Production and Transport of the Silencing Signal in Transgenic and Virus-Infected Plant Systems

  • Thomas HohnEmail author
  • Rashid Akbergenov
  • Mikhail M. Pooggin
Part of the Plant Cell Monographs book series (CELLMONO, volume 7)


In plants, RNA interference constitutes an important defense mechanism against viruses, transposons, and transgenes. Viruses, on the other hand, use suppressors to counteract silencing. In contrast to mammalian systems, silencing in plants spreads systemically through the whole organism. Since also viruses spread and consequently produce suppressors systemically, a race between silencing and virus replication occurs. Apparently, successful viruses win the race, but only until they reach the tissue around the meristem. There, the silencing mechanism is most capable by efficiently amplifying the silencing signal, bona fide 21-nt siRNA, leading to the well-known phenomenon of meristem exclusion.


Transcriptional Gene Silence Silence Suppressor Silence Signal African Cassava Mosaic Virus Mungbean Yellow Mosaic Virus 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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  1. Adenot X, Elmayan T, Lauressergues D, Boutet S, Bouché N, Gasciolli V, Vaucheret H (2006) DRB4-Dependent TAS3 trans-Acting siRNAs Control Leaf Morphology through AGO7. Curr Biol 16:927–932 PubMedGoogle Scholar
  2. Al-Kaff NS, Kreike MM, Covey SN, Pitcher R, Page AM, Dale PJ (2000) Plants rendered herbicide-susceptible by cauliflower mosaic virus-elicited suppression of a 35S promoter-regulated transgene. Nat Biotechnol 18:995–999 PubMedGoogle Scholar
  3. Akbergenov RZ, Si-Ammour A, Blevins T, Amin I, Kutter C, Vanderschuren H, Zhang P, Gruissem W, Meins F Jr, Hohn T, Pooggin MM (2006) Molecular characterization of geminivirus-derived small RNAs in different plant species. Nucleic Acids Res 34:462–471 PubMedGoogle Scholar
  4. Allen E, Xie Z, Gustafson AM, Carrington JC (2005) microRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell 121:207–221 PubMedGoogle Scholar
  5. Amedeo P, Habu Y, Afsar K, Mittelsten SO, Paszkowski J (2000) Disruption of the plant gene MOM releases transcriptional silencing of methylated genes. Nature 405:203–206 PubMedGoogle Scholar
  6. Anandalakshmi R, Pruss GJ, Ge X, Marathe R, Mallory AC, Smith TH, Vance VB (1998) A viral suppressor of gene silencing in plants. Proc Natl Acad Sci USA 95:13079–13084 PubMedGoogle Scholar
  7. Anandalakshmi R, Marathe R, Ge X, Herr JM, Mallory A, Mau C, Pruss G, Bowman L, Vance VB (2000) A calmodulin-related protein from tobacco suppresses post-transcriptional gene silencing. Science 290:142–144 PubMedGoogle Scholar
  8. Balachandran S, Hull RJ, Martins RA, Vaadia Y, Lucas WJ (1997) Influence of Environmental Stress on Biomass Partitioning in Transgenic Tobacco Plants Expressing the Movement Protein of Tobacco Mosaic Virus. Plant Physiol 114:475–481 PubMedGoogle Scholar
  9. Baulcombe DC (2005) RNA silencing. Trends Biochem Sci 30:290–293 PubMedGoogle Scholar
  10. Baulcombe DC, Molnar A (2004) Crystal structure of p19 – a universal suppressor of RNA silencing. Trends Biochem Sci 29:279–281 PubMedGoogle Scholar
  11. Baumberger N, Baulcombe DC (2005) Arabidopsis ARGONAUTE1 is an RNA Slicer that selectively recruits microRNAs and short interfering RNAs. Proc Natl Acad Sci USA 102:11928–11933 PubMedGoogle Scholar
  12. Bayne EH, Rakitina DV, Morozov SY, Baulcombe DC (2005) Cell-to-cell movement of potato potexvirus X is dependent on suppression of RNA silencing. Plant J 44:471–482 PubMedGoogle Scholar
  13. Bendahmane A, Kanyuka KV, Baulcombe DC (1997) High resolution and physical mapping of the Rx gene for extreme resistance to potato virus X in tetraploid potato. Theor Appl Genet 95:153–162 Google Scholar
  14. Blevins T, Rajeswaran R, Shivaprasad P, Beknazariants D, Si-Ammour A, Park H-S, Vazquez F, Robertson D, Meins F Jr, Hohn T, Pooggin M (2006) Four plant dicers mediate viral small RNA biogenesis and DNA virus induced silencing. Nucleic Acids Res 34:6233–6246 PubMedGoogle Scholar
  15. Borsani O, Zhu J, Verslues PE, Sunkar R, Zhu JK (2005) Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis. Cell 123:1279–1291 PubMedGoogle Scholar
