine how DENV populations adapt to these different host environments, we used serial passage in human and mosquito cell lines and estimated fitness effects for all single-nucleotide variants in these populations using ultra-deep sequencing. This allowed us to determine the contributions of beneficial and deleterious mutations to the collective fitness of the population. Our analysis revealed that the continuous influx of a large burden of deleterious mutations counterbalances the effect of rare, host-specific beneficial mutations to shape the path of adaptation. Beneficial mutations preferentially map to intrinsically disordered domains in the viral proteome and cluster to defined regions in the genome. These phenotypically redundant adaptive alleles may facilitate host-specific DENV adaptation. Importantly, the evolutionary constraints described in our simple system mirror trends observed across DENV and Zika strains, indicating it recapitulates key biophysical and biological constraints shaping long-term viral evolution.
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Affiliation(s)
- Patrick T Dolan
- Stanford University, Department of BiologyStanfordUnited States
- University of California, Microbiology and Immunology, San FranciscoSan FranciscoUnited States
| | - Shuhei Taguwa
- Stanford University, Department of BiologyStanfordUnited States
| | | | - Ashley Acevedo
- University of California, Microbiology and Immunology, San FranciscoSan FranciscoUnited States
| | - Tzachi Hagai
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv UniversityTel AvivIsrael
| | - Raul Andino
- University of California, Microbiology and Immunology, San FranciscoSan FranciscoUnited States
| | - Judith Frydman
- Stanford University, Department of BiologyStanfordUnited States
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16
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Torabi SF, Vaidya AT, Tycowski KT, DeGregorio SJ, Wang J, Shu MD, Steitz TA, Steitz JA. RNA stabilization by a poly(A) tail 3'-end binding pocket and other modes of poly(A)-RNA interaction. Science 2021; 371:science.abe6523. [PMID: 33414189 DOI: 10.1126/science.abe6523] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 11/20/2020] [Indexed: 12/16/2022]
Abstract
Polyadenylate [poly(A)] tail addition to the 3' end of a wide range of RNAs is a highly conserved modification that plays a central role in cellular RNA function. Elements for nuclear expression (ENEs) are cis-acting RNA elements that stabilize poly(A) tails by sequestering them in RNA triplex structures. A crystal structure of a double ENE from a rice hAT transposon messenger RNA complexed with poly(A)28 at a resolution of 2.89 angstroms reveals multiple modes of interaction with poly(A), including major-groove triple helices, extended minor-groove interactions with RNA double helices, a quintuple-base motif that transitions poly(A) from minor-groove associations to major-groove triple helices, and a poly(A) 3'-end binding pocket. Our findings both expand the repertoire of motifs involved in long-range RNA interactions and provide insights into how polyadenylation can protect an RNA's extreme 3' end.
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Affiliation(s)
- Seyed-Fakhreddin Torabi
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06536, USA.,Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06536, USA
| | - Anand T Vaidya
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06536, USA.,Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06536, USA.,TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research, Hyderabad 500046, India
| | - Kazimierz T Tycowski
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06536, USA.,Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06536, USA
| | - Suzanne J DeGregorio
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06536, USA.,Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06536, USA
| | - Jimin Wang
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06536, USA
| | - Mei-Di Shu
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06536, USA.,Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06536, USA
| | - Thomas A Steitz
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06536, USA.,Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06536, USA
| | - Joan A Steitz
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06536, USA. .,Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06536, USA
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17
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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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18
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Bellone R, Lequime S, Jupille H, Göertz GP, Aubry F, Mousson L, Piorkowski G, Yen PS, Gabiane G, Vazeille M, Sakuntabhai A, Pijlman GP, de Lamballerie X, Lambrechts L, Failloux AB. Experimental adaptation of dengue virus 1 to Aedes albopictus mosquitoes by in vivo selection. Sci Rep 2020; 10:18404. [PMID: 33110109 PMCID: PMC7591890 DOI: 10.1038/s41598-020-75042-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 10/06/2020] [Indexed: 12/23/2022] Open
Abstract
In most of the world, Dengue virus (DENV) is mainly transmitted by the mosquito Aedes aegypti while in Europe, Aedes albopictus is responsible for human DENV cases since 2010. Identifying mutations that make DENV more competent for transmission by Ae. albopictus will help to predict emergence of epidemic strains. Ten serial passages in vivo in Ae. albopictus led to select DENV-1 strains with greater infectivity for this vector in vivo and in cultured mosquito cells. These changes were mediated by multiple adaptive mutations in the virus genome, including a mutation at position 10,418 in the DENV 3′UTR within an RNA stem-loop structure involved in subgenomic flavivirus RNA production. Using reverse genetics, we showed that the 10,418 mutation alone does not confer a detectable increase in transmission efficiency in vivo. These results reveal the complex adaptive landscape of DENV transmission by mosquitoes and emphasize the role of epistasis in shaping evolutionary trajectories of DENV variants.
