High-throughput sequencing of Hop stunt viroid-derived small RNAs from cucumber leaves and phloem

Molecular Plant Pathology

Volumn 11, Issue 3, 2010, Pages 347-359

  Martinez, German ^a   Donaire, Livia ^b   Llave, Cesar ^b   Pallas, Vicente ^a   Gomez, Gustavo ^a  

^a Ciudad Politécnica de la Innovación   (Spain)

^b CENTRO DE INVESTIGACIONES BIOLÓGICAS   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMALIA; CUCUMIS SATIVUS; HOP STUNT VIROID; HUMULUS; VIROIDS;

EID: 77953035621     PISSN: 14646722     EISSN: 13643703     Source Type: Journal    
DOI: 10.1111/j.1364-3703.2009.00608.x     Document Type: Article

References (58)

1. Aung K, Lin SI, Wu CC, Huang YT, Su CI, Chiou TJ. pho2, a phosphate over accumulator, is caused by a nonsense mutation in a microRNA399 target gene. Plant Physiol. 2006, 141:1000-1011.
2. Bari R, Pant BD, Stitt M, Scheible WR. PHO2, microRNA399, and PHR1 define a phosphate-signaling pathway in plants. Plant Physiol. 2006, 141:988-999.
3. Baulcombe D. RNA silencing in plants. Nature 2004, 431:356-363.
4. Bouche N, Lauressergues D, Gasciolli V, Vaucheret H. An antagonistic function for Arabidopsis DCL2 in development and a new function for DCL4 in generating viral siRNAs. EMBO J. 2006, 25:3347-3356.
5. Brodersen P, Voinnet O. The diversity of RNA silencing pathways in plants. Trends Genet. 2006, 22:268-280.
6. Brosnan CA, Mitter N, Christie M, Smith NA, Waterhouse PM, Carrol BJ. Nuclear gene silencing directs reception of long-distance mRNA silencing in Arabidopsis. Proc. Natl. Acad. Sci. USA 2007, 104:14741-14746.
7. Buhtz A, Springer F, Chappell L, Baulcombe D, Kehr J. Identification and characterization of small RNAs from the phloem of Brassica napus. Plant J. 2008, 53:739-749.
8. Carbonell A, Martínez de Alba AE, Flores R, Gago S. Double-stranded RNA interferes in a sequence-specific manner with the infection of representative members of the two viroid families. Virology 2008, 371:44-53.
9. Carra A, Mica E, Gambino G, Pindo M, Moser C, Pè M, Schubert A. Cloning and characterization of small non-coding RNAs from grape. Plant J. 2009, 59:750-753.
10. Chapman EJ, Carrington JC. Specialization and evolution of endogenous small RNA pathways. Nat. Rev. Genet. 2007, 8:884-896.
11. Daròs JA, Elena SF, Flores R. Viroids: an Ariadne's thread into the RNA labyrinth. EMBO Rep. 2006, 7:593-598.
12. Deleris A, Gallego-Bartolome J, Bao J, Kasschau KD, Carrington JC, Voinnet O. Hierarchical action and inhibition of plant Dicer-like proteins in antiviral defense. Science 2006, 313:68-71.
13. Denti MA, Boutla A, Tsagris M, Tabler M. Short interfering RNAs specific for Potato spindle tuber viroid are found in the cytoplasm but not in the nucleus. Plant J. 2004, 37:762-769.
14. Ding B. Biology of viroid-host interactions. Annu. Rev. Phytopathol. 2009, 47:105-131.
15. Donaire L, Barajas D, Martinez-Garcia B, Martinez-Priego L, Pagan I, Llave C. Structural and genetic requirements for the biogenesis of Tobacco rattle virus-derived small interfering RNAs. J. Virol. 2008, 82:5167-5177.
16. Donaire L, Wang Y, Gonzalez-Ibeas D, Mayer K, Aranda M, Llave C. Deep-sequencing of plant viral small RNAs reveals effective and widespread targeting of viral genomes. Virology 2009, 30:203-214.
17. Dunoyer P, Voinnet O. Mixing and matching: the essence of plant systemic silencing? Trends Genet. 2008, 24:151-154.
18. Flores R, Hernández C, Martínez de Alba AE, Daròs JA, Di Serio F. Viroids and viroid-host interactions. Ann. Rev. Phytopathol. 2005, 43:117-139.