  16. Bouche N, Lauressergues D, Gasciolli V, Vaucheret H (2006) An antagonistic function for Arabidopsis DCL2 in development and a new function for DCL4 in generating viral siRNAs. EMBO J 25:3347–3356 PubMedGoogle Scholar
  17. Brigneti G, Voinnet O, Li WX, Ji LH, Ding SW, Baulcombe DC (1998) Viral pathogenicity determinants are suppressors of transgene silencing in Nicotiana benthamiana. EMBO J 17:6739–6746 PubMedGoogle Scholar
  18. Brodersen P, Voinnet O (2006) The diversity of RNA silencing pathways in plants. Trends Genet 22:268–280 PubMedGoogle Scholar
  19. Brzeski J, Jerzmanowski A (2003) Deficient in DNA methylation 1 (DDM1) defines a novel family of chromatin-remodeling factors. J Biol Chem 278:823–828 PubMedGoogle Scholar
  20. Bucher E, Sijen T, de Haan P, Goldbach R, Prins M (2003) Negative-strand tospoviruses and tenuiviruses carry a gene for a suppressor of gene silencing at analogous genomic positions. J Virol 77:1329–1336 PubMedGoogle Scholar
  21. Bucher E, Hemmes H, de Haan P, Goldbach R, Prins M (2004) The influenza A virus NS1 protein binds small interfering RNAs and suppresses RNA silencing in plants. J Gen Virol 85:983–991 PubMedGoogle Scholar
  22. Cao X, Aufsatz W, Zilberman D, Mette MF, Huang MS, Matzke MA, Jacobsen SE (2003) Role of the DRM and CMT3 methyltransferases in RNA-directed DNA methylation. Curr Biol 13:2212–2217 PubMedGoogle Scholar
  23. Cao X, Jacobsen SE (2002) Locus-specific control of asymmetric and CpNpG methylation by the DRM and CMT3 methyltransferase genes. Proc Natl Acad Sci USA 99:16491–16498 PubMedGoogle Scholar
  24. Cao X, Jacobsen SE (2002) Role of the arabidopsis DRM methyltransferases in de novo DNA methylation and gene silencing. Curr Biol 9:1138–1144 Google Scholar
  25. Cao X, Zhou P, Zhang X, Zhu S, Zhong X, Xiao Q, Ding B, Li Y (2005) Identification of an RNA silencing suppressor from a plant double-stranded RNA virus. J Virol 79:13018–13027 PubMedGoogle Scholar
  26. Canizares MC, Taylor KM, Lomonossoff GP (2004) Surface-exposed C-terminal amino acids of the small coat protein of Cowpea mosaic virus are required for suppression of silencing. J Gen Virol 85:3431–3435 PubMedGoogle Scholar
  27. Carrington JC (2005) Small RNAs and Arabidopsis. A fast forward look. Plant Physiol 13:565–566 Google Scholar
  28. Chan SW, Zilberman D, Xie Z, Johansen LK, Carrington JC, Jacobsen SE (2004) RNA silencing genes control de novo DNA methylation. Science 303:1336 PubMedGoogle Scholar
  29. Chellappan P, Vanitharani R, Ogbe F, Fauquet CM (2005) Effect of temperature on geminivirus-induced RNA silencing in plants. Plant Physiol 138:1828–1841 PubMedGoogle Scholar
  30. Chellappan P, Vanitharani R, Fauquet CM (2005) MicroRNA-binding viral protein interferes with Arabidopsis development. Proc Natl Acad Sci USA 102:10381–10386 Chan SW, Henderson IR, Zhang X, Shah G, Chien JS, Jacobsen SE (2006) RNAi, DRD1, and histone methylation actively target developmentally important non-CG DNA methylation in Arabidopsis. PLoS Genet 2:e83 Google Scholar
  31. Chen J, Li WX, Xie D, Peng JR, Ding SW (2004) Viral virulence protein suppresses RNA silencing-mediated defense but upregulates the role of microRNA in host gene expression. Plant Cell 16:1302–1313 PubMedGoogle Scholar
  32. Covey SN, Al-Kaff NS, Langara A, Turner DS (1997) Plants combat infection by gene silencing. Nature 385:781–782 Google Scholar
  33. Covey SN, Al Kaff NS (2000) Plant DNA viruses and gene silencing. Plant Mol Biol 43:307–322 PubMedGoogle Scholar
  34. Cui X, Li G, Wang D, Hu D, Zhou X (2005) A Begomovirus DNAbeta-encoded protein binds DNA, functions as a suppressor of RNA silencing, and targets the cell nucleus. J Virol 79:10764–10775 PubMedGoogle Scholar
  35. Deleris A, Gallego-Bartolome J, Bao J, Kasschau KD, Carrington JC, Voinnet O (2006) A molecular framework for induction and suppression of antiviral RNA silencing in plants. Science 313:68–71 PubMedGoogle Scholar
  36. Delgadillo MO, Saenz P, Salvador B, Garcia JA, Simon-Mateo C (2004) Human influenza virus NS1 protein enhances viral pathogenicity and acts as an RNA silencing suppressor in plants. J Gen Virol 85:993–999 PubMedGoogle Scholar
