Nicotiana Small RNA Sequences Support a Host Genome Origin of Cucumber Mosaic Virus Satellite RNA

PLoS Genetics

Volumn 11, Issue 1, 2015, Pages

  Zahid, Kiran ^a,b,d   Zhao, Jian Hua ^c   Smith, Neil A ^a   Schumann, Ulrike ^a   Fang, Yuan Yuan ^c   Dennis, Elizabeth S ^a   Zhang, Ren ^b   Guo, Hui Shan ^c   Wang, Ming Bo ^a  

^a CSIRO   (Australia)

^b UNIVERSITY OF WOLLONGONG   (Australia)

^c INSTITUTE OF GENETICS AND DEVELOPMENTAL BIOLOGY   (China)

^d NATIONAL UNIVERSITY OF SCIENCES AND TECHNOLOGY   (Pakistan)

Author keywords

[No Author keywords available]

Indexed keywords

SATELLITE RNA; BETA GLUCURONIDASE; SMALL INTERFERING RNA;

ARTICLE; CONTROLLED STUDY; CUCUMBER MOSAIC VIRUS; DNA METHYLATION; DNA SEQUENCE; GENE ACTIVITY; GENE EXPRESSION; GENE FUSION; NICOTIANA TABACUM; NONHUMAN; NORTHERN BLOTTING; PLANT GENOME; PROMOTER REGION; RNA SEQUENCE; SEQUENCE HOMOLOGY; SOUTHERN BLOTTING; TRANSGENE; CUCUMOVIRUS; GENE SILENCING; GENETICS; HELPER VIRUS; PATHOGENICITY; SEQUENCE ANALYSIS; TOBACCO; TRANSGENIC PLANT; VIROLOGY;

CUCUMBER MOSAIC VIRUS; CUCUMBER MOSAIC VIRUS SATELLITE RNA; NICOTIANA; NICOTIANA TABACUM;

CUCUMBER MOSAIC VIRUS SATELLITE; CUCUMOVIRUS; DNA METHYLATION; GENE SILENCING; GENOME, PLANT; GLUCURONIDASE; HELPER VIRUSES; PLANTS, GENETICALLY MODIFIED; RNA, SMALL INTERFERING; SEQUENCE ANALYSIS, RNA; TOBACCO; TRANSGENES;

EID: 84924370684     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1004906     Document Type: Article

References (46)

