Virus-derived siRNAs and piRNAs in immunity and pathogenesis

Current Opinion in Virology

Volumn 1, Issue 6, 2011, Pages 533-544

  Ding, Shou Wei ^a   Lu, Rui ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b LOUISIANA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; PIWI INTERACTING RNA; SMALL INTERFERING RNA;

ANTIGEN RECOGNITION; ARTICLE; GENE SEQUENCE; GENE SILENCING; GENETIC TRANSCRIPTION; HUMAN; IMMUNITY; NONHUMAN; POSTTRANSCRIPTIONAL GENE SILENCING; PRIORITY JOURNAL; RNA INTERFERENCE; VIRUS CELL INTERACTION; VIRUS CULTURE; VIRUS PATHOGENESIS;

EID: 82955233640     PISSN: 18796257     EISSN: 18796265     Source Type: Journal    
DOI: 10.1016/j.coviro.2011.10.028     Document Type: Review

References (75)

1. M.C. Siomi, K. Sato, D. Pezic, and A.A. Aravin PIWI-interacting small RNAs: the vanguard of genome defence Nat Rev Mol Cell Biol 12 2011 246 258
2. V.N. Kim, J. Han, and M.C. Siomi Biogenesis of small RNAs in animals Nat Rev Mol Cell Biol 10 2009 126 139
3. X. Chen Small RNAs and their roles in plant development Annu Rev Cell Dev Biol 25 2009 21 44
4. A.J. Hamilton, and D.C. Baulcombe A species of small antisense RNA in posttranscriptional gene silencing in plants Science 286 1999 950 952
5. H.W. Li, W.X. Li, and S.W. Ding Induction and suppression of RNA silencing by an animal virus Science 296 2002 1319 1321 (Pubitemid 34522787)
6. P. Parameswaran, E. Sklan, C. Wilkins, T. Burgon, M.A. Samuel, R. Lu, K.M. Ansel, V. Heissmeyer, S. Einav, and W. Jackson Six RNA viruses and forty-one hosts: viral small RNAs and modulation of small RNA repertoires in vertebrate and invertebrate systems PLoS Pathog 6 2010 e1000764
7. S. Pfeffer, M. Zavolan, F.A. Grasser, M. Chien, J.J. Russo, J. Ju, B. John, A.J. Enright, D. Marks, and C. Sander Identification of virus-encoded microRNAs Science 304 2004 734 736 (Pubitemid 38560879)
8. Q. Wu, Y. Luo, R. Lu, N. Lau, E.C. Lai, W.X. Li, and S.W. Ding Virus discovery by deep sequencing and assembly of virus-derived small silencing RNAs Proc Natl Acad Sci USA 107 2010 1606 1611
9. S.-W. Ding RNA-based antiviral immunity Nat Rev Immunol 10 2010 632 644
10. L.R. Sabin, S.L. Hanna, and S. Cherry Innate antiviral immunity in Drosophila Curr Opin Immunol 22 2010 4 9
11. F. Qu Antiviral role of plant-encoded rna-dependent RNA polymerases revisited with deep sequencing of small interfering RNAs of virus origin Mol Plant Microbe Interact 23 2010 1248 1252
12. B.R. Cullen Herpesvirus microRNAs: phenotypes and functions Curr Opin Virol 1 2011 211 215
13. J.T. Perez, A. Varble, R. Sachidanandam, I. Zlatev, M. Manoharan, A. Garcia-Sastre, and B.R. tenOever Influenza A virus-generated small RNAs regulate the switch from transcription to replication Proc Natl Acad Sci USA 107 2010 11525 11530
14. J.L. Umbach, H.L. Yen, L.L. Poon, and B.R. Cullen Influenza A virus expresses high levels of an unusual class of small viral leader RNAs in infected cells MBio 2010 1