  37. Dunoyer P, Pfeffer S, Fritsch C, Hemmer O, Voinnet O, Richards KE (2002) Identification, subcellular localization and some properties of a cysteine-rich suppressor of gene silencing encoded by peanut clump virus. Plant J 29:555–567 PubMedGoogle Scholar
  38. Dunoyer P, Himber C, Voinnet O (2005) DICER-LIKE 4 is required for RNA interference and produces the 21-nucleotide small interfering RNA component of the plant cell-to-cell silencing signal. Nat Genet 37:1356–1360 PubMedGoogle Scholar
  39. Dunoyer P, Lecellier CH, Parizotto EA, Himber C, Voinnet O (2004) Probing the microRNA and small interfering RNA pathways with virus-encoded suppressors of RNA silencing. Plant Cell 16:1235–1250 PubMedGoogle Scholar
  40. Dunoyer P, Voinnet O (2005) The complex interplay between plant viruses and host RNA-silencing pathways. Curr Opin Plant Biol 8:415–423 PubMedGoogle Scholar
  41. Ebhardt HA, Thi EP, Wang MB, Unrau PJ (2005) Extensive 3′ modification of plant small RNAs is modulated by helper component-proteinase expression. Proc Natl Acad Sci USA 102:13398–13403 PubMedGoogle Scholar
  42. Ekwall K (2004) The RITS complex-A direct link between small RNA and heterochromatin. Mol Cell 13:304–305 PubMedGoogle Scholar
  43. English JJ, Mueller E, Baulcombe DC (1996) Suppression of virus accumulation in transgenic plants exhibiting silencing of nuclear genes. Plant Cell 8:179–188 PubMedGoogle Scholar
  44. Fitchen JH, Beachy RN (1993) Genetically engineered protection against viruses in transgenic plants. Annu Rev Microbiol 47:739–763 PubMedGoogle Scholar
  45. Gasciolli V, Mallory AC, Bartel DP, Vaucheret H (2005) Partially redundant functions of Arabidopsis DICER-like enzymes and a role for DCL4 in producing trans-acting siRNAs. Curr Biol 15:1494–1500 PubMedGoogle Scholar
  46. Gustafson AM, Allen E, Givan S, Smith D, Carrington JC, Kasschau KD (2005) ASRP: the Arabidopsis Small RNA Project Database. Nucleic Acids Res 33:D637–D640 PubMedGoogle Scholar
  47. Habu Y, Mathieu O, Tariq M, Probst AV, Smathajitt C, Zhu T, Paszkowski J (2006) Epigenetic regulation of transcription in intermediate heterochromatin. EMBO Rep 7:1279–1284 PubMedGoogle Scholar
  48. Hamilton AJ, Baulcombe DC (1999) A novel species of small antisense RNA in post-transcriptional gene silencing. Science 286:950–952 PubMedGoogle Scholar
  49. Hamilton A, Voinnet O, Chappell L, Baulcombe D (2002) Two classes of short interfering RNA in RNA silencing. EMBO J 21:4671–4679 PubMedGoogle Scholar
  50. Han MH, Goud S, Song L, Fedoroff N (2004) The Arabidopsis double-stranded RNA-binding protein HYL1 plays a role in microRNA-mediated gene regulation. Proc Natl Acad Sci USA 101:1093–1098 PubMedGoogle Scholar
  51. He B (2006) Viruses, endoplasmic reticulum stress, and interferon responses. Cell Death Differ 13:393–403 PubMedGoogle Scholar
  52. Heinlein M, Epel BL (2004) Macromolecular transport and signaling through plasmodesmata. Int Rev Cytol 235:93–164 PubMedCrossRefGoogle Scholar
  53. Henderson IR, Zhang X, Lu C, Johnson L, Meyers BC, Green PJ, Jacobsen SE (2006) Dissecting Arabidopsis thaliana DICER function in small RNA processing, gene silencing and DNA methylation patterning. Nat Genet 38:721–725 PubMedGoogle Scholar
  54. Herr AJ, Jensen MB, Dalmay T, Baulcombe DC (2005) RNA polymerase IV directs silencing of endogenous DNA. Science 308:118–120 PubMedGoogle Scholar
  55. Himber C, Dunoyer P, Moissiard G, Ritzenthaler C, Voinnet O (2003) Transitivity-dependent and -independent cell-to-cell movement of RNA silencing. EMBO J 22:4523–4533 PubMedGoogle Scholar
  56. Hiraguri A et al. (2005) Specific interactions between Dicer-like proteins and HYL1/DRB-family dsRNA-binding proteins in Arabidopsis thaliana. Plant Mol Biol 57:173–188 PubMedGoogle Scholar
  57. Huettel B, Kanno T, Daxinger L, Aufsatz W, Matzke AJ, Matzke M (2006) Endogenous targets of RNA-directed DNA methylation and Pol IV in Arabidopsis. EMBO J 25:2828–2836 PubMedGoogle Scholar
  58. Hunter C, Sun H, Poethig RS (2003) The Arabidopsis heterochronic gene ZIPPY is an ARGONAUTE family member. Curr Biol 13:1734–1739 PubMedGoogle Scholar
  59. Jones-Rhoades MW, Bartel DP, Bartel B (2006) MicroRNAs and their regulatory roles in plants. Annu Rev Plant Biol 57:19–53 PubMedGoogle Scholar
