A Human Torque Teno Virus Encodes a MicroRNA That Inhibits Interferon Signaling
Torque teno viruses (TTVs) are a group of viruses with small, circular DNA genomes. Members of this family are thought to ubiquitously infect humans, although causal disease associations are currently lacking. At present, there is no understanding of how infection with this diverse group of viruses is so prevalent. Using a combined computational and synthetic approach, we predict and identify miRNA-coding regions in diverse human TTVs and provide evidence for TTV miRNA production in vivo. The TTV miRNAs are transcribed by RNA polymerase II, processed by Drosha and Dicer, and are active in RISC. A TTV mutant defective for miRNA production replicates as well as wild type virus genome; demonstrating that the TTV miRNA is dispensable for genome replication in a cell culture model. We demonstrate that a recombinant TTV genome is capable of expressing an exogenous miRNA, indicating the potential utility of TTV as a small RNA vector. Gene expression profiling of host cells identifies N-myc (and STAT) interactor (NMI) as a target of a TTV miRNA. NMI transcripts are directly regulated through a binding site in the 3′UTR. SiRNA knockdown of NMI contributes to a decreased response to interferon signaling. Consistent with this, we show that a TTV miRNA mediates a decreased response to IFN and increased cellular proliferation in the presence of IFN. Thus, we add Annelloviridae to the growing list of virus families that encode miRNAs, and suggest that miRNA-mediated immune evasion can contribute to the pervasiveness associated with some of these viruses.
Vyšlo v časopise:
A Human Torque Teno Virus Encodes a MicroRNA That Inhibits Interferon Signaling. PLoS Pathog 9(12): e32767. doi:10.1371/journal.ppat.1003818
Kategorie:
Research Article
prolekare.web.journal.doi_sk:
https://doi.org/10.1371/journal.ppat.1003818
Souhrn
Torque teno viruses (TTVs) are a group of viruses with small, circular DNA genomes. Members of this family are thought to ubiquitously infect humans, although causal disease associations are currently lacking. At present, there is no understanding of how infection with this diverse group of viruses is so prevalent. Using a combined computational and synthetic approach, we predict and identify miRNA-coding regions in diverse human TTVs and provide evidence for TTV miRNA production in vivo. The TTV miRNAs are transcribed by RNA polymerase II, processed by Drosha and Dicer, and are active in RISC. A TTV mutant defective for miRNA production replicates as well as wild type virus genome; demonstrating that the TTV miRNA is dispensable for genome replication in a cell culture model. We demonstrate that a recombinant TTV genome is capable of expressing an exogenous miRNA, indicating the potential utility of TTV as a small RNA vector. Gene expression profiling of host cells identifies N-myc (and STAT) interactor (NMI) as a target of a TTV miRNA. NMI transcripts are directly regulated through a binding site in the 3′UTR. SiRNA knockdown of NMI contributes to a decreased response to interferon signaling. Consistent with this, we show that a TTV miRNA mediates a decreased response to IFN and increased cellular proliferation in the presence of IFN. Thus, we add Annelloviridae to the growing list of virus families that encode miRNAs, and suggest that miRNA-mediated immune evasion can contribute to the pervasiveness associated with some of these viruses.
Zdroje
1. King AMQ, Lefkowitz E, Adams MJ, Carstens EB (2012) Family - Anelloviridae. In: King AMQ, Lefkowitz E, Carstens EB, editors. Virus Taxonomy. San Diego: Elsevier. pp. 331–341.
2. Biagini P (2009) Classification of TTV and Related Viruses (Anelloviruses). In: de Villiers E-M, zur Hausen H, editors. TT Viruses. Current Topics in Microbiology and Immunology. Berlin: Springer. Vol. 331. pp. 21–33.
3. Zur Hausen H, de Villiers E-M (2009) TT Viruses: Oncogenic or Tumor-Suppressive Properties? In: de Villiers E-M, zur Hausen H, editors. TT Viruses. Current Topics in Microbiology and Immunology. Berlin: Springer. Vol. 331. pp.109–116.
4. LeppikL, GunstK, LehtinenM, DillnerJ, StrekerK, et al. (2007) In Vivo and In Vitro Intragenomic Rearrangement of TT Viruses. J Virol 81: 9346–9356.
5. NishizawaT, OkamotoH, KonishiK, YoshizawaH, MiyakawaY, et al. (1997) A Novel DNA Virus (TTV) Associated with Elevated Transaminase Levels in Posttransfusion Hepatitis of Unknown Etiology. Biochem Biophys Res Commun 241: 92–97.
