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Oishi K, Blanco-Melo D, Kurland AP, Johnson JR, tenOever BR. Archaeal Kink-Turn Binding Protein Mediates Inhibition of Orthomyxovirus Splicing Biology. J Virol 2023; 97:e0181322. [PMID: 36943134 PMCID: PMC10134859 DOI: 10.1128/jvi.01813-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 02/22/2023] [Indexed: 03/23/2023] Open
Abstract
Despite lacking a DNA intermediate, orthomyxoviruses complete their replication cycle in the nucleus and generate multiple transcripts by usurping the host splicing machinery. This biology results in dynamic changes of relative viral transcripts over time and dictates the replicative phase of the infection. Here, we demonstrate that the family of archaeal L7Ae proteins uniquely inhibit the splicing biology of influenza A virus, influenza B virus, and Salmon isavirus, revealing a common strategy utilized by Orthomyxoviridae members to achieve this dynamic. L7Ae-mediated inhibition of virus biology was lost with the generation of a splicing-independent strain of influenza A virus and attempts to select for an escape mutant resulted in variants that conformed to host splicing biology at significant cost to their overall fitness. As L7Ae recognizes conventional kink turns in various RNAs, these data implicate the formation of a similar structure as a shared strategy adopted by this virus family to coordinate their replication cycle. IMPORTANCE Here, we demonstrate that a family of proteins from archaea specifically inhibit this splicing biology of all tested members of the Orthomyxoviridae family. We show that this inhibition extends to influenza A virus, influenza B virus, and isavirus genera, while having no significant impact on the mammalian transcriptome or proteome. Attempts to generate an escape mutant against L7Ae-mediated inhibition resulted in mutations surrounding the viral splice sites and a significant loss of viral fitness. Together, these findings reveal a unique biology shared among diverse members of the Orthomyxoviridae family that may serve as a means to generate future universal therapeutics.
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Affiliation(s)
- Kohei Oishi
- Department of Microbiology, New York University, Grossman School of Medicine, New York, New York, USA
| | - Daniel Blanco-Melo
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Andrew P. Kurland
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Jeffrey R. Johnson
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Benjamin R. tenOever
- Department of Microbiology, New York University, Grossman School of Medicine, New York, New York, USA
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Shibata T, Suzuki Y, Sugiyama H, Endo M, Saito H. Folding RNA-Protein Complex into Designed Nanostructures. Methods Mol Biol 2021; 2323:221-32. [PMID: 34086284 DOI: 10.1007/978-1-0716-1499-0_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
RNA-protein (RNP) complexes are promising biomaterials for the fields of nanotechnology and synthetic biology. Protein-responsive RNA sequences (RNP motifs) can be integrated into various RNAs, such as messenger RNA, short-hairpin RNA, and synthetic RNA nanoobjects for a variety of purposes. Direct observation of RNP interaction in solution at high resolution is important in the design and construction of RNP-mediated nanostructures. Here we describe a method to construct and visualize RNP nanostructures that precisely arrange a target protein on the RNA scaffold with nanometer scale. High-speed AFM (HS-AFM) images of RNP nanostructures show that the folding of RNP complexes of defined sizes can be directly visualized at single RNP resolution in solution.
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Lai SM, Gopalan V. Using an L7Ae-Tethered, Hydroxyl Radical-Mediated Footprinting Strategy to Identify and Validate Kink-Turns in RNAs. Methods Mol Biol 2021; 2167:147-169. [PMID: 32712919 DOI: 10.1007/978-1-0716-0716-9_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Kink-turns are important RNA structural modules that facilitate long-range tertiary interactions and form binding sites for members of the L7Ae family of proteins. Present in a wide variety of functional RNAs, kink-turns play key organizational roles in many RNA-based cellular processes, including translation, modification, and tRNA biogenesis. It is important to determine the contribution of kink-turns to the overall architecture of resident RNAs, as these modules dictate ribonucleoprotein (RNP) assembly and function. This chapter describes a site-directed, hydroxyl radical-mediated footprinting strategy that utilizes L7Ae-tethered chemical nucleases to experimentally validate computationally identified kink-turns in any RNA and under a wide variety of conditions. The work plan described here uses the catalytic RNase P RNA as an example to provide a blueprint for using this footprinting method to map RNA-protein interactions in other RNP complexes.
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Affiliation(s)
- Stella M Lai
- Department of Chemistry and Biochemistry and Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Venkat Gopalan
- Department of Chemistry and Biochemistry and Center for RNA Biology, The Ohio State University, Columbus, OH, USA.