19. Gómez G, Pallás V. Identification of an in vitro ribonucleoprotein complex between a viroid RNA and a phloem protein from cucumber plants. Mol. Plant-Microbe Interact. 2001, 14:910-913.
20. Gómez G, Pallás V. A long-distance translocatable phloem protein from cucumber forms a ribonucleoprotein complex in vivo with Hop stunt viroid RNA. J. Virol. 2004, 78:10104-10110.
21. Gómez G, Pallás V. Hop stunt viroid is processed and translocated in transgenic N. benthamiana plants. Mol. Plant Pathol. 2006, 7:511-517.
22. Gómez G, Pallás V. Mature monomeric forms of Hop stunt viroid resist RNA silencing in transgenic plants. Plant J. 2007, 51:1041-1049.
23. Gómez G, Torres H, Pallás V. Identification of translocatable RNA-binding phloem proteins from melon, potential components of the long-distance RNA transport system. Plant J. 2005, 41:107-116.
24. Gómez G, Martinez G, Pallas V. Viroid-induced symptoms in Nicotiana benthamiana plants are dependent on RDR6 activity. Plant Physiol. 2008, 148:414-423.
25. Gómez G, Martinez G, Pallás V. Interplay between viroid-induced pathogenesis and RNA silencing pathways. Trends Plant Sci. 2009, 14:264-269.
26. Itaya A, Folimonov A, Matsuda Y, Nelson RS, Ding B. Potato spindle tuber viroid as inducer of RNA silencing in infected tomato. Mol. Plant-Microbe Interact. 2001, 14:1332-1334.
27. Itaya A, Zhong X, Bundschuh R, Qi Y, Wang Y, Takeda R, Harris AR, Molina C, Nelson RS, Ding B. A structured viroid RNA is substrate for Dicer-like cleavage to produce biologically active small RNAs but is resistant to RISC-mediated degradation. J. Virol. 2007, 81:2980-2994.
28. Jorgensen RA. RNA traffics information systemically in plants. Proc. Natl. Acad. Sci. USA 2002, 99:11561-11563.
29. Kalantidis K, Schumacher HT, Alexiadis T, Helm JM. RNA silencing movement in plants. Biol. Cell 2008, 100:13-26.
30. Kasschau KD, Fahlgren N, Chapman EJ, Sullivan CM, Cumbie JS, Givan SA, Carrington JC. Genome-wide profiling and analysis of Arabidopsis siRNAs. PLoS Biol. 2007, 5:e57.
31. Kim VN. Sorting out small RNAs. Cell 2008, 133:25-26.
32. Machida S, Yanahata N, Watanuki H, Owens RA, Sano T. Successive accumulation of two size classes of viroid-specific small RNA in Potato spindle tuber viroid-infected tomato plants. J. Gen. Virol. 2007, 88:3452-3457.
33. Markarian N, Li HW, Ding SW, Semancik JS. RNA silencing as related to viroid induced symptom expression. Arch. Virol. 2004, 149:397-406.
34. Martín R, Arenas C, Daròs JA, Covarrubias A, Reyes JL, Chua N. Characterization of small RNAs derived from Citrus exocortis viroid in infected tomato plants. Virology 2007, 367:135-146.
35. Martinez de Alba AE, Flores R, Hernandez C. Two chloroplastic viroids induce the accumulation of the small RNAs associated with post-transcriptional gene silencing. J. Virol. 2002, 76:13094-13096.
36. Matoušek J, Kozlová P, Orctová L, Schmitz A, Pesina K, Bannach O, Diermann N, Steger G, Riesner D. Accumulation of viroid-specific small RNAs and increase in nucleolytic activities linked to viroid-caused pathogenesis. Biol. Chem. 2007, 388:1-13.
37. Mi S, Cai T, Hu Y, Chen Y, Hodges E, Ni F, Wu L, Li S, Zhou H, Long C, Chen S, Hannon GJ, Qi Y. Sorting of small RNAs into Arabidopsis argonaute complexes is directed by the 5′ terminal nucleotide. Cell 2008, 133:116-127.
38. Montgomery TA, Howell MD, Cuperus JT, Li D, Hansen JE, Alexander AL, Chapman EJ, Fahlgren N, Allen E, Carrington JC. Specificity of ARGONAUTE7-miR390 interaction and dual functionality in TAS3 trans-acting siRNA formation. Cell 2008, 133:128-141.