  60. Kalantidis K, Tsagris M, Tabler M (2006) Spontaneous short-range silencing of a GFP transgene in Nicotiana benthamiana is possibly mediated by small quantities of siRNA that do not trigger systemic silencing. Plant J 45:1006–1016 PubMedCrossRefGoogle Scholar
  61. Kanno T, Mette MF, Kreil DP, Aufsatz W, Matzke M, Matzke AJ (2004) Involvement of putative SNF2 chromatin remodeling protein DRD1 in RNA-directed DNA methylation. Curr Biol 14:801–805 PubMedGoogle Scholar
  62. Kanno T, Huettel B, Mette MF, Aufsatz W, Jaligot E, Daxinger L, Kreil DP, Matzke M, Matzke AJ (2005) Atypical RNA polymerase subunits required for RNA-directed DNA methylation. Nat Genet 37:761–765 PubMedGoogle Scholar
  63. Kasschau KD, Carrington JC (1998) A counterdefensive strategy of plant viruses: suppression of posttranscriptional gene silencing. Cell 95:461–470 PubMedGoogle Scholar
  64. Katze MG (2002) Interferon, PKR, virology, and genomics: what is past and what is next in the new millennium? J Interferon Cytokine Res 22:283–286 PubMedGoogle Scholar
  65. Keene KM, Foy BD, Sanchez-Vargas I, Beaty BJ, Blair CD, Olson KE (2004) RNA interference acts as a natural antiviral response to O'nyong-nyong virus (Alphavirus; Togaviridae) infection of Anopheles gambiae. Proc Natl Acad Sci USA 101:17240–17245 PubMedGoogle Scholar
  66. Kubota K, Tsuda S, Tamai A, Meshi T (2003) Tomato mosaic virus replication protein suppresses virus-targeted posttranscriptional gene silencing. J Virol 77:11016–11026 PubMedGoogle Scholar
  67. Kumagai MH, Donson J, Dellacioppa G, Harvey D, Hanley K, Grill LK (1995) Cytoplasmic inhibition of carotenoid biosynthesis with virus-derived RNA. Proc Natl Acad Sci USA 92:1679–1683 PubMedGoogle Scholar
  68. Kurihara Y, Takashi Y, Watanabe Y (2006) The interaction between DCL1 and HYL1 is important for efficient and precise processing of pri-miRNA in plant microRNA biogenesis. RNA 12:206–212 PubMedGoogle Scholar
  69. Kurihara Y, Watanabe Y (2004) Arabidopsis micro-RNA biogenesis through Dicer-like 1 protein functions. Proc Natl Acad Sci USA 101:12753–12758 PubMedGoogle Scholar
  70. Lakatos L, Szittya G, Silhavy D, Burgyan J (2004) Molecular mechanism of RNA silencing suppression mediated by p19 protein of tombusviruses. EMBO J 23:876–884 PubMedGoogle Scholar
  71. Lakatos L, Csorba T, Pantaleo V, Chapman EJ, Carrington JC, Liu YP, Dolja VV, Fernández-Calvino L, López-Moya JJ, Burgyán J (2006) Small RNA binding is a common strategy to suppress RNA silencing by several viral suppressors. EMBO J 25:2768–2780 PubMedGoogle Scholar
  72. Li CF, Pontes O, El Shami M, Henderson IR, Bernatavichute YV, Chan SW, Lagrange T, Pikaard CS, Jacobsen SE (2006) An ARGONAUTE4-Containing Nuclear Processing Center Colocalized with Cajal Bodies in Arabidopsis thaliana. Cell 126:93–106 PubMedGoogle Scholar
  73. Li J, Yang Z, Yu B, Liu J, Che X (2005) Methylation protects miRNAs and siRNAs from a 3′-end uridylation activity in Arabidopsis. Curr Biol 15:1501–1507 PubMedGoogle Scholar
  74. Lindbo JA, Dougherty WG (2005) Plant pathology and RNAi: a brief history. Annu Rev Phytopathol 43:191–204 PubMedGoogle Scholar
  75. Lindbo JA, Dougherty WG (1992) Untranslatable transcripts of the tobacco etch virus coat protein gene sequence can interfere with tobacco etch virus replication in transgenic plants and protoplasts. Virology 189:725–733 PubMedGoogle Scholar
  76. Lindroth AM, Shultis D, Jasencakova Z, Fuchs J, Johnson L, Schubert D, Patnaik D, Pradhan S, Goodrich J, Schubert I, Jenuwein T, Khorasanizadeh S, Jacobsen SE (2004) Dual histone H3 methylation marks at lysines 9 and 27 required for interaction with CHROMOMETHYLASE3. EMBO J 23:4286–4296 PubMedGoogle Scholar
  77. Liu L, Grainger J, Canizares MC, Angell SM, Lomonossoff GP (2004) Cowpea mosaic virus RNA-1 acts as an amplicon whose effects can be counteracted by a RNA-2-encoded suppressor of silencing. Virology 323:37–48 PubMedGoogle Scholar
  78. Llave C, Kasschau KD, Rector MA, Carrington JC (2002) Endogenous and silencing-associated small RNAs in plants. Plant Cell 14:1605–1619 PubMedGoogle Scholar
  79. Lu R, Folimonov A, Shintaku M, Li WX, Falk BW, Dawson WO, Ding SW (2004) Three distinct suppressors of RNA silencing encoded by a 20-kb viral RNA genome. Proc Natl Acad Sci USA 101:15742–15747 PubMedGoogle Scholar