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Mc Cafferty S, De Temmerman J, Kitada T, Becraft JR, Weiss R, Irvine DJ, Devreese M, De Baere S, Combes F, Sanders NN. In Vivo Validation of a Reversible Small Molecule-Based Switch for Synthetic Self-Amplifying mRNA Regulation. Mol Ther 2020; 29:1164-1173. [PMID: 33186690 DOI: 10.1016/j.ymthe.2020.11.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 10/03/2020] [Accepted: 11/05/2020] [Indexed: 12/01/2022] Open
Abstract
Synthetic mRNA therapeutics have the potential to revolutionize healthcare, as they enable patients to produce therapeutic proteins inside their own bodies. However, convenient methods that allow external control over the timing and magnitude of protein production after in vivo delivery of synthetic mRNA are lacking. In this study, we validate the in vivo utility of a synthetic self-amplifying mRNA (RNA replicon) whose expression can be turned off using a genetic switch that responds to oral administration of trimethoprim (TMP), a US Food and Drug Administration (FDA)-approved small-molecule drug. After intramuscular electroporation, the engineered RNA replicon exhibited dose-dependent and reversible expression of its encoded protein upon TMP administration. The TMP serum level needed for maximal downregulation of protein translation was approximately 45-fold below that used in humans for therapeutic purposes. To demonstrate the therapeutic potential of the technology, we injected mice with a TMP-responsive RNA replicon encoding erythropoietin (EPO) and successfully controlled the timing and magnitude of EPO production as well as changes in hematocrit. This work demonstrates the feasibility of controlling mRNA kinetics in vivo, thereby broadly expanding the clinical versatility of mRNA therapeutics.
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Affiliation(s)
- Sean Mc Cafferty
- Laboratory of Gene Therapy, Department of Nutrition, Genetics and Ethology, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium; Cancer Research Institute Ghent (CRIG), Ghent University, 9000 Ghent, Belgium
| | - Joyca De Temmerman
- Laboratory of Gene Therapy, Department of Nutrition, Genetics and Ethology, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium; Cancer Research Institute Ghent (CRIG), Ghent University, 9000 Ghent, Belgium; Department of Pathology, Bacteriology and Poultry diseases, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium
| | | | | | - Ron Weiss
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA
| | - Darrell J Irvine
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA; Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Mathias Devreese
- Laboratory of Pharmacology and Toxicology, Department of Pharmacology, Toxicology and Biochemistry, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium
| | - Siegrid De Baere
- Laboratory of Pharmacology and Toxicology, Department of Pharmacology, Toxicology and Biochemistry, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium
| | - Francis Combes
- Laboratory of Gene Therapy, Department of Nutrition, Genetics and Ethology, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium; Cancer Research Institute Ghent (CRIG), Ghent University, 9000 Ghent, Belgium
| | - Niek N Sanders
- Laboratory of Gene Therapy, Department of Nutrition, Genetics and Ethology, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium; Cancer Research Institute Ghent (CRIG), Ghent University, 9000 Ghent, Belgium.
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Ashraf S, Huang L, Lilley DMJ. Sequence determinants of the folding properties of box C/D kink-turns in RNA. RNA 2017; 23:1927-1935. [PMID: 28956757 PMCID: PMC5689011 DOI: 10.1261/rna.063453.117] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 09/15/2017] [Indexed: 05/20/2023]
Abstract
Folding properties differ markedly between kink-turns (k-turns) that have different biological functions. While ribosomal and riboswitch k-turns generally fold into their kinked conformation on addition of metal ions, box C/D snoRNP k-turns remain completely unfolded under these conditions, although they fold on addition of L7Ae protein. Sequence elements have been systematically exchanged between a standard ribosomal k-turn (Kt-7) that folds on addition of metal ions, and a box C/D k-turn. Folding was studied using fluorescence resonance energy transfer and gel electrophoresis. Three sequence elements each contribute in an approximately additive manner to the different folding properties of Kt-7 and box C/D k-turns from archaea. Bioinformatic analysis indicates that k-turn sequences evolve sequences that suit their folding properties to their biological function. The majority of ribosomal and riboswitch k-turns have sequences allowing unassisted folding in response to the presence of metal ions. In contrast, box C/D k-turns have sequences that require the binding of proteins to drive folding into the kinked conformation, consistent with their role in the assembly of the box C/D snoRNP apparatus. The rules governing the influence of sequence on folding properties can be applied to other standard k-turns to predict their folding characteristics.
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Affiliation(s)
- Saira Ashraf
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Lin Huang
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dundee DD1 5EH, United Kingdom
| | - David M J Lilley
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dundee DD1 5EH, United Kingdom
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Kim J, Jun KM, Kim JS, Chae S, Pahk YM, Lee TH, Sohn SI, Lee SI, Lim MH, Kim CK, Hur Y, Nahm BH, Kim YK. RapaNet: A Web Tool for the Co-Expression Analysis of Brassica rapa Genes. Evol Bioinform Online 2017; 13:1176934317715421. [PMID: 28680265 PMCID: PMC5484627 DOI: 10.1177/1176934317715421] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 05/24/2017] [Indexed: 12/20/2022] Open
Abstract
Accumulated microarray data are used for assessing gene function by providing statistical values for co-expressed genes; however, only a limited number of Web tools are available for analyzing the co-expression of genes of Brassica rapa. We have developed a Web tool called RapaNet (http://bioinfo.mju.ac.kr/arraynet/brassica300k/query/), which is based on a data set of 143 B rapa microarrays compiled from various organs and at different developmental stages during exposure to biotic or abiotic stress. RapaNet visualizes correlated gene expression information via correlational networks and phylogenetic trees using Pearson correlation coefficient (r). In addition, RapaNet provides hierarchical clustering diagrams, scatterplots of log ratio intensities, related pathway maps, and cis-element lists of promoter regions. To ascertain the functionality of RapaNet, the correlated genes encoding ribosomal protein (L7Ae), photosystem II protein D1 (psbA), and cytochrome P450 monooxygenase in glucosinolate biosynthesis (CYP79F1) were retrieved from RapaNet and compared with their Arabidopsis homologues. An analysis of the co-expressed genes revealed their shared and unique features.
