A Viral Nuclear Noncoding RNA Binds Re-localized Poly(A) Binding Protein and Is Required for Late KSHV Gene Expression


During the lytic phase of infection, the gamma herpesvirus Kaposi's Sarcoma-Associated Herpesvirus (KSHV) expresses a highly abundant, 1.1 kb nuclear noncoding RNA of unknown function. We observe that this polyadenylated nuclear (PAN) RNA avidly binds host poly(A)-binding protein C1 (PABPC1), which normally functions in the cytoplasm to bind the poly(A) tails of mRNAs, regulating mRNA stability and translation efficiency. During the lytic phase of KSHV infection, PABPC1 is re-localized to the nucleus as a consequence of expression of the viral shutoff exonuclease (SOX) protein; SOX also mediates the host shutoff effect in which host mRNAs are downregulated while viral mRNAs are selectively expressed. We show that whereas PAN RNA is not required for the host shutoff effect or for PABPC1 re-localization, SOX strongly upregulates the levels of PAN RNA in transient transfection experiments. This upregulation is destroyed by the same SOX mutation that ablates the host shutoff effect and PABPC1 nuclear re-localization or by removal of the poly(A) tail of PAN. In cells induced into the KSHV lytic phase, depletion of PAN RNA using RNase H-targeting antisense oligonucleotides reveals that it is necessary for the production of late viral proteins from mRNAs that are themselves polyadenylated. Our results add to the repertoire of functions ascribed to long noncoding RNAs and suggest a mechanism of action for nuclear noncoding RNAs in gamma herpesvirus infection.


Vyšlo v časopise: A Viral Nuclear Noncoding RNA Binds Re-localized Poly(A) Binding Protein and Is Required for Late KSHV Gene Expression. PLoS Pathog 7(10): e32767. doi:10.1371/journal.ppat.1002300
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.ppat.1002300

Souhrn

During the lytic phase of infection, the gamma herpesvirus Kaposi's Sarcoma-Associated Herpesvirus (KSHV) expresses a highly abundant, 1.1 kb nuclear noncoding RNA of unknown function. We observe that this polyadenylated nuclear (PAN) RNA avidly binds host poly(A)-binding protein C1 (PABPC1), which normally functions in the cytoplasm to bind the poly(A) tails of mRNAs, regulating mRNA stability and translation efficiency. During the lytic phase of KSHV infection, PABPC1 is re-localized to the nucleus as a consequence of expression of the viral shutoff exonuclease (SOX) protein; SOX also mediates the host shutoff effect in which host mRNAs are downregulated while viral mRNAs are selectively expressed. We show that whereas PAN RNA is not required for the host shutoff effect or for PABPC1 re-localization, SOX strongly upregulates the levels of PAN RNA in transient transfection experiments. This upregulation is destroyed by the same SOX mutation that ablates the host shutoff effect and PABPC1 nuclear re-localization or by removal of the poly(A) tail of PAN. In cells induced into the KSHV lytic phase, depletion of PAN RNA using RNase H-targeting antisense oligonucleotides reveals that it is necessary for the production of late viral proteins from mRNAs that are themselves polyadenylated. Our results add to the repertoire of functions ascribed to long noncoding RNAs and suggest a mechanism of action for nuclear noncoding RNAs in gamma herpesvirus infection.


Zdroje

1. VermaSCRobertsonES 2003 Molecular biology and pathogenesis of Kaposi sarcoma-associated herpesvirus. FEMS Microbiol Lett 222 155 163

2. GanemD 2006 KSHV infection and the pathogenesis of Kaposi's sarcoma. Annu Rev Pathol 1 273 296

3. SunRLinSFGradovilleLMillerG 1996 Polyadenylylated nuclear RNA encoded by Kaposi sarcoma-associated herpesvirus. Proc Natl Acad Sci U S A 93 11883 11888

4. ZhongWGanemD 1997 Characterization of ribonucleoprotein complexes containing an abundant polyadenylated nuclear RNA encoded by Kaposi's sarcoma-associated herpesvirus (human herpesvirus 8). J Virol 71 1207 1212

5. ConradNKSteitzJA 2005 A Kaposi's sarcoma virus RNA element that increases the nuclear abundance of intronless transcripts. EMBO J 24 1831 1841

6. ConradNKMiliSMarshallELShuMDSteitzJA 2006 Identification of a rapid mammalian deadenylation-dependent decay pathway and its inhibition by a viral RNA element. Mol Cell 24 943 953

7. ConradNKShuMDUyhaziKESteitzJA 2007 Mutational analysis of a viral RNA element that counteracts rapid RNA decay by interaction with the polyadenylate tail. Proc Natl Acad Sci U S A 104 10412 10417

8. PawlickiJMSteitzJA 2008 Primary microRNA transcript retention at sites of transcription leads to enhanced microRNA production. J Cell Biol 182 61 76