  80. Lu S, Cullen BR (2004) Adenovirus VA1 noncoding RNA can inhibit small interfering RNA and MicroRNA biogenesis. J Virol 78:12868–12876 PubMedGoogle Scholar
  81. Lu C, Fedoroff N (2000) A mutation in the Arabidopsis HYL1 gene encoding a dsRNA binding protein affects responses to abscisic acid, auxin, and cytokinin. Plant Cell 12:2351–2366 PubMedGoogle Scholar
  82. Lu C, Fedoroff N (2000) A Mutation in the Arabidopsis HYL1 Gene Encoding a dsRNA Binding Protein Affects Responses to Abscisic Acid, Auxin, and Cytokinin. Plant Cell 12:2351–2365 PubMedGoogle Scholar
  83. Mallory AC, Parks G, Endres MW, Baulcombe DC, Bowman LH, Pruss GJ, Vance VB (2002) The amplicon-plus system for high-level expression of transgenes in plants. Nat Biotechnol 20:622–625 PubMedGoogle Scholar
  84. Merai Z, Kerenyi Z, Kertesz S, Magna M, Lakatos L, Silhavy D (2006) Double-stranded RNA binding may be a general plant RNA viral strategy to suppress RNA silencing. J Virol 80:5747–5756 PubMedGoogle Scholar
  85. Mittelsten-Scheid O, Afsar K, Paszkowski J (1998) Release of epigenetic gene silencing by trans-acting mutations in Arabidopsis. Proc Natl Acad Sci USA 95:632–637 PubMedGoogle Scholar
  86. Mittelsten SO, Probst AV, Afsar K, Paszkowski J (2002) Two regulatory levels of transcriptional gene silencing in Arabidopsis. Proc Natl Acad Sci USA 99:13659–13662 Google Scholar
  87. Mlotshwa S, Voinnet O, Mette MF, Matzke MA, Vaucheret H, Ding SW, Pruss G, Vance VB (2002) RNA silencing and the mobile silencing signal. Plant Cell 14(Suppl):289–301 Google Scholar
  88. Moissiard G, Voinnet O (2004) Viral suppression of RNA silencing in plants. Mol Plant Pathol 5:71–82 PubMedGoogle Scholar
  89. Mourrain P, Beclin C, Elmayan T, Feuerbach F, Godon C, Morel JB, Jouette D, Lacombe AM, Nikic S, Picault N, Remoue K, Sanial M, Vo TA, Vaucheret H (2000) Arabidopsis SGS2 and SGS3 genes are required for posttranscriptional gene silencing and natural virus resistance. Cell 101:533–542 PubMedGoogle Scholar
  90. Muangsan N, Beclin C, Vaucheret H, Robertson D (2004) Geminivirus VIGS of endogenous genes requires SGS2/SDE1 and SGS3 and defines a new branch in the genetic pathway for silencing in plants. Plant J 38:1004–1014 PubMedGoogle Scholar
  91. Noreen F, Akbergenov R, Hohn T, Richert-Pöggeler KR (2007) Distinct expression of endogenous Petunia vein clearing virus and the DNA transposon dTph1 in two Petunia hybrida lines is correlated with differences in histone modification and siRNA production. Plant J (in press) Google Scholar
  92. Onodera Y, Haag JR, Ream T, Nunes PC, Pontes O, Pikaard CS (2005) Plant nuclear RNA polymerase IV mediates siRNA and DNA methylation-dependent heterochromatin formation. Cell 120:613–622 PubMedGoogle Scholar
  93. Park MY, Wu G, Gonzalez-Sulser A, Vaucheret H, Poethig RS (2005) Nuclear processing and export of microRNAs in Arabidopsis. Proc Natl Acad Sci USA 102:3691–3696 PubMedGoogle Scholar
  94. Palauqui JC, Elmayan T, Pollien JM, Vaucheret H (1997) Systemic acquired silencing: transgene-specific post-transcriptional silencing is transmitted by grafting from silenced stocks to non-silenced scions [published erratum in EMBO J 1998 Apr 1;17(7):2137]. EMBO J 16:4738–4745 PubMedGoogle Scholar
  95. Papenbrock J, Pfundel E, Mock HP, Grimm B (2000) Decreased and increased expression of the subunit CHL I diminishes Mg chelatase activity and reduces chlorophyll synthesis in transgenic tobacco plants. Plant J 22:155–164 PubMedGoogle Scholar
  96. Peele C, Jordan CV, Muangsan N, Turnage M, Egelkrout E, Eagle P, Hanley-Bowdoin L, Robertson D (2001) Silencing of a meristematic gene using geminivirus-derived vectors. Plant J 27:357–366 PubMedGoogle Scholar
  97. Pelissier T, Thalmeir S, Kempe D, Sanger HL, Wassenegger M (1999) Heavy de novo methylation at symmetrical and non-symmetrical sites is a hallmark of RNA-directed DNA methylation. Nucleic Acids Res 27:1625–1634 PubMedGoogle Scholar
  98. Peragine A, Yoshikawa M, Wu G, Albrecht HL, Poethig RS (2004) SGS3 and SGS2/SDE1/RDR6 are required for juvenile development and the production of trans-acting siRNAs in Arabidopsis. Genes Dev 18:2368–2379 PubMedGoogle Scholar