15. S. Mueller, V. Gausson, N. Vodovar, S. Deddouche, L. Troxler, J. Perot, S. Pfeffer, J.A. Hoffmann, M.-C. Saleh, and J.-L. Imler RNAi-mediated immunity provides strong protection against the negative-strand RNA vesicular stomatitis virus in Drosophila Proc Natl Acad Sci 2010
16. Q. Wu, X. Wang, and S.W. Ding Viral suppressors of RNA-based viral immunity: host targets Cell Host Microbe 8 2010 12 15
17. N. Qi, D. Cai, Y. Qiu, J. Xie, Z. Wang, J. Si, J. Zhang, X. Zhou, and Y. Hu RNA binding by a novel helical fold of b2 protein from wuhan nodavirus mediates the suppression of RNA interference and promotes b2 dimerization J Virol 85 2011 9543 9554
18. A. Nayak, B. Berry, M. Tassetto, M. Kunitomi, A. Acevedo, C. Deng, A. Krutchinsky, J. Gross, C. Antoniewski, and R. Andino Cricket paralysis virus antagonizes Argonaute 2 to modulate antiviral defense in Drosophila Nat Struct Mol Biol 2010 advance online publication
19. P.A. Venter, and A. Schneemann Recent insights into the biology and biomedical applications of Flock House virus Cell Mol Life Sci 2008
20. W.X. Li, H. Li, R. Lu, F. Li, M. Dus, P. Atkinson, E.W. Brydon, K.L. Johnson, A. Garcia-Sastre, and L.A. Ball Interferon antagonist proteins of influenza and vaccinia viruses are suppressors of RNA silencing Proc Natl Acad Sci USA 101 2004 1350 1355 (Pubitemid 38182692)
21. R. Aliyari, Q. Wu, H.W. Li, X.H. Wang, F. Li, L.D. Green, C.S. Han, W.X. Li, and S.W. Ding Mechanism of induction and suppression of antiviral immunity directed by virus-derived small RNAs in Drosophila Cell Host Microbe 4 2008 387 397
22. D. Galiana-Arnoux, C. Dostert, A. Schneemann, J.A. Hoffmann, and J.L. Imler Essential function in vivo for Dicer-2 in host defense against RNA viruses in drosophila Nat Immunol 7 2006 590 597 (Pubitemid 43797340)
23. K.M. Myles, M.R. Wiley, E.M. Morazzani, and Z.N. Adelman Alphavirus-derived small RNAs modulate pathogenesis in disease vector mosquitoes Proc Natl Acad Sci USA 105 2008 19938 19943
24. I. Sanchez-Vargas, J.C. Scott, B.K. Poole-Smith, A.W. Franz, V. Barbosa-Solomieu, J. Wilusz, K.E. Olson, and C.D. Blair Dengue virus type 2 infections of Aedes aegypti are modulated by the mosquito's RNA interference pathway PLoS Pathog 5 2009 e1000299
25. Han YH, Luo YJ, Wu Q, Jovel J, Wang XH, Aliyari R, Han C, Li WX, Ding SW: RNA-based immunity terminates viral infection in adult Drosophila in absence of viral suppression of RNAi: characterization of viral siRNA populations in wildtype and mutant flies. J Virol published online ahead of print on 28 September 2011. doi:10.1128/JVI.05518-11
26. F. Li, and S.W. Ding Virus counterdefense: diverse strategies for evading the RNA-silencing immunity Annu Rev Microbiol 60 2006 503 531 (Pubitemid 44627959)
27. J. Burgyan, and Z. Havelda Viral suppressors of RNA silencing Trends Plant Sci 16 2011 265 272
28. J.E. Irazoqui, J.M. Urbach, and F.M. Ausubel Evolution of host innate defence: insights from Caenorhabditis elegans and primitive invertebrates Nat Rev Immunol 10 2010 47 58
29. M.-A. Félix, A. Ashe, J. Piffaretti, G. Wu, I. Nuez, T. Bélicard, Y. Jiang, G. Zhao, C.J. Franz, and L.D. Goldstein Natural and experimental infection of Caenorhabditis nematodes by novel viruses related to nodaviruses PLoS Biol 9 2011 e1000586