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Affiliation(s)
- Rachel Bellone
- Arboviruses and Insect Vectors Unit, Institut Pasteur, Paris, France.,Sorbonne Université, Collège doctoral, 75005, Paris, France
| | - Sebastian Lequime
- Sorbonne Université, Collège doctoral, 75005, Paris, France.,Insect-Virus Interactions Unit, Institut Pasteur, UMR2000, CNRS, Paris, France.,Cluster of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Henri Jupille
- Arboviruses and Insect Vectors Unit, Institut Pasteur, Paris, France
| | - Giel P Göertz
- Laboratory of Virology, Wageningen University, Wageningen, The Netherlands
| | - Fabien Aubry
- Insect-Virus Interactions Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
| | - Laurence Mousson
- Arboviruses and Insect Vectors Unit, Institut Pasteur, Paris, France
| | - Géraldine Piorkowski
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207-IHU Méditerranée Infection), Marseille, France
| | - Pei-Shi Yen
- Arboviruses and Insect Vectors Unit, Institut Pasteur, Paris, France
| | - Gaelle Gabiane
- Arboviruses and Insect Vectors Unit, Institut Pasteur, Paris, France
| | - Marie Vazeille
- Arboviruses and Insect Vectors Unit, Institut Pasteur, Paris, France
| | - Anavaj Sakuntabhai
- Functional Genetics of Infectious Diseases Unit, Institut Pasteur, Paris, France
| | - Gorben P Pijlman
- Laboratory of Virology, Wageningen University, Wageningen, The Netherlands
| | - Xavier de Lamballerie
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207-IHU Méditerranée Infection), Marseille, France
| | - Louis Lambrechts
- Insect-Virus Interactions Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
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19
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Schneider ADB, Wolfinger MT. Musashi binding elements in Zika and related Flavivirus 3'UTRs: A comparative study in silico. Sci Rep 2019; 9:6911. [PMID: 31061405 PMCID: PMC6502878 DOI: 10.1038/s41598-019-43390-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 04/23/2019] [Indexed: 12/16/2022] Open
Abstract
Zika virus (ZIKV) belongs to a class of neurotropic viruses that have the ability to cause congenital infection, which can result in microcephaly or fetal demise. Recently, the RNA-binding protein Musashi-1 (Msi1), which mediates the maintenance and self-renewal of stem cells and acts as a translational regulator, has been associated with promoting ZIKV replication, neurotropism, and pathology. Msi1 predominantly binds to single-stranded motifs in the 3' untranslated region (UTR) of RNA that contain a UAG trinucleotide in their core. We systematically analyzed the properties of Musashi binding elements (MBEs) in the 3'UTR of flaviviruses with a thermodynamic model for RNA folding. Our results indicate that MBEs in ZIKV 3'UTRs occur predominantly in unpaired, single-stranded structural context, thus corroborating experimental observations by a biophysical model of RNA structure formation. Statistical analysis and comparison with related viruses show that ZIKV MBEs are maximally accessible among mosquito-borne flaviviruses. Our study addresses the broader question of whether other emerging arboviruses can cause similar neurotropic effects through the same mechanism in the developing fetus by establishing a link between the biophysical properties of viral RNA and teratogenicity. Moreover, our thermodynamic model can explain recent experimental findings and predict the Msi1-related neurotropic potential of other viruses.
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Affiliation(s)
- Adriano de Bernardi Schneider
- Department of Medicine, University of California San Diego, 220 Dickinson St, Suite A, San Diego, CA, 92103, United States of America
| | - Michael T Wolfinger
- Department of Theoretical Chemistry, University of Vienna, Währingerstraße 17, 1090, Vienna, Austria.
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20
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Ochsenreiter R, Hofacker IL, Wolfinger MT. Functional RNA Structures in the 3'UTR of Tick-Borne, Insect-Specific and No-Known-Vector Flaviviruses. Viruses 2019; 11:E298. [PMID: 30909641 PMCID: PMC6466055 DOI: 10.3390/v11030298] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 03/19/2019] [Accepted: 03/20/2019] [Indexed: 12/21/2022] Open
Abstract
Untranslated regions (UTRs) of flaviviruses contain a large number of RNA structural elements involved in mediating the viral life cycle, including cyclisation, replication, and encapsidation. Here we report on a comparative genomics approach to characterize evolutionarily conserved RNAs in the 3 ' UTR of tick-borne, insect-specific and no-known-vector flaviviruses in silico. Our data support the wide distribution of previously experimentally characterized exoribonuclease resistant RNAs (xrRNAs) within tick-borne and no-known-vector flaviviruses and provide evidence for the existence of a cascade of duplicated RNA structures within insect-specific flaviviruses. On a broader scale, our findings indicate that viral 3 ' UTRs represent a flexible scaffold for evolution to come up with novel xrRNAs.
