1
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Ahmed N, Ahmed N, Bilodeau DA, Pezacki JP. An unnatural enzyme with endonuclease activity towards small non-coding RNAs. Nat Commun 2023; 14:3777. [PMID: 37355703 PMCID: PMC10290691 DOI: 10.1038/s41467-023-39105-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 05/25/2023] [Indexed: 06/26/2023] Open
Abstract
Endonucleases are enzymes that cleave internal phosphodiester bonds within double-stranded DNA or RNA and are essential for biological functions. Herein, we use genetic code expansion to create an unnatural endonuclease that cleaves non-coding RNAs including short interfering RNA (siRNA) and microRNAs (miRNAs), a function that does not exist in nature. We introduce a metal-chelating unnatural amino acid, (2,2'-bipyridin-5-yl)alanine (BpyAla) to impart endonuclease activity to the viral suppressor of RNA silencing protein p19. Upon binding of copper, the mutant p19-T111BpyAla displays catalytic site-specific cleavage of siRNA and human miRNAs. Catalysis is confirmed using fluorescence polarization and fluorescence turn-on. Global miRNA profiling reveals that the engineered enzyme cleaves miRNAs in a human cell line. The therapeutic potential is demonstrated by targeting miR-122, a critical host factor for the hepatitis C virus (HCV). Unnatural endonuclease function is shown to deplete miR-122 levels with similar effects to an antagomir that reduces HCV levels therapeutically.
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Affiliation(s)
- Noreen Ahmed
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Nadine Ahmed
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Didier A Bilodeau
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - John Paul Pezacki
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada.
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2
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Foss DV, Schirle NT, MacRae IJ, Pezacki JP. Structural insights into interactions between viral suppressor of RNA silencing protein p19 mutants and small RNAs. FEBS Open Bio 2019; 9:1042-1051. [PMID: 31021526 PMCID: PMC6551489 DOI: 10.1002/2211-5463.12644] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 04/03/2019] [Accepted: 04/24/2019] [Indexed: 12/31/2022] Open
Abstract
Viral suppressors of RNA silencing (VSRSs) are a diverse group of viral proteins that have evolved to disrupt eukaryotic RNA silencing pathways, thereby contributing to viral pathogenicity. The p19 protein is a VSRS that selectively binds to short interfering RNAs (siRNAs) over microRNAs (miRNAs). Mutational analysis has identified single amino acid substitutions that reverse this selectivity through new high-affinity interactions with human miR-122. Herein, we report crystal structures of complexed p19-T111S (2.6 Å), p19-T111H (2.3 Å) and wild-type p19 protein (2.2 Å) from the Carnation Italian ringspot virus with small interfering RNA (siRNA) ligands. Structural comparisons reveal that these mutations do not lead to major changes in p19 architecture, but instead promote subtle rearrangement of residues and solvent molecules along the p19 midline. These observations suggest p19 uses many small interactions to distinguish siRNAs from miRNAs and perturbing these interactions can create p19 variants with novel RNA-recognition properties. DATABASE: Model data are deposited in the PDB database under the accession numbers 6BJG, 6BJH and 6BJV.