6. Okamoto H (2009) History of Discoveries and Pathogenicity of TT Viruses. In: de Villiers E-M, zur Hausen H, editors. TT Viruses. Current Topics in Microbiology and Immunology. Berlin: Springer. Vol. 331. pp.1–20.
7. LeeRC, FeinbaumRL, AmbrosV (1993) The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75: 843–854.
8. CullenBR (2006) Viruses and microRNAs. Nat Genet 38: S25–S30.
9. KincaidRP, SullivanCS (2012) Virus-Encoded microRNAs: An Overview and a Look to the Future. PLoS Pathog 8: e1003018.
10. CullenBR (2013) MicroRNAs as mediators of viral evasion of the immune system. Nat Immunol 14: 205–210.
11. BossIW, RenneR (2010) Viral miRNAs: tools for immune evasion. Host–Microbe Interactions FungiParasitesViruses 13: 540–545.
12. KincaidRP, BurkeJM, SullivanCS (2012) RNA virus microRNA that mimics a B-cell oncomiR. Proc Natl Acad Sci 109: 3077–3082.
13. ZhuM, JohnS, BergM, LeonardWJ (1999) Functional Association of Nmi with Stat5 and Stat1 in IL-2- and IFN γ-Mediated Signaling. Cell 96: 121–130.
14. WangJ, WangY, LiuJ, DingL, ZhangQ, et al. (2012) A critical role of N-myc and STAT interactor (Nmi) in foot-and-mouth disease virus (FMDV) 2C-induced apoptosis. Virus Res 170: 59–65.
15. De VilliersE-M, BorkoskySS, KimmelR, GunstK, FeiJ-W (2011) The Diversity of Torque Teno Viruses: In Vitro Replication Leads to the Formation of Additional Replication-Competent Subviral Molecules. J Virol 85: 7284–7295.
16. WheelerDL, BarrettT, BensonDA, BryantSH, CaneseK, et al. (2008) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 36: D13–D21.
17. VazC, AhmadH, SharmaP, GuptaR, KumarL, et al. (2010) Analysis of microRNA transcriptome by deep sequencing of small RNA libraries of peripheral blood. BMC Genomics 11: 288.
18. BartelDP (2004) MicroRNAs: Genomics, Biogenesis, Mechanism, and Function. Cell 116: 281–297.
19. KimVN, HanJ, SiomiMC (2009) Biogenesis of small RNAs in animals. Nat Rev Mol Cell Biol 10: 126–139.
20. AmeresSL, MartinezJ, SchroederR (2007) Molecular Basis for Target RNA Recognition and Cleavage by Human RISC. Cell 130: 101–112.
21. BogerdHP, KarnowskiHW, CaiX, ShinJ, PohlersM, et al. (2010) A Mammalian Herpesvirus Uses Noncanonical Expression and Processing Mechanisms to Generate Viral MicroRNAs. Mol Cell 37: 135–142.
22. CazallaD, XieM, SteitzJA (2011) A Primate Herpesvirus Uses the Integrator Complex to Generate Viral MicroRNAs. Mol Cell 43: 982–992.
23. HanJ, PedersenJS, KwonSC, BelairCD, KimY-K, et al. (2009) Posttranscriptional Crossregulation between Drosha and DGCR8. Cell 136: 75–84.
24. CumminsJM, HeY, LearyRJ, PagliariniR, DiazLA, et al. (2006) The colorectal microRNAome. Proc Natl Acad Sci U S A 103: 3687–3692.
25. PedenKW, PipasJM, Pearson-WhiteS, NathansD (1980) Isolation of mutants of an animal virus in bacteria. Science 209: 1392–1396.
26. SullivanCS, GrundhoffAT, TevethiaS, PipasJM, GanemD (2005) SV40-encoded microRNAs regulate viral gene expression and reduce susceptibility to cytotoxic T cells. Nature 435: 682–686.
27. SullivanCS, SungCK, PackCD, GrundhoffA, LukacherAE, et al. (2009) Murine Polyomavirus encodes a microRNA that cleaves early RNA transcripts but is not essential for experimental infection. Virology 387: 157–167.
28. FabianMR, SonenbergN (2012) The mechanics of miRNA-mediated gene silencing: a look under the hood of miRISC. Nat Struct Mol Biol 19: 586–593.
29. BazziniAA, LeeMT, GiraldezAJ (2012) Ribosome Profiling Shows That miR-430 Reduces Translation Before Causing mRNA Decay in Zebrafish. Science 336: 233–237.
30. LimLP, LauNC, Garrett-EngeleP, GrimsonA, SchelterJM, et al. (2005) Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature 433: 769–773.