30. R. Lu, M. Maduro, F. Li, H.W. Li, G. Broitman-Maduro, W.X. Li, and S.W. Ding Animal virus replication and RNAi-mediated antiviral silencing in Caenorhabditis elegans Nature 436 2005 1040 1043 (Pubitemid 41191689)
31. C. Wilkins, R. Dishongh, S.C. Moore, M.A. Whitt, M. Chow, and K. Machaca RNA interference is an antiviral defence mechanism in Caenorhabditis elegans Nature 436 2005 1044 1047 (Pubitemid 41191690)
32. D.H. Schott, D.K. Cureton, S.P. Whelan, and C.P. Hunter An antiviral role for the RNA interference machinery in Caenorhabditis elegans Proc Natl Acad Sci USA 102 2005 18420 18424 (Pubitemid 43011241)
33. W.H. Liu, Y.L. Lin, J.P. Wang, W. Liou, R.F. Hou, Y.C. Wu, and C.L. Liao Restriction of vaccinia virus replication by a ced-3 and ced-4-dependent pathway in Caenorhabditis elegans Proc Natl Acad Sci USA 103 2006 4174 4179
34. R. Lu, E. Yigit, W.X. Li, and S.W. Ding An RIG-I-Like RNA helicase mediates antiviral RNAi downstream of viral siRNA biogenesis in Caenorhabditis elegans PLoS Pathog 5 2009 e1000286
35. J. Rehwinkel, and C. Reis e Sousa RIGorous detection: exposing virus through RNA sensing Science 327 2010 284 286
36. M. Yoneyama, and T. Fujita RNA recognition and signal transduction by RIG-I-like receptors Immunol Rev 227 2009 54 65
37. O. Takeuchi, and S. Akira Innate immunity to virus infection Immunol Rev 227 2009 75 86
38. C. Lipardi, and B.M. Paterson Retraction Proc Natl Acad Sci USA 108 2011 15010
39. A. Deleris, J. Gallego-Bartolome, J. Bao, K.D. Kasschau, J.C. Carrington, and O. Voinnet Hierarchical action and inhibition of plant dicer-like proteins in antiviral defense Science 313 2006 68 71 (Pubitemid 44051252)
40. J.A. Diaz-Pendon, F. Li, W.X. Li, and S.W. Ding Suppression of antiviral silencing by cucumber mosaic virus 2b protein in Arabidopsis is associated with drastically reduced accumulation of three classes of viral small interfering RNAs Plant Cell 19 2007 2053 2063 (Pubitemid 47218858)
41. F. Qu, X. Ye, and T.J. Morris Arabidopsis DRB4, AGO1, AGO7, and RDR6 participate in a DCL4-initiated antiviral RNA silencing pathway negatively regulated by DCL1 Proc Natl Acad Sci USA 105 2008 14732 14737
42. X.B. Wang, Q. Wu, T. Ito, F. Cillo, W.X. Li, X. Chen, J.L. Yu, and S.W. Ding RNAi-mediated viral immunity requires amplification of virus-derived siRNAs in Arabidopsis thaliana Proc Natl Acad Sci USA 107 2010 484 489
43. H. Garcia-Ruiz, A. Takeda, E.J. Chapman, C.M. Sullivan, N. Fahlgren, K.J. Brempelis, and J.C. Carrington Arabidopsis RNA-dependent RNA polymerases and dicer-like proteins in antiviral defense and small interfering RNA biogenesis during Turnip Mosaic Virus infection Plant Cell 22 2010 481 496
44. X.B. Wang, J. Jovel, P. Udomporn, Y. Wang, Q. Wu, W.X. Li, V. Gasciolli, H. Vaucheret, and S.W. Ding The 21-nucleotide, but not 22-nucleotide, viral secondary small interfering RNAs direct potent antiviral defense by two cooperative argonautes in Arabidopsis thaliana Plant Cell 23 2011 1625 1638