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Affiliation(s)
- Dana V Foss
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Canada
| | - Nicole T Schirle
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ian J MacRae
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - John Paul Pezacki
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Canada
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3
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Ahmed N, De Graaf JF, Ahmed N, Foss DV, Delcorde J, Schultz PG, Pezacki JP. Visualization of the Delivery and Release of Small RNAs Using Genetic Code Expansion and Unnatural RNA-Binding Proteins. Bioconjug Chem 2018; 29:3982-3986. [DOI: 10.1021/acs.bioconjchem.8b00649] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Noreen Ahmed
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie Curie Pvt., Ottawa, Ontario K1N 6N5, Canada
| | - Joanna Fréderique De Graaf
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie Curie Pvt., Ottawa, Ontario K1N 6N5, Canada
| | - Nadine Ahmed
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie Curie Pvt., Ottawa, Ontario K1N 6N5, Canada
| | - Dana V. Foss
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie Curie Pvt., Ottawa, Ontario K1N 6N5, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
| | - Julie Delcorde
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie Curie Pvt., Ottawa, Ontario K1N 6N5, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
| | - Peter G. Schultz
- Department of Chemistry and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N Torrey Pines Road, La Jolla, California 92037, United States
| | - John Paul Pezacki
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie Curie Pvt., Ottawa, Ontario K1N 6N5, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
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4
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Yang NJ, Kauke MJ, Sun F, Yang LF, Maass KF, Traxlmayr MW, Yu Y, Xu Y, Langer RS, Anderson DG, Wittrup KD. Cytosolic delivery of siRNA by ultra-high affinity dsRNA binding proteins. Nucleic Acids Res 2017. [PMID: 28641400 PMCID: PMC5570165 DOI: 10.1093/nar/gkx546] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Protein-based methods of siRNA delivery are capable of uniquely specific targeting, but are limited by technical challenges such as low potency or poor biophysical properties. Here, we engineered a series of ultra-high affinity siRNA binders based on the viral protein p19 and developed them into siRNA carriers targeted to the epidermal growth factor receptor (EGFR). Combined in trans with a previously described endosome-disrupting agent composed of the pore-forming protein Perfringolysin O (PFO), potent silencing was achieved in vitro with no detectable cytotoxicity. Despite concerns that excessively strong siRNA binding could prevent the discharge of siRNA from its carrier, higher affinity continually led to stronger silencing. We found that this improvement was due to both increased uptake of siRNA into the cell and improved pharmacodynamics inside the cell. Mathematical modeling predicted the existence of an affinity optimum that maximizes silencing, after which siRNA sequestration decreases potency. Our study characterizing the affinity dependence of silencing suggests that siRNA-carrier affinity can significantly affect the intracellular fate of siRNA and may serve as a handle for improving the efficiency of delivery. The two-agent delivery system presented here possesses notable biophysical properties and potency, and provide a platform for the cytosolic delivery of nucleic acids.
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Affiliation(s)
- Nicole J Yang
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Monique J Kauke
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Fangdi Sun
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Lucy F Yang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Katie F Maass
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Michael W Traxlmayr
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Yao Yu
- Protein Analytics, Adimab LLC, Lebanon, NH 03766, USA
| | - Yingda Xu
- Protein Analytics, Adimab LLC, Lebanon, NH 03766, USA
| | - Robert S Langer
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Harvard-MIT Division of Health Science and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Daniel G Anderson
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Harvard-MIT Division of Health Science and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - K Dane Wittrup
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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5
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Campuzano S, Yánez-Sedeño P, Pingarrón JM. Electrochemical biosensing of microribonucleic acids using antibodies and viral proteins with affinity for ribonucleic acid duplexes. Electrochim Acta 2017. [DOI: 10.1016/j.electacta.2017.02.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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6
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Campuzano S, Pedrero M, Pingarrón JM. Viral protein-based bioanalytical tools for small RNA biosensing. Trends Analyt Chem 2016. [DOI: 10.1016/j.trac.2015.09.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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7
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Chen KI, Pan CY, Li KH, Huang YC, Lu CW, Tang CY, Su YW, Tseng LW, Tseng KC, Lin CY, Chen CD, Lin SS, Chen YT. Isolation and Identification of Post-Transcriptional Gene Silencing-Related Micro-RNAs by Functionalized Silicon Nanowire Field-effect Transistor. Sci Rep 2015; 5:17375. [PMID: 26616332 PMCID: PMC4663627 DOI: 10.1038/srep17375] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 10/29/2015] [Indexed: 02/08/2023] Open
Abstract
Many transcribed RNAs are non-coding RNAs, including microRNAs (miRNAs), which bind to complementary sequences on messenger RNAs to regulate the translation efficacy. Therefore, identifying the miRNAs expressed in cells/organisms aids in understanding genetic control in cells/organisms. In this report, we determined the binding of oligonucleotides to a receptor-modified silicon nanowire field-effect transistor (SiNW-FET) by monitoring the changes in conductance of the SiNW-FET. We first modified a SiNW-FET with a DNA probe to directly and selectively detect the complementary miRNA in cell lysates. This SiNW-FET device has 7-fold higher sensitivity than reverse transcription-quantitative polymerase chain reaction in detecting the corresponding miRNA. Next, we anchored viral p19 proteins, which bind the double-strand small RNAs (ds-sRNAs), on the SiNW-FET. By perfusing the device with synthesized ds-sRNAs of different pairing statuses, the dissociation constants revealed that the nucleotides at the 3′-overhangs and pairings at the terminus are important for the interactions. After perfusing the total RNA mixture extracted from Nicotiana benthamiana across the device, this device could enrich the ds-sRNAs for sequence analysis. Finally, this bionanoelectronic SiNW-FET, which is able to isolate and identify the interacting protein-RNA, adds an additional tool in genomic technology for the future study of direct biomolecular interactions.