  99. Petersen BO, Albrechtsen M (2005) Evidence implying only unprimed RdRP activity during transitive gene silencing in plants. Plant Mol Biol 58:575–583 PubMedGoogle Scholar
  100. Pfeffer S, Dunoyer P, Heim F, Richards KE, Jonard G, Ziegler-Graff V (2002) P0 of beet Western yellows virus is a suppressor of posttranscriptional gene silencing. J Virol 76:6815–6824 PubMedGoogle Scholar
  101. Pillai RS, Bhattacharyya SN, Artus CG, Zoller T, Cougot N, Basyuk E, Bertrand E, Filipowicz W (2005) Inhibition of translational initiation by Let-7 MicroRNA in human cells. Science 309:1573–1576 PubMedGoogle Scholar
  102. Pontes O, Li CF, Nunes PC, Haag J, Ream T, Vitins A, Jacobsen SE, Pikaard CS (2006) The Arabidopsis Chromatin-Modifying Nuclear siRNA Pathway Involves a Nucleolar RNA Processing Center. Cell 126:79–92 PubMedGoogle Scholar
  103. Pontier D, Yahubyan G, Vega D, Bulski A, Saez-Vasquez J, Hakimi MA, Lerbs-Mache S, Colot V, Lagrange T (2005) Reinforcement of silencing at transposons and highly repeated sequences requires the concerted action of two distinct RNA polymerases IV in Arabidopsis. Genes Dev 19:2030–2040 PubMedGoogle Scholar
  104. Pooggin M, Shivaprasad PV, Veluthambi K, Hohn T (2003) RNAi targeting of DNA virus in plants. Nat Biotechnol 21:131–132 PubMedGoogle Scholar
  105. Probst AV, Fagard M, Proux F, Mourrain P, Boutet S, Earley K, Lawrence RJ, Pikaard CS, Murfett J, Furner I, Vaucheret H, Mittelsten SO (2004) Arabidopsis histone deacetylase HDA6 is required for maintenance of transcriptional gene silencing and determines nuclear organization of rDNA repeats. Plant Cell 16:1021–1034 PubMedGoogle Scholar
  106. Qi Y, Denli A, Hannon G (2005) Biochemical specialization within Arabidopsis RNA silencing pathways. Molecular Cell 19:421–428 PubMedGoogle Scholar
  107. Qi Y, He X, Wang XJ, Kohany O, Jurka J, Hannon GJ (2006) Distinct catalytic and non-catalytic roles of ARGONAUTE4 in RNA-directed DNA methylation. Nature 443:1008–1012 PubMedGoogle Scholar
  108. Qu F, Ren T, Morris TJ (2003) The coat protein of turnip crinkle virus suppresses posttranscriptional gene silencing at an early initiation step. J Virol 77:511–522 PubMedGoogle Scholar
  109. Qu F, Ye X, Hou G, Sato S, Clemente TE, Morris TJ (2005) RDR6 has a broad-spectrum but temperature-dependent antiviral defense role in Nicotiana benthamiana. J Virol 79:15209–15217 PubMedGoogle Scholar
  110. Rand TA, Petersen S, Du F, Wang X (2005) Argonaute2 cleaves the anti-guide strand of siRNA during RISC activation. Cell 123:621–629 PubMedGoogle Scholar
  111. Reed JC, Kasschau KD, Prokhnevsky AI, Gopinath K, Pogue GP, Carrington JC, Dolja VV (2003) Suppressor of RNA silencing encoded by Beet yellows virus. Virology 306:203–209 PubMedGoogle Scholar
  112. Richert-Poeggeler KR, Noreen F, Schwarzacher T, Harper G, Hohn T (2003) Induction of infectious petunia vein clearing (pararetro) virus from endogenous provirus in petunia. EMBO J 22:4836–4845 Google Scholar
  113. Roth BM, Pruss GJ, Vance VB (2004) Plant viral suppressors of RNA silencing. Virus Res 102:97–108 PubMedGoogle Scholar
  114. Ruiz-Medrano R, Xonocosle-Cazares B, Kragler F (2004) The plasmodesmatal transport pathway for homeotic proteins, silencing signals and virases. Curr Opin Plant Biol 7:641–650 PubMedGoogle Scholar
  115. Sanford JC, Johnston SA (1985) The concept of parasite derived resistance. J Theor Biol 113:395–405 Google Scholar
  116. Sarmiento C, Nigul L, Kazantseva J, Buschmann M, Truve E (2006) AtRLI2 is an endogenous suppressor of RNA silencing. Plant Mol Biol 61:153–163 PubMedGoogle Scholar
  117. Schwach F, Vaistij FE, Jones L, Baulcombe DC (2005) An RNA-dependent RNA polymerase prevents meristem invasion by potato virus X and is required for the activity but not the production of a systemic silencing signal. Plant Physiol 138:1842–1852 PubMedGoogle Scholar
  118. Shi BJ, Ding SW and Symons RH (1997) In vivo expression of an overlapping gene encoded by the cucumoviruses. J Gen Virol 78:237–241 PubMedGoogle Scholar
  119. Shivaprasad PV, Akbergenov R, Trinks D, Rajeswaran R, Veluthambi K, Hohn T, Pooggin MM (2005) Promoters, transcripts, and regulatory proteins of Mungbean yellow mosaic geminivirus. J Virol 79:8149–8163 PubMedGoogle Scholar