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Affiliation(s)
- Jiye Kim
- Insilicogen, Inc., Suwon-si, Republic of Korea
| | - Kyong Mi Jun
- GreenGene Biotech Inc., Yongin, Republic of Korea
| | - Joung Sug Kim
- Division of Biosciences and Bioinformatics, Myongji University, Yongin, Republic of Korea
| | - Songhwa Chae
- Division of Biosciences and Bioinformatics, Myongji University, Yongin, Republic of Korea
| | | | - Tae-Ho Lee
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Jeonju, Republic of Korea
| | - Soo-In Sohn
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Jeonju, Republic of Korea
| | - Soo In Lee
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Jeonju, Republic of Korea
| | - Myung-Ho Lim
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Jeonju, Republic of Korea
| | - Chang-Kug Kim
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Jeonju, Republic of Korea
| | - Yoonkang Hur
- Department of Biology, College of Biological Sciences and Biotechnology, Chungnam National University, Daejeon, Republic of Korea
| | - Baek Hie Nahm
- GreenGene Biotech Inc., Yongin, Republic of Korea.,Division of Biosciences and Bioinformatics, Myongji University, Yongin, Republic of Korea
| | - Yeon-Ki Kim
- Division of Biosciences and Bioinformatics, Myongji University, Yongin, Republic of Korea
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Bhuiya MW, Suryadi J, Zhou Z, Brown BA. Structure of the Aeropyrum pernix L7Ae multifunctional protein and insight into its extreme thermostability. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:979-88. [PMID: 23989144 PMCID: PMC3758144 DOI: 10.1107/s1744309113021799] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 08/05/2013] [Indexed: 11/11/2022]
Abstract
Archaeal ribosomal protein L7Ae is a multifunctional RNA-binding protein that directs post-transcriptional modification of archaeal RNAs. The L7Ae protein from Aeropyrum pernix (Ap L7Ae), a member of the Crenarchaea, was found to have an extremely high melting temperature (>383 K). The crystal structure of Ap L7Ae has been determined to a resolution of 1.56 Å. The structure of Ap L7Ae was compared with the structures of two homologs: hyperthermophilic Methanocaldococcus jannaschii L7Ae and the mesophilic counterpart mammalian 15.5 kD protein. The primary stabilizing feature in the Ap L7Ae protein appears to be the large number of ion pairs and extensive ion-pair network that connects secondary-structural elements. To our knowledge, Ap L7Ae is among the most thermostable single-domain monomeric proteins presently observed.
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Affiliation(s)
| | - Jimmy Suryadi
- Department of Chemistry, Wake Forest University, Winston-Salem, NC 27109, USA
| | - Zholi Zhou
- Bristol-Myers Squibb, Syracuse, NY 13221, USA
| | - Bernard Andrew Brown
- Womble Carlyle Sandridge and Rice LLP, One West Fourth Street, Winston-Salem, NC 27101, USA
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Abstract
RNA, at the forefront of biochemical research due to its central role in biology, is recognized by proteins through various mechanisms. Analysis of the RNA-protein interface provides insight into the recognition determinants and function. As such, there is a demand for developing new methods to characterize RNA-protein interactions. Saturation transfer difference (STD) NMR can identify binding ligands for proteins in a rather short period of time, with data acquisitions of just a few hours. Two RNA-protein systems involved in RNA modification were studied using STD NMR. The N (6)-threonylcarbamoyltransferase, YrdC, with nucleoside-specific recognition, was shown to bind the anticodon stem-loop of tRNA(Lys)UUU. The points of contact on the RNA were assigned and a binding interface was identified. STD NMR was also applied to the interaction of the archaeal ribosomal protein, L7Ae, with the box C/D K-turn RNA. The distinctiveness of the two RNA-protein interfaces was evident. Both RNAs exhibited strong STD signals indicative of direct contact with the respective protein, but reflected the nature of recognition. Characterization of nucleic acid recognition determinants traditionally involves cost and time prohibitive methods. This approach offers significant insight into interaction interfaces fairly rapidly, and complements existing structural methods.
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Affiliation(s)
- Kimberly A Harris
- The RNA Institute; University at Albany; Albany, NY USA; Department of Biological Sciences; University at Albany; Albany, NY USA
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