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Affiliation(s)
- Kuan-I Chen
- Department of Chemistry, National Taiwan University, Taipei 106, Taiwan.,Institute of Atomic and Molecular Sciences, Academia Sinica, P.O. Box 23-166, Taipei 106, Taiwan
| | - Chien-Yuan Pan
- Department of Life Science, National Taiwan University, Taipei 106, Taiwan
| | - Keng-Hui Li
- Department of Chemistry, National Taiwan University, Taipei 106, Taiwan
| | - Ying-Chih Huang
- Institute of Biotechnology, National Taiwan University, Taipei 106, Taiwan
| | - Chia-Wei Lu
- Institute of Biotechnology, National Taiwan University, Taipei 106, Taiwan
| | - Chuan-Yi Tang
- Department of Computer Science, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Ya-Wen Su
- National Nano Device Laboratories, Hsinchu 300, Taiwan
| | - Ling-Wei Tseng
- Department of Chemistry, National Taiwan University, Taipei 106, Taiwan
| | - Kun-Chang Tseng
- Department of Chemistry, National Taiwan University, Taipei 106, Taiwan.,Institute of Atomic and Molecular Sciences, Academia Sinica, P.O. Box 23-166, Taipei 106, Taiwan
| | - Chi-Yun Lin
- Department of Chemistry, National Taiwan University, Taipei 106, Taiwan
| | - Chii-Dong Chen
- Institute of Physics, Academia Sinica, Taipei 115, Taiwan
| | - Shih-Shun Lin
- Institute of Biotechnology, National Taiwan University, Taipei 106, Taiwan.,Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Yit-Tsong Chen
- Department of Chemistry, National Taiwan University, Taipei 106, Taiwan.,Institute of Atomic and Molecular Sciences, Academia Sinica, P.O. Box 23-166, Taipei 106, Taiwan
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8
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Suppressing RNA silencing with small molecules and the viral suppressor of RNA silencing protein p19. Biochem Biophys Res Commun 2015; 463:1135-40. [PMID: 26079891 DOI: 10.1016/j.bbrc.2015.06.071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 06/09/2015] [Indexed: 11/22/2022]
Abstract
RNA silencing is a gene regulatory and host defense mechanism whereby small RNA molecules are engaged by Argonaute (AGO) proteins, which facilitate gene knockdown of complementary mRNA targets. Small molecule inhibitors of AGO represent a convenient method for reversing this effect and have applications in human therapy and biotechnology. Viral suppressors of RNA silencing, such as p19, can also be used to suppress the pathway. Here we assess the compatibility of these two approaches, by examining whether synthetic inhibitors of AGO would inhibit p19-siRNA interactions. We observe that aurintricarboxylic acid (ATA) is a potent inhibitor of p19's ability to bind siRNA (IC50 = 0.43 μM), oxidopamine does not inhibit p19:siRNA interactions, and suramin is a mild inhibitor of p19:siRNA interactions (IC50 = 430 μM). We observe that p19 and suramin are compatible inhibitors of RNA silencing in human hepatoma cells. Our data suggests that at least some inhibitors of AGO may be used in combination with p19 to inhibit RNA silencing at different points in the pathway.
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9
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Chen CD, La M, Zhou BB. Strategies for Designing of Electrochemical MicroRNA Genesensors Based on the Difference in the Structure of RNA and DNA. INT J ELECTROCHEM SC 2014; 9:7228-7238. [DOI: 10.1016/s1452-3981(23)10962-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
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10
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He YC, Yin BC, Jiang L, Ye BC. The rapid detection of microRNA based on p19-enhanced fluorescence polarization. Chem Commun (Camb) 2014; 50:6236-9. [PMID: 24788879 DOI: 10.1039/c4cc00705k] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Via a molecular caliper p19 protein, we have developed an amplified fluorescence polarization method for rapid microRNA detection. This proposed assay has several intrinsic features including rapidity, simplicity, and accuracy.