  120. Silhavy D, Burgyan J (2004) Effects and side-effects of viral RNA silencing suppressors on short RNAs. Trends Plant Sci 9:76–83 PubMedGoogle Scholar
  121. Szittya G, Silhavy D, Molnar A, Havelda Z, Lovas A, Lakatos L, Banfalvi Z, Burgyan J (2003) Low temperature inhibits RNA silencing-mediated defence by the control of siRNA generation. EMBO J 22:633–640 PubMedGoogle Scholar
  122. Takeda A, Sugiyama K, Nagano H, Mori M, Kaido M, Mise K, Tsuda S, Okuno T (2002) Identification of a novel RNA silencing suppressor, NSs protein of Tomato spotted wilt virus. FEBS Lett 532:75–79 PubMedGoogle Scholar
  123. Thomas CL, Leh V, Lederer C, Maule AJ (2003) Turnip crinkle virus coat protein mediates suppression of RNA silencing in Nicotiana benthamiana. Virology 306:33–41 PubMedGoogle Scholar
  124. Tomari Y, Du T, Haley B, Schwarz DS, Bennett R, Cook HA, Koppetsch BS, Theurkauf WE, Zamore PD (2004) RISC assembly defects in the Drosophila RNAi mutant armitage. Cell 116:831–841 PubMedGoogle Scholar
  125. Trinks D, Rajeswaran R, Shivaprasad PV, Akbergenov R, Oakeley EJ, Veluthambi K, Hohn T, Pooggin MM (2005) Suppression of RNA silencing by a geminivirus nuclear protein, AC2, correlates with transactivation of host genes. J Virol 79:2517–2527 PubMedGoogle Scholar
  126. Valle RP, Skrzeczkowski J, Morch MD, Joshi RL, Gargouri R, Drugeon G, Boyer JC, Chapeville F, Haenni AL (1988). Plant viruses and new perspectives in cross-protection. Biochimie 70:695–703 PubMedGoogle Scholar
  127. Vaucheret H (2005) RNA polymerase IV and transcriptional silencing. Nat Genet 37:659–660 PubMedGoogle Scholar
  128. Vaistij FE, Jones L, Baulcombe DC (2002) Spreading of RNA targeting and DNA methylation in RNA silencing requires transcription of the target gene and a putative RNA-dependent RNA polymerase. Plant Cell 14:857–867 PubMedGoogle Scholar
  129. Vanitharani R, Chellappan P, Pita JS, Fauquet CM (2004) Differential roles of AC2 and AC4 of cassava geminiviruses in mediating synergism and suppression of posttranscriptional gene silencing. J Virol 78:9487–9498 PubMedGoogle Scholar
  130. Vargason JM, Szittya G, Burgyan J, Tanaka Hall TM (2003) Size selective recognition of siRNA by an RNA silencing suppressor. Cell 115:799–811 PubMedGoogle Scholar
  131. Vaughn MW, Martienssen RA (2005) Finding the right template: RNA Pol IV, a plant-specific RNA polymerase. Mol Cell 17:754–756 PubMedGoogle Scholar
  132. Vazquez F, Gasciolli V, Crete P, Vaucheret H (2004) The nuclear dsRNA binding protein HYL1 is required for microRNA accumulation and plant development, but not posttranscriptional transgene silencing. Curr Biol 14:346–351 PubMedGoogle Scholar
  133. Vazquez F, Vaucheret H, Rajagopalan R, Lepers C, Gasciolli V, Mallory AC, Hilbert JL, Bartel DP, Crete P (2004) Endogenous trans-acting siRNAs regulate the accumulation of Arabidopsis mRNAs. Mol Cell 16:69–79 PubMedGoogle Scholar
  134. Voinnet O (2005a) Induction and suppression of RNA silencing:insights from viral infections. Nat Rev Genet 6:206–220 PubMedGoogle Scholar
  135. Voinnet O (2005b) Non-cell autonomous RNA silencing. FEBS Lett 579:5858–5871 PubMedGoogle Scholar
  136. Voinnet O, Baulcombe DC (1997) Systemic signalling in gene silencing. Nature 389:553 PubMedGoogle Scholar
  137. Voinnet O, Lederer C, Baulcombe DC (2000) A viral movement protein prevents spread of the gene silencing signal in Nicotiana benthamiana. Cell 103:157–167 PubMedGoogle Scholar
  138. Voinnet O, Pinto YM, Baulcombe DC (1999) Suppression of gene silencing: a general strategy used by diverse DNA and RNA viruses of plants. Proc Natl Acad Sci USA 96:14147–14152 PubMedGoogle Scholar
  139. Voinnet O, Vain P, Angell S, Baulcombe DC (1998) Systemic spread of sequence-specific transgene RNA degradation in plants is initiated by localized introduction of ectopic promoterless DNA. Cell 95:177–187 PubMedGoogle Scholar
  140. Wang MB, Bian XY, Wu LM, Liu LX, Smith NA, Isenegger D, Wu RM, Masuta C, Vance VB, Watson JM, Rezaian A, Dennis ES, Waterhouse PM (2004) On the role of RNA silencing in the pathogenicity and evolution of viroids and viral satellites. Proc Natl Acad Sci USA 101:3275–3280 PubMedGoogle Scholar