9. Mitton-FryRMDeGregorioSJWangJSteitzTASteitzJA 2010 Poly(A) tail recognition by a viral RNA element through assembly of a triple helix. Science 330 1244 1247

10. BernsteinPPeltzSWRossJ 1989 The poly(A)-poly(A)-binding protein complex is a major determinant of mRNA stability in vitro. Mol Cell Biol 9 659 670

11. FordLPBaggaPSWiluszJ 1997 The poly(A) tail inhibits the assembly of a 3′-to-5′ exonuclease in an in vitro RNA stability system. Mol Cell Biol 17 398 406

12. KornerCGWormingtonMMuckenthalerMSchneiderSDehlinE 1998 The deadenylating nuclease (DAN) is involved in poly(A) tail removal during the meiotic maturation of Xenopus oocytes. EMBO J 17 5427 5437

13. WiluszCJGaoMJonesCLWiluszJPeltzSW 2001 Poly(A)-binding proteins regulate both mRNA deadenylation and decapping in yeast cytoplasmic extracts. RNA 7 1416 1424

14. MangusDAEvansMCJacobsonA 2003 Poly(A)-binding proteins: multifunctional scaffolds for the post-transcriptional control of gene expression. Genome Biol 4 223

15. TarunSZJrSachsAB 1996 Association of the yeast poly(A) tail binding protein with translation initiation factor eIF-4G. EMBO J 15 7168 7177

16. TarunSZJrWellsSEDeardorffJASachsAB 1997 Translation initiation factor eIF4G mediates in vitro poly(A) tail-dependent translation. Proc Natl Acad Sci U S A 94 9046 9051

17. WellsSEHillnerPEValeRDSachsAB 1998 Circularization of mRNA by eukaryotic translation initiation factors. Mol Cell 2 135 140

18. KannoTSatoYSataTKatanoH 2006 Expression of Kaposi's sarcoma-associated herpesvirus-encoded K10/10.1 protein in tissues and its interaction with poly(A)-binding protein. Virology 352 100 109

19. LeeYJGlaunsingerBA 2009 Aberrant herpesvirus-induced polyadenylation correlates with cellular messenger RNA destruction. PLoS Biol 7 e1000107

20. AriasCWalshDHarbellJWilsonACMohrI 2009 Activation of host translational control pathways by a viral developmental switch. PLoS Pathog 5 e1000334

21. GlaunsingerBGanemD 2004 Highly selective escape from KSHV-mediated host mRNA shutoff and its implications for viral pathogenesis. J Exp Med 200 391 398

22. GlaunsingerBGanemD 2004 Lytic KSHV infection inhibits host gene expression by accelerating global mRNA turnover. Mol Cell 13 713 723

23. ChandrianiSGanemD 2007 Host transcript accumulation during lytic KSHV infection reveals several classes of host responses. PLoS ONE 2 e811

24. KumarGRGlaunsingerBA 2010 Nuclear import of cytoplasmic poly(A) binding protein restricts gene expression via hyperadenylation and nuclear retention of mRNA. Mol Cell Biol 30 4996 5008

25. BryanBADysonOFAkulaSM 2006 Identifying cellular genes crucial for the reactivation of Kaposi's sarcoma-associated herpesvirus latency. J Gen Virol 87 519 529

26. McAllisterSCHansenSGMessaoudiINikolich-ZugichJMosesAV 2005 Increased efficiency of phorbol ester-induced lytic reactivation of Kaposi's sarcoma-associated herpesvirus during S phase. J Virol 79 2626 2630

27. LernerEALernerMRJanewayCAJrSteitzJA 1981 Monoclonal antibodies to nucleic acid-containing cellular constituents: probes for molecular biology and autoimmune disease. Proc Natl Acad Sci U S A 78 2737 2741

28. IdeueTHinoKKitaoSYokoiTHiroseT 2009 Efficient oligonucleotide-mediated degradation of nuclear noncoding RNAs in mammalian cultured cells. RNA 15 1578 1587

29. SasakiYTIdeueTSanoMMituyamaTHiroseT 2009 MENepsilon/beta noncoding RNAs are essential for structural integrity of nuclear paraspeckles. Proc Natl Acad Sci U S A 106 2525 2530

30. YooSMAhnAKSeoTHongHBChungMA 2008 Centrifugal enhancement of Kaposi's sarcoma-associated virus infection of human endothelial cells in vitro. J Virol Methods 154 160 166

31. SunRLinSFGradovilleLYuanYZhuF 1998 A viral gene that activates lytic cycle expression of Kaposi's sarcoma-associated herpesvirus. Proc Natl Acad Sci U S A 95 10866 10871