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Affiliation(s)
- Yuan-Chen He
- Lab of Biosystem and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science & Technology, Shanghai 200237, P.R. China.
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11
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Vargason JM, Burch CJ, Wilson JW. Identification and RNA binding characterization of plant virus RNA silencing suppressor proteins. Methods 2013; 64:88-93. [PMID: 23981361 DOI: 10.1016/j.ymeth.2013.08.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Revised: 08/06/2013] [Accepted: 08/13/2013] [Indexed: 10/26/2022] Open
Abstract
Suppression is a common mechanism employed by viruses to evade the antiviral effects of the host's RNA silencing pathway. The activity of suppression has commonly been localized to gene products in the virus, but the variety of mechanisms used in suppression by these viral proteins spans nearly the complete biochemical pathway of RNA silencing in the host. This review describes the agrofiltration assay and a slightly modified version of the agro-infiltration assay called co-infiltration, which are common methods used to observe RNA silencing and identify viral silencing suppressor proteins in plants, respectively. In addition, this review will provide an overview of two methods, electrophoretic mobility shift assay and fluorescence polarization, used to assess the binding of a suppressor protein to siRNA which has been shown to be a general mechanism to suppress RNA silencing by plant viruses.
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Affiliation(s)
- Jeffrey M Vargason
- Department of Biology and Chemistry, George Fox University, 414 North Meridian Street, Newberg, OR 97132, USA.
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12
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A new insight into electrochemical microRNA detection: a molecular caliper, p19 protein. Biosens Bioelectron 2013; 48:165-71. [PMID: 23680935 DOI: 10.1016/j.bios.2013.04.011] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Revised: 03/28/2013] [Accepted: 04/08/2013] [Indexed: 11/21/2022]
Abstract
microRNA (miRNA) has drawn a great attention in biomedical research due to its functions on biological processes. Detection of miRNAs is a big challenge since the amount present in real samples is very low and the length of them is short. In this study, for the first time an electrochemical biosensor for detection of mir21 using the oxidation signal of protein 19 (p19) as a molecular caliper was designed. The proposed method enables detection of mir21 in direct, rapid, sensitive, inexpensive and label-free way. Binding specificity of the p19 to 20-23 base pair length double stranded RNA (dsRNA) and direct/water-mediated intermolecular contacts between the fusion protein and miRNA allows detection of miRNA-antimiRNA hybrid structure. The detection of mir21 was achieved in picomole sensitivity through the changes of intrinsic p19 oxidation signals observed at +0.80 V with Differential Pulse Voltammetry (DPV) and the specifity of the designed sensor was proved by control studies.
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13
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Danielson DC, Pezacki JP. Studying the RNA silencing pathway with the p19 protein. FEBS Lett 2013; 587:1198-205. [PMID: 23376479 DOI: 10.1016/j.febslet.2013.01.036] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Revised: 01/17/2013] [Accepted: 01/18/2013] [Indexed: 01/05/2023]
Abstract
The origins of the RNA silencing pathway are in defense against invading viruses and in response, viruses have evolved counter-measures to interfere with the host pathway. The p19 protein is expressed by tombusviruses as a suppressor of RNA silencing and functions to sequester small RNA duplexes, thereby preventing induction of the pathway. p19 exhibits size-specific and sequence-independent binding of its small RNA ligands, binding with high affinity to duplexes 20-22 nucleotides long. p19's binding specificity and its ability to sequester small RNAs has made it a unique protein-based tool for probing the molecular mechanisms of the highly complex RNA silencing pathway in a variety of systems. Furthermore, protein engineering of this 'molecular caliper' promises novel applications in biotechnology and medicine where small RNA molecules are of remarkable interest given their potent gene regulatory abilities.
