Characterization of small interfering RNAs derived from the Geminivirus/Betasatellite complex using deep sequencing

PLoS ONE

Volumn 6, Issue 2, 2011, Pages

  Yang, Xiuling ^a   Wang, Yu ^b   Guo, Wei ^a   Xie, Yan ^a   Xie, Qi ^c   Fan, Longjiang ^b   Zhou, Xueping ^a  

^a ZHEJIANG UNIVERSITY   (China)

^b ZHEJIANG UNIVERSITY   (China)

^c INSTITUTE OF GENETICS AND DEVELOPMENTAL BIOLOGY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

DOUBLE STRANDED RNA; SMALL INTERFERING RNA; COMPLEMENTARY RNA; VIRUS RNA;

ARTICLE; BEGOMOVIRUS; CONTROLLED STUDY; DNA BETASATELLITE; DNA LIBRARY; DNA STRUCTURE; GEMINIVIRUS; NICOTIANA BENTHAMIANA; NONHUMAN; PLANT LEAF; RNA EXTRACTION; SEQUENCE ANALYSIS; SOLANUM; SOLANUM LYCOPERSICUM; TOMATO YELLOW LEAF CURL CHINA VIRUS; VIRUS GENOME; BIOSYNTHESIS; GENETICS; HIGH THROUGHPUT SEQUENCING; METHODOLOGY; PHYSIOLOGY; TOBACCO; TOMATO; VIROLOGY; VIRUS GENE;

BEGOMOVIRUS; EUKARYOTA; LYCOPERSICON; LYCOPERSICON ESCULENTUM; NICOTIANA BENTHAMIANA; TOMATO YELLOW LEAF CURL CHINA VIRUS;

GEMINIVIRIDAE; GENES, VIRAL; GENOME, VIRAL; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; LYCOPERSICON ESCULENTUM; PLANT LEAVES; RNA, ANTISENSE; RNA, SMALL INTERFERING; RNA, VIRAL; SEQUENCE ANALYSIS, RNA; TOBACCO;

EID: 79951778843     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0016928     Document Type: Article

References (54)