32. StaudtMRDittmerDP 2007 The Rta/Orf50 transactivator proteins of the gamma-herpesviridae. Curr Top Microbiol Immunol 312 71 100

33. LukacDMRenneRKirshnerJRGanemD 1998 Reactivation of Kaposi's sarcoma-associated herpesvirus infection from latency by expression of the ORF 50 transactivator, a homolog of the EBV R protein. Virology 252 304 312

34. ConradNK 2008 Chapter 15. Co-immunoprecipitation techniques for assessing RNA-protein interactions in vivo. Methods Enzymol 449 317 342

35. GlaunsingerBChavezLGanemD 2005 The exonuclease and host shutoff functions of the SOX protein of Kaposi's sarcoma-associated herpesvirus are genetically separable. J Virol 79 7396 7401

36. CovarrubiasSRichnerJMClydeKLeeYJGlaunsingerBA 2009 Host shutoff is a conserved phenotype of gammaherpesvirus infection and is orchestrated exclusively from the cytoplasm. J Virol 83 9554 9566

37. KumarGRShumLGlaunsingerBA 2011 Importin α-mediated nuclear import of cytoplasmic poly(A) binding protein occurs as a direct consequence of cytoplasmic mRNA depletion. Mol Cell Biol 31 3113 3125

38. WiluszJEFreierSMSpectorDL 2008 3′ end processing of a long nuclear-retained noncoding RNA yields a tRNA-like cytoplasmic RNA. Cell 135 919 932

39. SunwooHDingerMEWiluszJEAmaralPPMattickJS 2009 MEN epsilon/beta nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles. Genome Res 19 347 359

40. WangHWSharpTVKoumiAKoentgesGBoshoffC 2002 Characterization of an anti-apoptotic glycoprotein encoded by Kaposi's sarcoma-associated herpesvirus which resembles a spliced variant of human survivin. EMBO J 21 2602 2615

41. VieiraJO'HearnPM 2004 Use of the red fluorescent protein as a marker of Kaposi's sarcoma-associated herpesvirus lytic gene expression. Virology 325 225 240

42. MyoungJGanemD 2011 Generation of a doxycycline-inducible KSHV producer cell line of endothelial origin: Maintenance of tight latency with efficient reactivation upon induction. J Virol Methods 174 12 21

43. KedesDHGanemD 1997 Sensitivity of Kaposi's sarcoma-associated herpesvirus replication to antiviral drugs. Implications for potential therapy. J Clin Invest 99 2082 2086

44. FauldsDHeelRC 1990 Ganciclovir. A review of its antiviral activity, pharmacokinetic properties and therapeutic efficacy in cytomegalovirus infections. Drugs 39 597 638

45. HollandLEAndersonKPShipmanCJrWagnerEK 1980 Viral DNA synthesis is required for the efficient expression of specific herpes simplex virus type 1 mRNA species. Virology 101 10 24

46. PowellKLPurifoyDJCourtneyRJ 1975 The synthesis of herpes simplex virus proteins in the absence of virus DNA synthesis. Biochem Biophys Res Commun 66 262 271

47. JonesPCRoizmanB 1979 Regulation of herpesvirus macromolecular synthesis. VIII. The transcription program consists of three phases during which both extent of transcription and accumulation of RNA in the cytoplasm are regulated. J Virol 31 299 314

48. ZhangYJBonaparteRSPatelDSteinDAIversenPL 2008 Blockade of viral interleukin-6 expression of Kaposi's sarcoma-associated herpesvirus. Mol Cancer Ther 7 712 720

49. GregorySMWestJADillonPJHilscherCDittmerDP 2009 Toll-like receptor signaling controls reactivation of KSHV from latency. Proc Natl Acad Sci U S A 106 11725 11730

50. GorlachMBurdCGDreyfussG 1994 The mRNA poly(A)-binding protein: localization, abundance, and RNA-binding specificity. Exp Cell Res 211 400 407

51. RoweMGlaunsingerBvan LeeuwenDZuoJSweetmanD 2007 Host shutoff during productive Epstein-Barr virus infection is mediated by BGLF5 and may contribute to immune evasion. Proc Natl Acad Sci U S A 104 3366 3371

52. BoyneJRJacksonBRWhitehouseA 2010 ORF57: Master regulator of KSHV mRNA biogenesis. Cell Cycle 9 2702 2703

53. BoyneJRColganKJWhitehouseA 2008 Recruitment of the complete hTREX complex is required for Kaposi's sarcoma-associated herpesvirus intronless mRNA nuclear export and virus replication. PLoS Pathog 4 e1000194

54. SahinBBPatelDConradNK 2010 Kaposi's sarcoma-associated herpesvirus ORF57 protein binds and protects a nuclear noncoding RNA from cellular RNA decay pathways. PLoS Pathog 6 e1000799