  141. Wang MB, Metzlaff M (2005) RNA silencing and antiviral defense in plants. Curr Opin Plant Biol 8:216–222 PubMedGoogle Scholar
  142. Wassenegger M (2005) The role of the RNAi machinery in heterochromatin formation. Cell 122:13–16 PubMedGoogle Scholar
  143. Wassenegger M, Heimes S, Riedel L, Sanger HL (1994) RNA-directed de novo methylation of genomic sequences in plants. Cell 76:567–576 PubMedGoogle Scholar
  144. Wassenegger M, Krczal G (2006) Nomenclature and functions of RNA-directed RNA polymerases. Trends Plant Sci 11:142–151 PubMedGoogle Scholar
  145. Wilkins C, Dishongh R, Moore SC, Whitt MA, Chow M, Machaca K (2005) RNA interference is an antiviral defence mechanism in Caenorhabditis elegans. Nature 436:1044–1047 PubMedGoogle Scholar
  146. Wille AC, Lucas WJ (1984) Ultrastructural and histochemical studies on guard cells. Planta 160:129–42 Google Scholar
  147. Xie M, He Y, Gan S (2001) Bidirectionalization of polar promoters in plants. Nat Biotechnol 19:677–679 PubMedGoogle Scholar
  148. Xie Z, Johansen LK, Gustafson AM, Kasschau KD, Lellis AD, Zilberman D, Jacobsen SE, Carrington JC (2004) Genetic and functional diversification of small RNA pathways in plants. PLoS Biol 2:E104 PubMedGoogle Scholar
  149. Xie Z, Allen E, Fahlgren N, Calamar A, Givan SA, Carrington JC (2005a) Expression of Arabidopsis miRNA genes. Plant Physiol 138:2145–2154 PubMedGoogle Scholar
  150. Xie Z, Allen E, Wilken A, Carrington JC (2005b) DICER-LIKE 4 functions in trans-acting small interfering RNA biogenesis and vegetative phase change in Arabidopsis thaliana. Proc Natl Acad Sci USA 102:12984–12989 PubMedGoogle Scholar
  151. Yang SJ, Carter SA, Cole AB, Cheng NH, Nelson RS (2004) A natural variant of a host RNA-dependent RNA polymerase is associated with increased susceptibility to viruses by Nicotiana benthamiana. Proc Natl Acad Sci USA 101:6297–6302 PubMedGoogle Scholar
  152. Yang Z, Ebright YW, Yu B, Chen X (2006) HEN1 recognizes 21–24 nt small RNA duplexes and deposits a methyl group onto the 2′ OH of the 3′ terminal nucleotide. Nucleic Acids Res 34:667–675 PubMedGoogle Scholar
  153. Ye K, Malinina L, Patel DJ (2003) Recognition of small interfering RNA by a viral suppressor of RNA silencing. Nature 426:874–878 PubMedGoogle Scholar
  154. Ye K, Patel DJ (2005) RNA silencing suppressor p21 of Beet yellows virus forms an RNA binding octameric ring structure. Structure 13:1375–1384 PubMedGoogle Scholar
  155. Yelina NE, Savenkov EI, Solovyev AG, Morozov SY, Valkonen JP (2002) Long-distance movement, virulence, and RNA silencing suppression controlled by a single protein in hordei- and potyviruses: complementary functions between virus families. J Virol 76:12981–12991 PubMedGoogle Scholar
  156. Yoo BC, Kragler F, Varkonyi-Gasic E, Haywood V, Archer-Evans S, Lee YM, Lough TJ, Lucas WJ (2004) A systemic small RNA signaling system in plants. Plant Cell 16:1979–2000 PubMedGoogle Scholar
  157. Yoshikawa M, Peragine A, Park MY, Poethig RS (2005) A pathway for the biogenesis of trans-acting siRNAs in Arabidopsis. Genes Dev 19:2164–2175 PubMedGoogle Scholar
  158. Yu B, Yang Z, Li J, Minakhina S, Yang M, Padgett RW, Steward R, Chen X (2005) Methylation as a crucial step in plant microRNA biogenesis. Science 307:932–935 PubMedGoogle Scholar
  159. Zamore PD, Haley B (2005) Ribo-gnome: the big world of small RNAs. Science 3092:1519–1524 Google Scholar
  160. Zhang X, Yuan Y-R, Pei Y, Lin S-S, Tuschl T, Patel DJ, Chua N-H (2007) Cucumber mosaic virus-encoded 2b suppressor inhibits Arabidopsis Argonaute1 cleavage activity to counter plant defense. Genesdev 20:3255–3268 Google Scholar
  161. Zilberman D, Cao X, Johansen LK, Xie Z, Carrington JC, Jacobsen SE (2004) Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted repeats. Curr Biol 14:1214–1220 PubMedGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2007

Authors and Affiliations

  • Thomas Hohn
    • 1
    • 2
    Email author
  • Rashid Akbergenov
    • 1
  • Mikhail M. Pooggin
    • 1
  1. 1.Department of Plant Physiology, Botanical InstituteUniversity of BaselBaselSwitzerland
  2. 2.Friedrich-Miescher InstituteUniversity of BaselBaselSwitzerland

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