1. Lee RC, Feinbaum RL, Ambros V, (1993) The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75: 843-854.
2. Ruiz-Ferrer V, Voinnet O, (2009) Roles of plant small RNAs in biotic stress responses. Ann Rev Plant Biol 60: 485-510.
3. Baulcombe D, (2004) RNA silencing in plants. Nature 431: 356-363.
4. Xie ZX, Qi XP, (2008) Diverse small RNA-directed silencing pathways in plants. Biochim Biophys Acta 1779: 720-724.
5. Qi X, Bao FS, Xie Z, (2009) Small RNA deep sequencing reveals role for Arabidopsis thaliana RNA-dependent RNA polymerases in viral siRNA biogenesis. PLoS ONE 4: e4971.
6. Pilartz M, Jeske H, (1992) Abutilon mosaic geminivirus double-stranded DNA is packed into minichromosomes. Virology 189: 800-802.
7. Gutierrez C, (1999) Geminivirus DNA replication. Cell Mol Life Sci 56: 313-329.
8. Jeske H, Lutgemeier M, Preiss W, (2001) DNA forms indicate rolling circle and recombination-dependent replication of Abutilon mosaic virus. Embo J 20: 6158-6167.
9. Pilartz M, Jeske H, (2003) Mapping of Abutilon mosaic geminivirus minichromosomes. J Virol 77: 10808-10818.
10. Fauquet CM, Briddon RW, Brown JK, Moriones E, Stanley J, et al. (2008) Geminivirus strain demarcation and nomenclature. Arch Virol 153: 783-821.
11. Saunders K, Bedford ID, Briddon RW, Markham PG, Wong SM, et al. (2000) A unique virus complex causes Ageratum yellow vein disease. Proc Natl Acad Sci U S A 97: 6890-6895.
12. Mansoor S, Zafar Y, Briddon RW, (2006) Geminivirus disease complexes: the threat is spreading. Trends Plant Sci 11: 209-212.
13. Guo W, Jiang T, Zhang X, Li G, Zhou X, (2008) Molecular variation of satellite DNAβ molecules associated with Malvastrum yellow vein virus and their role in pathogenicity. Appl Environ Microbiol 74: 1909-1913.
14. Akbergenov R, Si-Ammour A, Blevins T, Amin I, Kutter C, et al. (2006) Molecular characterization of geminivirus-derived small RNAs in different plant species. Nucleic Acids Res 34: 462-471.
15. Blevins T, Rajeswaran R, Shivaprasad PV, Beknazariants D, Si-Ammour A, et al. (2006) Four plant Dicers mediate viral small RNA biogenesis and DNA virus induced silencing. Nucleic Acids Res 34: 6233-6246.
16. Rodriguez-Negrete EA, Carrillo-Tripp J, Rivera-Bustamante RF, (2008) RNA silencing against Geminivirus: complementary action of posttranscriptional gene silencing and transcriptional gene silencing in host-recovery. J Virol 83: 1332-1340.
17. Cui X, Li G, Wang D, Hu D, Zhou X, (2005) A Begomovirus DNAβ-encoded protein binds DNA, functions as a suppressor of RNA silencing, and targets the cell nucleus. J Virol 79: 10764-10775.
18. Bisaro DM, (2006) Silencing suppression by geminivirus proteins. Virology 344: 158-168.
19. Ding SW, Voinnet O, (2007) Antiviral immunity directed by small RNAs. Cell 130: 413-426.
20. Sharma P, Ikegami M, (2008) RNA-silencing suppressors of geminiviruses. J Gen Plant Pathol 74: 189-202.
21. Raja P, Wolf JN, Bisaro DM, (2010) RNA silencing directed against geminiviruses: Post-transcriptional and epigenetic components. Biochim Biophys Acta 1799: 337-351.
22. Cui X, Tao X, Xie Y, Fauquet CM, Zhou X, (2004) A DNAβ associated with Tomato yellow leaf curl China virus is required for symptom induction. J Virol 78: 13966-13974.
23. Donaire L, Wang Y, Gonzalez-Ibeas D, Mayer KF, Aranda MA, et al. (2009) Deep-sequencing of plant viral small RNAs reveals effective and widespread targeting of viral genomes. Virology 392: 203-214.
24. Mlotshwa S, Pruss GJ, Peragine A, Endres MW, Li J, et al. (2008) DICER-LIKE2 plays a primary role in transitive silencing of transgenes in Arabidopsis. PLoS One 3: e1755.
25. Mi S, Cai T, Hu Y, Chen Y, Hodges E, et al. (2008) Sorting of small RNAs into Arabidopsis Argonaute complexes is directed by the 5′ terminal nucleotide. Cell 133: 116-127.
26. Montgomery TA, Howell MD, Cuperus JT, Li DW, Hansen JE, et al. (2008) Specificity of ARGONAUTE7-miR390 interaction and dual functionality in TAS3 trans-acting siRNA formation. Cell 133: 128-141.
27. Takeda A, Iwasaki S, Watanabe T, Utsumi M, Watanabe Y, (2008) The mechanism selecting the guide strand from small RNA duplexes is different among Argonaute proteins. Plant and Cell Physiol 49: 493-500.
28. Wu L, Zhang QQ, Zhou HY, Ni FR, Wu XY, et al. (2009) Rice microRNA effector complexes and targets. Plant Cell 21: 3421-3435.