55. JoachimsMVan BreugelPCLloydRE 1999 Cleavage of poly(A)-binding protein by enterovirus proteases concurrent with inhibition of translation in vitro. J Virol 73 718 727

56. KerekatteVKeiperBDBadorffCCaiAKnowltonKU 1999 Cleavage of Poly(A)-binding protein by coxsackievirus 2A protease in vitro and in vivo: another mechanism for host protein synthesis shutoff? J Virol 73 709 717

57. Kuyumcu-MartinezMBelliotGSosnovtsevSVChangKOGreenKY 2004 Calicivirus 3C-like proteinase inhibits cellular translation by cleavage of poly(A)-binding protein. J Virol 78 8172 8182

58. PironMVendePCohenJPoncetD 1998 Rotavirus RNA-binding protein NSP3 interacts with eIF4GI and evicts the poly(A) binding protein from eIF4F. EMBO J 17 5811 5821

59. HarbMBeckerMMVitourDBaronCHVendeP 2008 Nuclear localization of cytoplasmic poly(A)-binding protein (PABP-C1) upon rotavirus infection involves interaction of NSP3 with eIF4G and RoXaN. J Virol

60. MonteroHRojasMAriasCFLopezS 2008 Rotavirus infection induces the phosphorylation of eIF2alpha but prevents the formation of stress granules. J Virol 82 1496 1504

61. BlakqoriGvan KnippenbergIElliottRM 2009 Bunyamwera orthobunyavirus S-segment untranslated regions mediate poly(A) tail-independent translation. J Virol 83 3637 3646

62. ChenZLiYKrugRM 1999 Influenza A virus NS1 protein targets poly(A)-binding protein II of the cellular 3′-end processing machinery. EMBO J 18 2273 2283

63. HuangYCarmichaelGG 1996 Role of polyadenylation in nucleocytoplasmic transport of mRNA. Mol Cell Biol 16 1534 1542

64. FortesPBelosoAOrtinJ 1994 Influenza virus NS1 protein inhibits pre-mRNA splicing and blocks mRNA nucleocytoplasmic transport. EMBO J 13 704 712

65. AlexanderLDenekampLKnappAAuerbachMRDamaniaB 2000 The primary sequence of rhesus monkey rhadinovirus isolate 26-95: sequence similarities to Kaposi's sarcoma-associated herpesvirus and rhesus monkey rhadinovirus isolate 17577. J Virol 74 3388 3398

66. DittmerDPGonzalezCMVahrsonWDeWireSMHines-BoykinR 2005 Whole-genome transcription profiling of rhesus monkey rhadinovirus. J Virol 79 8637 8650

67. SchneiderRJWeinbergerCShenkT 1984 Adenovirus VAI RNA facilitates the initiation of translation in virus-infected cells. Cell 37 291 298

68. LuSCullenBR 2004 Adenovirus VA1 noncoding RNA can inhibit small interfering RNA and MicroRNA biogenesis. J Virol 78 12868 12876

69. AfoninaEStauberRPavlakisGN 1998 The human poly(A)-binding protein 1 shuttles between the nucleus and the cytoplasm. J Biol Chem 273 13015 13021

70. BruneCMunchelSEFischerNPodtelejnikovAVWeisK 2005 Yeast poly(A)-binding protein Pab1 shuttles between the nucleus and the cytoplasm and functions in mRNA export. RNA 11 517 531

71. ChekanovaJABelostotskyDA 2003 Evidence that poly(A) binding protein has an evolutionarily conserved function in facilitating mRNA biogenesis and export. RNA 9 1476 1490

72. HosodaNLejeuneFMaquatLE 2006 Evidence that poly(A) binding protein C1 binds nuclear pre-mRNA poly(A) tails. Mol Cell Biol 26 3085 3097

73. ThakurtaAGHo YoonJDharR 2002 Schizosaccharomyces pombe spPABP, a homologue of Saccharomyces cerevisiae Pab1p, is a non-essential, shuttling protein that facilitates mRNA export. Yeast 19 803 810

74. MeyerSUrbankeCWahleE 2002 Equilibrium studies on the association of the nuclear poly(A) binding protein with poly(A) of different lengths. Biochemistry 41 6082 6089

75. HillerenPParkerR 2001 Defects in the mRNA export factors Rat7p, Gle1p, Mex67p, and Rat8p cause hyperadenylation during 3′-end formation of nascent transcripts. RNA 7 753 764

76. JensenTHPatricioKMcCarthyTRosbashM 2001 A block to mRNA nuclear export in S. cerevisiae leads to hyperadenylation of transcripts that accumulate at the site of transcription. Mol Cell 7 887 898

77. WyersFRougemailleMBadisGRousselleJCDufourME 2005 Cryptic pol II transcripts are degraded by a nuclear quality control pathway involving a new poly(A) polymerase. Cell 121 725 737

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