1. Simon AE, Roossinck MJ, Havelda Z, (2004) Plant virus satellite and defective interfering RNAs: new paradigms for a new century. Annu Rev Phytopathol 42: 415–437.
2. Hu C-C, Hsu Y-H, Lin N-S, (2009) Satellite RNAs and satellite viruses of plants. Viruses 1: 1325–1350.
3. Roossinck M, Sleat D, Palukaitis P, (1992) Satellite RNAs of plant viruses: structures and biological effects. Microbiological Reviews 56: 265–279.
4. Garcia-Arenal F, Palukaitis P (1999) Structure and functional relationships of satellite RNAs of cucumber mosaic virus. Satellites and Defective Viral RNAs: Springer. pp. 37–63.
5. Wang X-B, Wu Q, 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 USA 107: 484–489.
6. Choi SH, Seo JK, Kwon SJ, Rao AL, (2012) Helper virus-independent transcription and multimerization of a satellite RNA associated with cucumber mosaic virus. J Virol 86: 4823–4832.
7. Chaturvedi S, Kalantidis K, Rao AL, (2014) A bromodomain-containing host protein mediates the nuclear importation of a satellite RNA of Cucumber mosaic virus. J Virol 88: 1890–1896.
8. Collmer CW, Howell SH, (1992) Role of satellite RNA in the expression of symptoms caused by plant viruses. AnnRev Phytopathol 30: 419–442.
9. Shimura H, Pantaleo V, Ishihara T, Myojo N, Inaba J-i, et al. (2011) 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: e1002021.
10. Smith NA, Eamens AL, Wang M-B, (2011) Viral small interfering RNAs target host genes to mediate disease symptoms in plants. PLoS Pathog 7: e1002022.
11. Simon AE, Howell SH, (1986) The virulent satellite RNA of turnip crinkle virus has a major domain homologous to the 3'end of the helper virus genome. The EMBO J 5: 3423.
12. Hajimorad M, Ghabrial S, Roossinck M, (2009) De novo emergence of a novel satellite RNA of cucumber mosaic virus following serial passages of the virus derived from RNA transcripts. Arch Virol 154: 137–140.
13. Collmer CW, Hadidi A, Kaper J, (1985) Nucleotide sequence of the satellite of peanut stunt virus reveals structural homologies with viroids and certain nuclear and mitochondrial introns. Proc Natl Acad Sci USA 82: 3110–3114.
14. Meister G, Tuschl T, (2004) Mechanisms of gene silencing by double-stranded RNA. Nature 431: 343–349.
15. Baulcombe D, (2005) RNA silencing. Trends Biochem Sci 30: 290–293.
16. Baulcombe D, (2004) RNA silencing in plants. Nature 431: 356–363.
17. Eamens A, Wang M-B, Smith NA, Waterhouse PM, (2008) RNA silencing in plants: yesterday, today, and tomorrow. Plant Physiol 147: 456–468.
18. Bartel DP, (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116: 281–297.
19. Ding S-W, Voinnet O, (2007) Antiviral immunity directed by small RNAs. Cell 130: 413–426.
20. Matzke MA, Birchler JA, (2005) RNAi-mediated pathways in the nucleus. Nat Rev Genet 6: 24–35.
21. Zhang H, Zhu J-K, (2011) RNA-directed DNA methylation. Curr Opin Plant Biol 14: 142–147.
22. Wang M-B, Wesley SV, Finnegan EJ, Smith NA, Waterhouse PM, (2001) Replicating satellite RNA induces sequence-specific DNA methylation and truncated transcripts in plants. RNA 7: 16–28.
23. Masuta C, Kuwata S, Takanami Y, (1988) Effects of extra 5'non-viral bases on the infectivity of transcripts from a cDNA clone of satellite RNA (strain Y) of cucumber mosaic virus. J Biochem 104: 841–846.
24. Park YD, Papp I, Moscone E, Iglesias V, Vaucheret H, et al. (1996) Gene silencing mediated by promoter homology occurs at the level of transcription and results in meiotically heritable alterations in methylation and gene activity. Plant J 9: 183–194.
25. Clark SJ, Harrison J, Paul CL, Frommer M, (1994) High sensitivity mapping of methylated cytosines. Nucleic Acids Res 22: 2990–2997.
26. Le TN, Schumann U, Smith NA, Tiwari S, Au P, et al. (2014) DNA demethylases target promoter transposable elements to positively regulate stress responsive genes in Arabidopsis. Genome Biol 15: 458.
27. Mosher RA, Melnyk CW, Kelly KA, Dunn RM, Studholme DJ, et al. (2009) Uniparental expression of PolIV-dependent siRNAs in developing endosperm of Arabidopsis. Nature 460: 283–286.
28. Wang H, Zhang X, Liu J, Kiba T, Woo J, et al. (2011) Deep sequencing of small RNAs specifically associated with Arabidopsis AGO1 and AGO4 uncovers new AGO functions. Plant J 67: 292–304.
29. Hou WN, Duan CG, Fang RX, Zhou XY, Guo HS, (2011) Satellite RNA reduces expression of the 2b suppressor protein resulting in the attenuation of symptoms caused by Cucumber mosaic virus infection. Mol Plant Pathol 12: 595–605.
30. Kasschau KD, Fahlgren N, Chapman EJ, Sullivan CM, Cumbie JS, et al. (2007) Genome-wide profiling and analysis of Arabidopsis siRNAs. PLoS Biol 5: e57.
31. Waterhouse PM, Wang M-B, Lough T, (2001) Gene silencing as an adaptive defence against viruses. Nature 411: 834–842.
32. Matzke MA, Aufsatz W, Kanno T, Mette MF, Matzke AJ, (2002) Homology-dependent gene silencing and host defense in plants. Advances in Genetics 46: 235–275.
33. Wang M-B, Helliwell CA, Wu L-M, Waterhouse PM, Peacock WJ, et al. (2008) Hairpin RNAs derived from RNA polymerase II and polymerase III promoter-directed transgenes are processed differently in plants. RNA 14: 903–913.
34. Duan C-G, Fang Y-Y, Zhou B-J, Zhao J-H, Hou W-N, et al. (2012) Suppression of Arabidopsis ARGONAUTE1-mediated slicing, transgene-induced RNA silencing, and DNA methylation by distinct domains of the Cucumber mosaic virus 2b protein. Plant Cell 24: 259–274.
35. Steinhauer D, Holland J, (1987) Rapid evolution of RNA viruses. Ann Rev Microbiol 41: 409–431.
36. Horie M, Honda T, Suzuki Y, Kobayashi Y, Daito T, et al. (2010) Endogenous non-retroviral RNA virus elements in mammalian genomes. Nature 463: 84–87.
37. Chiba S, Kondo H, Tani A, Saisho D, Sakamoto W, et al. (2011) Widespread endogenization of genome sequences of non-retroviral RNA viruses into plant genomes. PLoS Pathog 7: e1002146.
38. Gleave AP, (1992) A versatile binary vector system with a T-DNA organisational structure conducive to efficient integration of cloned DNA into the plant genome. Plant Mol Biol 20: 1203–1207.
39. Chen S, Helliwell CA, Wu L-M, Dennis ES, Upadhyaya NM, et al. (2005) A novel T-DNA vector design for selection of transgenic lines with simple transgene integration and stable transgene expression. Funct Plant Biol 32: 671–681.
40. Cazzonelli CI, Velten J, (2006) An in vivo, luciferase-based, Agrobacterium-infiltration assay system: implications for post-transcriptional gene silencing. Planta 224: 582–597.
41. Wood CC, Petrie JR, Shrestha P, Mansour MP, Nichols PD, et al. (2009) A leaf-based assay using interchangeable design principles to rapidly assemble multistep recombinant pathways. Plant Biotech J 7: 914–924.
42. Draper J, Scott R, Armitage P, Walden R (1988) Plant genetic transformation and gene expression: a laboratory manual: Blackwell Scientific Publications.
43. De Vries S, Hoge H, Bisseling T (1989) Isolation of total and polysomal RNA from plant tissues. Plant Molecular Biology Manual: Springer. pp. 323–335.
44. Finn TE, Wang L, Smolilo D, Smith NA, White R, et al. (2011) Transgene expression and transgene-induced silencing in diploid and autotetraploid Arabidopsis. Genetics 187: 409–423.
45. Meng L, Lemaux P, (2003) A simple and rapid method for nuclear run-on transcription assays in plants. Plant Mol Biol Rep 21: 65–71.
46. He X-F, Fang Y-Y, Feng L, Guo H-S, (2008) Characterization of conserved and novel microRNAs and their targets, including a TuMV-induced TIR–NBS–LRR class R gene-derived novel miRNA in Brassica. FEBS letters 582: 2445–2452.