39. Pak J, Fire A. Distinct populations of primary and secondary effectors during RNAi in C. elegans. Science 2007, 315:241-244.
40. Palauqui JC, Elmayan T, Pollien JM, Vaucheret H. Systemic acquired silencing: transgene-specific post-transcriptional silencing is transmitted by grafting from silenced stocks to non-silenced scions. EMBO J. 1997, 16:4738-4745.
41. Pallás V, Navarro A, Flores R. Isolation of a viroid-like RNA from Hop different to Hop stunt viroid. J. Gen. Virol. 1987, 68:3201-3205.
42. Papaefthimiou I, Hamilton AJ, Denti MA, Baulcombe DC, Tsagris M, Tabler M. Replicating Potato spindle tuber viroid RNA is accompanied by short RNA fragments that are characteristic of post-transcriptional gene silencing. Nucleic Acids Res. 2001, 29:2395-2400.
43. Qi X, Bao FS, Xie Z. Small RNA deep sequencing reveals role for Arabidopsis thaliana RNA-dependent RNA polymerases in viral siRNA biogenesis. PLoS ONE 2009, 4:e4971.
44. Ramachandran V, Chen X. Small RNA metabolism in Arabidopsis. Trends Plant Sci. 2008, 13:368-374.
45. Ruiz-Ferrer V, Voinnet O. Roles of plant small RNAs in biotic stress responses. Annu. Rev. Plant Biol. 2009, 60:485-510.
46. Schiebel W, Pélissier T, Riedel L, Thalmeir S, Schiebel R, Kempe D, Lottspeich F, Sänger HL, Wassenegger M. Isolation of an RNA-directed RNA polymerase-specific cDNA clone from tomato. Plant Cell 1998, 10:2087-2101.
47. Sijen T, Steiner FA, Thijssen KL, Plasterk RH. Secondary siRNAs result from unprimed RNA synthesis and form a distinct class. Science 2007, 315:244-247.
48. St-Pierre P, Hassen FI, Thompson D, Perreault JP. Characterization of the siRNAs associated with peach latent mosaic viroid infection. Virology 2009, 383:178-182.
49. Takeda A, Iwasaki S, Watanabe T, Utsumi M, Watanabe Y. The mechanism selecting the guide strand from small RNA duplexes is different among argonaute proteins. Plant Cell Physiol. 2008, 49:493-500.
50. Tsagris M, Martinez de Alba AE, Gozmanova M, Kalantidis K. Viroids. Cell Microbiol. 2008, 10:2168-2179.
51. Válóczi A, Várallyay E, Kauppinen S, Burgyán J, Havelda Z. Spatio-temporal accumulation of microRNAs is highly coordinated in developing plant tissues. Plant J. 2006, 47:140-151.
52. Vaucheret H. Post-transcriptional small RNA pathways in plants: mechanisms and regulations. Genes Dev. 2006, 20:759-771.
53. Vogt U, Pelissier T, Putz A, Razvi F, Fischer R, Wassenneger M. Viroid-induced RNA silencing of GFP-viroid fusion transgenes does not induce extensive spreading of methylation or transitive silencing. Plant J. 2004, 38:107-118.
54. Voinnet O. Use, tolerance and avoidance of amplified RNA silencing by plants. Trends Plant Sci. 2008, 13:317-328.
55. Voinnet O, Vain P, Angel S, Baulcombe D. Systemic spread of sequence specific transgene RNA degradation in plants is initiated by localized introduction of ectopic promotorless DNA. Cell 1998, 95:177-187.
56. 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. On the role of RNA silencing in the pathogenicity and evolution of viroids and viral satellites. Proc. Natl. Acad. Sci. USA 2004, 101:3275-3280.
57. Wassenegger M, Krczal G. Nomenclature and functions of RNA-directed RNA polymerases. Trends Plant Sci. 2006, 11:142-151.
58. Yoo BC, Kragler F, Varkonyi-Gasic E, Haywood V, Archer-Evans S, Lee YM, Lough TJ, Lucas WJ. A systemic small RNA signaling system in plants. Plant Cell 2004, 16:1979-2000.