29. Chellappan P, Vanitharani R, Pita J, Fauquet CM, (2004) Short interfering RNA accumulation correlates with host recovery in DNA virus-infected hosts, and gene silencing targets specific viral sequences. J Virol 78: 7465-7477.
30. Vanitharani R, Chellappan P, Fauquet CM, (2005) Geminiviruses and RNA silencing. Trends Plant Sci 10: 144-151.
31. German M, Livia D, Cesar L, Vicente P, Gustavo G, (2010) High-throughput sequencing of Hop stunt viroid-derived small RNAs from cucumber leaves and phloem. Mol Plant Pathol 11: 347-359.
32. 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.
33. Vaucheret H, (2006) Post-transcriptional small RNA pathways in plants: mechanisms and regulations. Genes Dev 20: 759-771.
34. Wang XB, Wu QF, Ito T, Cillo F, Li WX, et al. (2010) RNAi-mediated viral immunity requires amplification of virus-derived siRNAs in Arabidopsis thaliana. Proc Natl Acad Sci U S A 107: 484-489.
35. Aragao FJL, Faria JC, (2009) First transgenic geminivirus-resistant plant in the field. Nat Biotechnol 27: 1086-1088.
36. Smith NA, Singh SP, Wang MB, Stoutjesdijk PA, Green AG, et al. (2000) Gene expression- Total silencing by intron-spliced hairpin RNAs. Nature 407: 319-320.
37. Morel JB, Godon C, Mourrain P, Beclin C, Boutet S, et al. (2002) Fertile hypomorphic ARGONAUTE (ago1) mutants impaired in post-transcriptional gene silencing and virus resistance. Plant Cell 14: 629-639.
38. Zhang XR, Yuan YR, Pei Y, Lin SS, Tuschl T, et al. (2006) Cucumber mosaic virus-encoded 2b suppressor inhibits Arabidopsis Argonaute1 cleavage activity to counter plant defense. Genes Dev 20: 3255-3268.
39. Pantaleo V, Szittya G, Burgyan J, (2007) Molecular bases of viral RNA targeting by viral small interfering RNA-programmed RISC. J Virol 81: 3797-3806.
40. Qu F, Ye XH, Morris TJ, (2008) Arabidopsis DRB4, AGO1, AGO7, and RDR6 participate in a DCL4-initiated antiviral RNA silencing pathway negatively regulated by DCL1. Proc Natl Acad Sci U S A 105: 14732-14737.
41. Qi YJ, He XY, Wang XJ, Kohany O, Jurka J, et al. (2006) Distinct catalytic and non-catalytic roles of ARGONAUTE4 in RNA-directed DNA methylation. Nature 443: 1008-1012.
42. Raja P, Sanville BC, Buchmann RC, Bisaro DM, (2008) Viral genome methylation as an epigenetic defense against geminiviruses. J Virol 82: 8997-9007.
43. Deleris A, Gallego-Bartolome J, Bao JS, Kasschau KD, Carrington JC, et al. (2006) Hierarchical action and inhibition of plant Dicer-like proteins in antiviral defense. Science 313: 68-71.
44. Diaz-Pendon JA, Li F, Li WX, Ding SW, (2007) 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: 2053-2063.
45. Garcia-Ruiz H, Takeda A, Chapman EJ, Sullivan CM, Fahlgren N, et al. (2010) 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: 481-496.
46. Chen HM, Chen LT, Patel K, Li YH, Baulcombe DC, et al. (2010) 22-nucleotide RNAs trigger secondary siRNA biogenesis in plants. Proc Natl Acad Sci U S A 107: 15269-15274.
47. Cuperus JT, Carbonell A, Fahlgren N, Garcia-Ruiz H, Burke RT, et al. (2010) Unique functionality of 22-nt miRNAs in triggering RDR6-dependent siRNA biogenesis from target transcripts in Arabidopsis. Nat Struct Mol Biol 17: 997-1003.
48. 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.
49. Yang S-J, Carter SA, Cole AB, Cheng N-H, 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 U S A 101: 6297-6302.
50. Ribeiro SG, Lohuis H, Goldbach R, Prins M, (2007) Tomato chlorotic mottle virus is a target of RNA silencing but the presence of specific short interfering RNAs does not guarantee resistance in transgenic plants. J Virol 81: 1563-1573.
51. Hagen C, Rojas MR, Kon T, Gilbertson RL, (2008) Recovery from Cucurbit leaf crumple virus (Family Geminiviridae, genus Begomovirus) infection is an adaptive antiviral response associated with changes in viral small RNAs. Phytopathology 98: 1029-1037.
52. Xie Y, Zhou XP, Zhang ZK, Qi YJ, (2002) Tobacco curly shoot virus isolated in Yunnan is a distinct species of Begomovirus. Chinese Sci Bull 47: 197-200.
53. Mette MF, Aufsatz W, van der Winden J, Matzke MA, Matzke AJM, (2000) Transcriptional silencing and promoter methylation triggered by double-stranded RNA. Embo J 19: 5194-5201.
54. Itaya A, Zhong X, Bundschuh R, Qi Y, Wang Y, et al. (2007) A structured viroid RNA serves as a substrate for Dicer-Like cleavage to produce biologically active small RNAs but is resistant to RNA-induced silencing complex-mediated degradation. J Virol 81: 2980-2994.