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Affiliation(s)
- Dana C Danielson
- Department of Biochemistry, Microbiology & Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Canada K1H 8M5
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14
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Fujii T, Urushihara M, Kashida H, Ito H, Liang X, Yagi-Utsumi M, Kato K, Asanuma H. Reversed assembly of dyes in an RNA duplex compared with those in DNA. Chemistry 2012; 18:13304-13. [PMID: 22996355 DOI: 10.1002/chem.201201956] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2012] [Indexed: 12/26/2022]
Abstract
We prepared reversed dye clusters by hybridizing two RNA oligomers, each of which tethered dyes (Methyl Red, 4'-methylthioazobenzene, and thiazole orange) on D-threoninols (threoninol nucleotides) at the center of their strands. NMR spectroscopic analyses revealed that two dyes from each strand were axially stacked in an antiparallel manner to each other in the duplex, and were located adjacent to the 3'-side of a natural nucleobase. Interestingly, this positional relationship of the dyes was completely the opposite of that assembled in DNA that we reported previously: dyes in DNA were located adjacent to the 5'-side of a natural nucleobase. This observation was also consistent with the circular dichroism of dimerized dyes in which the Cotton effect of the dyes (i.e., the winding properties of two dyes) was inverted in RNA relative to that in DNA. Further spectroscopic analyses revealed that clustering of the dyes on RNA duplexes induced distinct hypsochromicity and narrowing of the band, thus demonstrating that the dyes were axially stacked (i.e., H-aggregates) even on an A-type helix. On the basis of these results, we also prepared heterodimers of a fluorophore (thiazole orange) and quencher (Methyl Red) in an RNA duplex. Fluorescence from thiazole orange was found to be strongly quenched by Methyl Red due to the excitonic interaction, so that the ratio of fluorescent intensities of the RNA-thiazole orange conjugate with and without its complementary strand carrying a quencher became as high as 27. We believe that these RNA-dye conjugates are potentially useful probes for real-time monitoring of RNA interference (RNAi) mechanisms.
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Affiliation(s)
- Taiga Fujii
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
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15
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Cheng J, Danielson DC, Nasheri N, Singaravelu R, Pezacki JP. Enhanced specificity of the viral suppressor of RNA silencing protein p19 toward sequestering of human microRNA-122. Biochemistry 2011; 50:7745-55. [PMID: 21819044 DOI: 10.1021/bi2008273] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Tombusviruses express a 19 kDa protein (p19) that, as a dimeric protein, suppresses the RNAs silencing pathway during infection by binding short-interfering RNA (siRNA) and preventing their association with the RNA-induced silencing complex (RISC). The p19 protein can bind to both endogenous and synthetic siRNAs with a high degree of size selectivity but with little sequence dependence. It also binds to other endogenous small RNAs such as microRNAs (miRNAs) but with lower affinity than to canonical siRNAs. It has become apparent, however, that miRNAs play a large role in gene regulation; their influence extends to expression and processing that affects virtually all eukaryotic processes. In order to develop new tools to study endogenous small RNAs, proteins that suppress specific miRNAs are required. Herein we describe mutational analysis of the p19 binding surface with the aim of creating p19 mutants with increased affinity for miR-122. By site-directed mutagenesis of a single residue, we describe p19 mutants with a nearly 50-fold increased affinity for miR-122 without altering the affinity for siRNA. Upon further mutational analysis of this site, we postulate that the higher affinity relies on hydrogen-bonding interactions but can be sterically hindered by residues with bulky side chains. Finally, we demonstrate the effectiveness of a mutant p19, p19-T111S, at sequestering miR-122 in human hepatoma cell lines, as compared to wild-type p19. Overall, our results suggest that p19 can be engineered to enhance its affinity toward specific small RNA molecules, particularly noncanonical miRNAs that are distinguishable based on locations of base-pair mismatches. The p19-T111S mutant also represents a new tool for the study of the function of miR-122 in post-transcriptional silencing in the human liver.