31. SamolsMA, SkalskyRL, MaldonadoAM, RivaA, LopezMC, et al. (2007) Identification of Cellular Genes Targeted by KSHV-Encoded MicroRNAs. PLoS Pathog 3: e65.
32. ZiegelbauerJM, SullivanCS, GanemD (2008) Tandem array-based expression screens identify host mRNA targets of virus-encoded microRNAs. Nat Genet 41: 130–134.
33. SuffertG, MaltererG, HausserJ, ViiliäinenJ, FenderA, et al. (2011) Kaposi's Sarcoma Herpesvirus microRNAs Target Caspase 3 and Regulate Apoptosis. PLoS Pathog 7: e1002405.
34. GottweinE, MukherjeeN, SachseC, FrenzelC, MajorosWH, et al. (2007) A viral microRNA functions as an orthologue of cellular miR-155. Nature 450: 1096–1099.
35. HjortsbergL, LindvallC, CorcoranM, ArulampalamV, ChanD, et al. (2007) Phosphoinositide 3-kinase regulates a subset of interferon-alpha-stimulated genes. Exp Cell Res 313: 404–414.
36. PfefferS, ZavolanM, GrasserFA, ChienM, RussoJJ, et al. (2004) Identification of Virus-Encoded MicroRNAs. Science 304: 734–736.
37. FillmoreRA, MitraA, XiY, JuJ, ScammellJ, et al. (2009) Nmi (N-Myc interactor) inhibits Wnt/β-catenin signaling and retards tumor growth. Int J Cancer 125: 556–564.
38. LiZ, HouJ, SunL, WenT, WangL, et al. (2012) NMI mediates transcription-independent ARF regulation in response to cellular stresses. Mol Biol Cell 23: 4635–4646.
39. SeoGJ, FinkLHL, O'HaraB, AtwoodWJ, SullivanCS (2008) Evolutionarily Conserved Function of a Viral MicroRNA. J Virol 82: 9823–9828.
40. KawaiT, AkiraS (2010) The role of pattern-recognition receptors in innate immunity: update on Toll-like receptors. Nat Immunol 11: 373–384 doi:10.1038/ni.1863
41. HinoS, MiyataH (2007) Torque teno virus (TTV): current status. Rev Med Virol 17: 45–57.
42. KatoT, MisashiM, MukaideM, OritoE, OhnoT, et al. (2000) Development of a TT virus DNA quantification system using Real-Time Detection PCR. J Clin Microbiol 38: 94–98.
43. VasilyevE, TrofimovD, TonevitskyA, IlinskyV, KorostinD, et al. (2009) Torque Teno Virus (TTV) distribution in healthy Russian population. Virol J 6: 134.
44. BuckCB, PastranaDV, LowyDR, SchillerJT (2004) Efficient Intracellular Assembly of Papillomaviral Vectors. J Virol 78: 751–757.
45. LinY-T, SullivanCS (2011) Expanding the role of Drosha to the regulation of viral gene expression. Proc Natl Acad Sci 108: 11229–11234.
46. HofackerIL, FontanaW, StadlerPF, BonhoefferLS, TackerM, et al. (1994) Fast folding and comparison of RNA secondary structures. Monatshefte Für Chem Chem Mon 125: 167–188.
47. CockPJA, AntaoT, ChangJT, ChapmanBA, CoxCJ, et al. (2009) Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 25: 1422–1423.
48. McClureLV, LinY-T, SullivanCS (2011) Detection of Viral microRNAs by Northern Blot Analysis. Methods Mol Biol Clifton NJ 721: 153–171.
49. Strauss WM (2001) Preparation of Genomic DNA from Mammalian Tissue. Current Protocols in Molecular Biology. John Wiley & Sons, Inc.
50. WeberK, BolanderM, SarkarG (1998) PIG-B: A homemade monophasic cocktail for the extraction of RNA. Mol Biotechnol 9: 73–77 doi:10.1007/BF02752699
51. DavidM, DzambaM, ListerD, IlieL, BrudnoM (2011) SHRiMP2: Sensitive yet Practical Short Read Mapping. Bioinformatics 27: 1011–1012.
52. ZukerM (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31: 3406–3415.
53. MathewsDH, SabinaJ, ZukerM, TurnerDH (1999) Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J Mol Biol 288: 911–940 doi:10.1006/jmbi.1999.2700
Štítky
Hygiena a epidemiológia Infekčné lekárstvo LaboratóriumČlánok vyšiel v časopise
PLOS Pathogens
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