45. L. Donaire, D. Barajas, B. Martinez-Garcia, L. Martinez-Priego, I. Pagan, and C. Llave Structural and genetic requirements for the biogenesis of tobacco rattle virus-derived small interfering RNAs J Virol 82 2008 5167 5177 (Pubitemid 351705226)
46. J.T. Cuperus, A. Carbonell, N. Fahlgren, H. Garcia-Ruiz, R.T. Burke, A. Takeda, C.M. Sullivan, S.D. Gilbert, T.A. Montgomery, and J.C. Carrington Unique functionality of 22-nt miRNAs in triggering RDR6-dependent siRNA biogenesis from target transcripts in Arabidopsis Nat Struct Mol Biol 17 2010 997 1003
47. H.M. Chen, L.T. Chen, K. Patel, Y.H. Li, D.C. Baulcombe, and S.H. Wu 22-Nucleotide RNAs trigger secondary siRNA biogenesis in plants Proc Natl Acad Sci USA 107 2010 15269 15274
48. J.J. Harvey, M.G. Lewsey, K. Patel, J. Westwood, S. Heimstadt, J.P. Carr, and D.C. Baulcombe An Antiviral defense role of AGO2 in plants PLoS ONE 6 2011 e14639
49. M. Jaubert, S. Bhattacharjee, A.F. Mello, K.L. Perry, and P. Moffett ARGONAUTE2 mediates RNA-silencing antiviral defenses against Potato virus X in Arabidopsis Plant Physiol 156 2011 1556 1564
50. F. Jay, Y. Wang, A. Yu, L. Taconnat, S. Pelletier, V. Colot, J.P. Renou, and O. Voinnet Misregulation of AUXIN RESPONSE FACTOR 8 underlies the developmental abnormalities caused by three distinct viral silencing suppressors in Arabidopsis PLoS Pathog 7 2011 e1002035
51. H. Shimura, V. Pantaleo, T. Ishihara, N. Myojo, Inaba J-i, K. Sueda, J. Burgyán, and C. Masuta A viral satellite RNA induces yellow symptoms on tobacco by targeting a gene involved in chlorophyll biosynthesis using the RNA silencing machinery PLoS Pathog 7 2011 e1002021
52. N.A. Smith, A.L. Eamens, and M.-B. Wang Viral small interfering RNAs target host genes to mediate disease symptoms in plants PLoS Pathog 7 2011 e1002022
53. K.B. Scholthof Taking some of the mystery out of host:virus interactions PLoS Pathog 7 2011 e1002033
54. A.F. Fusaro, L. Matthew, N.A. Smith, S.J. Curtin, J. Dedic-Hagan, G.A. Ellacott, J.M. Watson, M.B. Wang, C. Brosnan, and B.J. Carroll RNA interference-inducing hairpin RNAs in plants act through the viral defence pathway EMBO Rep 7 2006 1168 1175 (Pubitemid 44660575)
55. Q.S. Du, C.G. Duan, Z.H. Zhang, Y.Y. Fang, R.X. Fang, Q. Xie, and H.S. Guo DCL4 targets Cucumber mosaic virus satellite RNA at novel secondary structures J Virol 81 2007 9142 9151 (Pubitemid 47311457)
56. J.A. Diaz-Pendon, and S.W. Ding Direct and indirect roles of viral suppressors of RNA silencing in pathogenesis Annu Rev Phytopathol 46 2008 303 326
57. N.C. Lau, N. Robine, R. Martin, W.J. Chung, Y. Niki, E. Berezikov, and E.C. Lai Abundant primary piRNAs, endo-siRNAs, and microRNAs in a Drosophila ovary cell line Genome Res 19 2009 1776 1785
58. K. Saito, S. Inagaki, T. Mituyama, Y. Kawamura, Y. Ono, E. Sakota, H. Kotani, K. Asai, H. Siomi, and M.C. Siomi A regulatory circuit for piwi by the large Maf gene traffic jam in Drosophila Nature 461 2009 1296 1299
59. J.C. Scott, D.E. Brackney, C.L. Campbell, V. Bondu-Hawkins, B. Hjelle, G.D. Ebel, K.E. Olson, and C.D. Blair Comparison of dengue virus type 2-specific small RNAs from RNA interference-competent and -incompetent mosquito cells PLoS Negl Trop Dis 4 2010 e848