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Affiliation(s)
- Jenny Cheng
- Steacie Institute for Molecular Sciences, National Research Council of Canada, Ottawa, Canada K1A 0R6
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16
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Nasheri N, Cheng J, Singaravelu R, Wu P, McDermott MT, Pezacki JP. An enzyme-linked assay for the rapid quantification of microRNAs based on the viral suppressor of RNA silencing protein p19. Anal Biochem 2011; 412:165-72. [DOI: 10.1016/j.ab.2011.01.030] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2010] [Revised: 01/24/2011] [Accepted: 01/25/2011] [Indexed: 12/21/2022]
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17
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van der Wiel IM, Cheng J, Koukiekolo R, Lyn RK, Stevens N, O'Connor N, Turro NJ, Pezacki JP. FLEth RNA intercalating probe is a convenient reporter for small interfering RNAs. J Am Chem Soc 2009; 131:9872-3. [PMID: 19583254 DOI: 10.1021/ja902636m] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Here we report that the phenanthridine derivative covalently linked to a fluorescein moiety (FLEth) can act as a fluorescence based probe for duplex short interfering RNA (siRNA) and that this probe can also be used to report on protein-RNA interactions. A fluorescence resonance energy transfer (FRET) signal that is observed at 600 nm occurs when FLEth is complexed with siRNA. At least 2 molecules of FLEth can bind to 21 nt duplex siRNA, and the dissociation constants for these interactions are reported. We find that FLEth can also report on the interaction of siRNAs with the Carnation Italian ringspot viral suppressor of RNA silencing p19. FLEth does not bind to the siRNA-p19 complex nor can p19 bind to the siRNA-FLEth complex; rather FLEth can report on the fraction of siRNA that is unbound. FLEth can also bind siRNA in delivery systems such as liposomes. Once the siRNA reaches the interior of Huh 7.5 cells, FLEth dissociates from the siRNA and is found in the nucleoli suggesting that FLEth cannot bind to siRNAs that are associated with the RNA silencing machinery.
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Affiliation(s)
- Ingrid M van der Wiel
- Steacie Institute for Molecular Sciences, National Research Council, 100 Sussex Drive, Ottawa, ON, Canada K1A 0R6
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18
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Cheng J, Koukiekolo R, Kieliszkiewicz K, Sagan SM, Pezacki JP. Cysteine residues of Carnation Italian Ringspot virus p19 suppressor of RNA silencing maintain global structural integrity and stability for siRNA binding. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1794:1197-203. [DOI: 10.1016/j.bbapap.2009.03.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2009] [Revised: 03/06/2009] [Accepted: 03/17/2009] [Indexed: 01/05/2023]
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19
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Koukiekolo R, Jakubek ZJ, Cheng J, Sagan SM, Pezacki JP. Studies of a viral suppressor of RNA silencing p19-CFP fusion protein: A FRET-based probe for sensing double-stranded fluorophore tagged small RNAs. Biophys Chem 2009; 143:166-9. [DOI: 10.1016/j.bpc.2009.05.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2009] [Revised: 05/06/2009] [Accepted: 05/06/2009] [Indexed: 01/14/2023]
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Hsieh YC, Omarov RT, Scholthof HB. Diverse and newly recognized effects associated with short interfering RNA binding site modifications on the Tomato bushy stunt virus p19 silencing suppressor. J Virol 2009; 83:2188-200. [PMID: 19052093 PMCID: PMC2643727 DOI: 10.1128/jvi.02186-08] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2008] [Accepted: 11/21/2008] [Indexed: 12/15/2022] Open
Abstract
The Tomato bushy stunt virus-encoded P19 forms dimers that bind duplex short interfering RNAs (siRNAs) to suppress RNA silencing. P19 is also involved in multiple host-specific activities, including the elicitation of symptoms, and in local and/or systemic spread. To study the correlation between those various roles and the siRNA binding by P19, predicted siRNA-interacting sites were modified. Twenty-two mutants were generated and inoculated onto Nicotiana benthamiana plants, to reveal that (i) they were all infectious, (ii) symptom differences did not correlate strictly with mutation-associated variation in P19 accumulation, and (iii) substitutions affecting a central domain of P19 generally exhibited symptoms more severe than for mutations affecting peripheral regions. Three mutants selected to represent separate phenotypic categories all displayed a substantially reduced ability to sequester siRNA. Consequently, these three mutants were compromised for systemic virus spread in P19-dependent hosts but had differential plant species-dependent effects on the symptom severity. One mutant in particular caused relatively exacerbated symptoms, exemplified by extensive morphological leaf deformations in N. benthamiana; this was especially remarkable because P19 was undetectable. Another striking feature of this mutant was that only within a few days after infection, viral RNA was cleared by silencing. One more original property was that host RNAs and proteins (notably, the P19-interactive Hin19 protein) were also susceptible to degradation in these infected N. benthamiana plants but not in spinach. In conclusion, even though siRNA binding by P19 is a key functional property, compromised siRNA sequestration can result in novel and diverse host-dependent properties.
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Affiliation(s)
- Yi-Cheng Hsieh
- Department of Plant Pathology and Microbiology, Texas A&M University, 2132 TAMU, College Station, Texas 77843, USA
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