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Affiliation(s)
- Roman Ochsenreiter
- Department of Theoretical Chemistry, University of Vienna, Währingerstraße 17, 1090 Vienna, Austria.
| | - Ivo L Hofacker
- Department of Theoretical Chemistry, University of Vienna, Währingerstraße 17, 1090 Vienna, Austria.
- Research Group BCB, Faculty of Computer Science, University of Vienna, Währingerstraße 29, 1090 Vienna, Austria.
| | - Michael T Wolfinger
- Department of Theoretical Chemistry, University of Vienna, Währingerstraße 17, 1090 Vienna, Austria.
- Research Group BCB, Faculty of Computer Science, University of Vienna, Währingerstraße 29, 1090 Vienna, Austria.
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21
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Du S, Liu X, Cai Q. Viral-Mediated mRNA Degradation for Pathogenesis. Biomedicines 2018; 6:biomedicines6040111. [PMID: 30501096 PMCID: PMC6315618 DOI: 10.3390/biomedicines6040111] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 11/25/2018] [Accepted: 11/29/2018] [Indexed: 11/21/2022] Open
Abstract
Cellular RNA decay machinery plays a vital role in regulating gene expression by altering the stability of mRNAs in response to external stresses, including viral infection. In the primary infection, viruses often conquer the host cell’s antiviral immune response by controlling the inherently cellular mRNA degradation machinery to facilitate viral gene expression and establish a successful infection. This review summarizes the current knowledge about the diverse strategies of viral-mediated regulatory RNA shutoff for pathogenesis, and particularly sheds a light on the mechanisms that viruses evolve to elude immune surveillance during infection.
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Affiliation(s)
- Shujuan Du
- MOE& MOH Key Laboratory of Medical Molecular Virology, School of Basic Medicine, Shanghai Medical College, Fudan University, Shanghai 200032, China.
| | - Xiaoqing Liu
- MOE& MOH Key Laboratory of Medical Molecular Virology, School of Basic Medicine, Shanghai Medical College, Fudan University, Shanghai 200032, China.
| | - Qiliang Cai
- MOE& MOH Key Laboratory of Medical Molecular Virology, School of Basic Medicine, Shanghai Medical College, Fudan University, Shanghai 200032, China.
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22
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Charley PA, Wilusz CJ, Wilusz J. Identification of phlebovirus and arenavirus RNA sequences that stall and repress the exoribonuclease XRN1. J Biol Chem 2017; 293:285-295. [PMID: 29118186 DOI: 10.1074/jbc.m117.805796] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 11/06/2017] [Indexed: 12/22/2022] Open
Abstract
Regulated mRNA decay plays a vital role in determining both the level and quality of cellular gene expression. Viral RNAs must successfully evade this host RNA decay machinery to establish a productive infection. One way for RNA viruses to accomplish this is to target the cellular exoribonuclease XRN1, because this enzyme is accessible in the cytoplasm and plays a major role in mRNA decay. Members of the Flaviviridae use RNA structures in their 5'- or 3'-untranslated regions to stall and repress XRN1, effectively stabilizing viral RNAs while also causing significant dysregulation of host cell mRNA stability. Here, we use a series of biochemical assays to demonstrate that the 3'-terminal portion of the nucleocapsid (N) mRNA of Rift Valley fever virus, a phlebovirus of the Bunyaviridae family, also can effectively stall and repress XRN1. The region responsible for impeding XRN1 includes a G-rich portion that likely forms a G-quadruplex structure. The 3'-terminal portions of ambisense-derived transcripts of multiple arenaviruses also stalled XRN1. Therefore, we conclude that RNAs from two additional families of mammalian RNA viruses stall and repress XRN1. This observation. emphasizes the importance and commonality of this viral strategy to interfere with the 5'-to-3'-exoribonuclease component of the cytoplasmic RNA decay machinery.
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Affiliation(s)
- Phillida A Charley
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523
| | - Carol J Wilusz
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523
| | - Jeffrey Wilusz
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523.