60. D.E. Brackney, J.C. Scott, F. Sagawa, J.E. Woodward, N.A. Miller, F.D. Schilkey, J. Mudge, J. Wilusz, K.E. Olson, and C.D. Blair C6/36 Aedes albopictus cells have a dysfunctional antiviral RNA interference response PLoS Negl Trop Dis 4 2010 e856
61. H.L. Chotkowski, A.T. Ciota, Y. Jia, F. Puig-Basagoiti, L.D. Kramer, P.Y. Shi, and R.L. Glaser West Nile virus infection of Drosophila melanogaster induces a protective RNAi response Virology 377 2008 197 206
62. R.A. Zambon, V.N. Vakharia, and L.P. Wu RNAi is an antiviral immune response against a dsRNA virus in Drosophila melanogaster Cell Microbiol 8 2006 880 889
63. C.A. Mims Vertical transmission of viruses Microbiol Rev 45 1981 267 286 (Pubitemid 11032200)
64. E. Allen, Z. Xie, A.M. Gustafson, and J.C. Carrington microRNA-directed phasing during trans-acting siRNA biogenesis in plants Cell 121 2005 207 221 (Pubitemid 40546389)
65. V.V. Vagin, A. Sigova, C. Li, H. Seitz, V. Gvozdev, and P.D. Zamore A distinct small RNA pathway silences selfish genetic elements in the germline Science 313 2006 320 324 (Pubitemid 44480950)
66. L. Donaire, Y. Wang, D. Gonzalez-Ibeas, K.F. Mayer, M.A. Aranda, and C. Llave Deep-sequencing of plant viral small RNAs reveals effective and widespread targeting of viral genomes Virology 392 2009 203 214
67. N. Vodovar, B. Goic, H. Blanc, and M.C. Saleh In silico reconstruction of viral genomes from small RNAs improves viral-derived siRNA profiling J Virol 85 2011 11016 11021
68. C. Hagen, A. Frizzi, J. Kao, L. Jia, M. Huang, Y. Zhang, and S. Huang Using small RNA sequences to diagnose, sequence, and investigate the infectivity characteristics of vegetable-infecting viruses Arch Virol 156 2011 1209 1216
69. J.F. Kreuze, A. Perez, M. Untiveros, D. Quispe, S. Fuentes, I. Barker, and R. Simon Complete viral genome sequence and discovery of novel viruses by deep sequencing of small RNAs: a generic method for diagnosis, discovery and sequencing of viruses Virology 388 2009 1 7
70. W.I. Lipkin Microbe hunting Microbiol Mol Biol Rev 74 2010 363 377
71. X.H. Wang, R. Aliyari, W.X. Li, H.W. Li, K. Kim, R. Carthew, P. Atkinson, and S.W. Ding RNA interference directs innate immunity against viruses in adult Drosophila Science 312 2006 452 454
72. B. Lemaitre, E. Nicolas, L. Michaut, J.M. Reichhart, and J.A. Hoffmann The dorsoventral regulatory gene cassette spatzle/Toll/cactus controls the potent antifungal response in Drosophila adults Cell 86 1996 973 983 (Pubitemid 26336801)
73. S.W. Ding, and O. Voinnet Antiviral immunity directed by small RNAs Cell 130 2007 413 426 (Pubitemid 47198311)
74. E.S. Machlin, P. Sarnow, and S.M. Sagan Masking the 5′ terminal nucleotides of the hepatitis C virus genome by an unconventional microRNA-target RNA complex Proc Natl Acad Sci USA 108 2011 3193 3198
75. I.A. Drinnenberg, G.R. Fink, and D.P. Bartel Compatibility with killer explains the rise of RNAi-deficient fungi Science 333 2011 1592