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23
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Rohilla KJ, Gagnon KT. RNA biology of disease-associated microsatellite repeat expansions. Acta Neuropathol Commun 2017; 5:63. [PMID: 28851463 PMCID: PMC5574247 DOI: 10.1186/s40478-017-0468-y] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 08/22/2017] [Indexed: 12/13/2022] Open
Abstract
Microsatellites, or simple tandem repeat sequences, occur naturally in the human genome and have important roles in genome evolution and function. However, the expansion of microsatellites is associated with over two dozen neurological diseases. A common denominator among the majority of these disorders is the expression of expanded tandem repeat-containing RNA, referred to as xtrRNA in this review, which can mediate molecular disease pathology in multiple ways. This review focuses on the potential impact that simple tandem repeat expansions can have on the biology and metabolism of RNA that contain them and underscores important gaps in understanding. Merging the molecular biology of repeat expansion disorders with the current understanding of RNA biology, including splicing, transcription, transport, turnover and translation, will help clarify mechanisms of disease and improve therapeutic development.
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24
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Boehm V, Gerbracht JV, Marx MC, Gehring NH. Interrogating the degradation pathways of unstable mRNAs with XRN1-resistant sequences. Nat Commun 2016; 7:13691. [PMID: 27917860 PMCID: PMC5150221 DOI: 10.1038/ncomms13691] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 10/25/2016] [Indexed: 12/22/2022] Open
Abstract
The turnover of messenger RNAs (mRNAs) is a key regulatory step of gene expression in eukaryotic cells. Due to the complexity of the mammalian degradation machinery, the contribution of decay factors to the directionality of mRNA decay is poorly understood. Here we characterize a molecular tool to interrogate mRNA turnover via the detection of XRN1-resistant decay fragments (xrFrag). Using nonsense-mediated mRNA decay (NMD) as a model pathway, we establish xrFrag analysis as a robust indicator of accelerated 5'-3' mRNA decay. In tethering assays, monitoring xrFrag accumulation allows to distinguish decapping and endocleavage activities from deadenylation. Moreover, xrFrag analysis of mRNA degradation induced by miRNAs, AU-rich elements (AREs) as well as the 3' UTRs of cytokine mRNAs reveals the contribution of 5'-3' decay and endonucleolytic cleavage. Our work uncovers formerly unrecognized modes of mRNA turnover and establishes xrFrag as a powerful tool for RNA decay analyses.
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Affiliation(s)
- Volker Boehm
- Institute for Genetics, Department of Biology, University of Cologne, Zuelpicher Straße 47a, 50674 Cologne, Germany
| | - Jennifer V Gerbracht
- Institute for Genetics, Department of Biology, University of Cologne, Zuelpicher Straße 47a, 50674 Cologne, Germany
| | - Marie-Charlotte Marx
- Institute for Genetics, Department of Biology, University of Cologne, Zuelpicher Straße 47a, 50674 Cologne, Germany
| | - Niels H Gehring
- Institute for Genetics, Department of Biology, University of Cologne, Zuelpicher Straße 47a, 50674 Cologne, Germany
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25
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D'Ascenzo L, Leonarski F, Vicens Q, Auffinger P. 'Z-DNA like' fragments in RNA: a recurring structural motif with implications for folding, RNA/protein recognition and immune response. Nucleic Acids Res 2016; 44:5944-56. [PMID: 27151194 PMCID: PMC4937326 DOI: 10.1093/nar/gkw388] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 04/28/2016] [Indexed: 01/09/2023] Open
Abstract
Since the work of Alexander Rich, who solved the first Z-DNA crystal structure, we have known that d(CpG) steps can adopt a particular structure that leads to forming left-handed helices. However, it is still largely unrecognized that other sequences can adopt ‘left-handed’ conformations in DNA and RNA, in double as well as single stranded contexts. These ‘Z-like’ steps involve the coexistence of several rare structural features: a C2’-endo puckering, a syn nucleotide and a lone pair–π stacking between a ribose O4’ atom and a nucleobase. This particular arrangement induces a conformational stress in the RNA backbone, which limits the occurrence of Z-like steps to ≈0.1% of all dinucleotide steps in the PDB. Here, we report over 600 instances of Z-like steps, which are located within r(UNCG) tetraloops but also in small and large RNAs including riboswitches, ribozymes and ribosomes. Given their complexity, Z-like steps are probably associated with slow folding kinetics and once formed could lock a fold through the formation of unique long-range contacts. Proteins involved in immunologic response also specifically recognize/induce these peculiar folds. Thus, characterizing the conformational features of these motifs could be a key to understanding the immune response at a structural level.
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Affiliation(s)
- Luigi D'Ascenzo
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg 67084, France
| | - Filip Leonarski
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg 67084, France Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Quentin Vicens
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg 67084, France
| | - Pascal Auffinger
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg 67084, France
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