Virus-based microRNA silencing in plants

Plant Physiology

Volumn 164, Issue 1, 2014, Pages 36-47

  Sha, Aihua ^a,b   Zhao, Jinping ^a   Yin, Kangquan ^a   Tang, Yang ^a,d   Wang, Yan ^a   Wei, Xiang ^a   Hong, Yiguo ^c   Liu, Yule ^a  

^a TSINGHUA UNIVERSITY   (China)

^b INSTITUTE OF PLANT PROTECTION   (China)

^c HANGZHOU NORMAL UNIVERSITY   (China)

^d ELI LILLY AND COMPANY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; PLANT RNA;

ARTICLE; FLOWER; GENE EXPRESSION REGULATION; GENE SILENCING; GENE VECTOR; GENETICS; GROWTH, DEVELOPMENT AND AGING; HISTOLOGY; PLANT LEAF; PLANT VIRUS; TOBACCO; TOMATO;

FLOWERS; GENE EXPRESSION REGULATION, PLANT; GENE SILENCING; GENETIC VECTORS; LYCOPERSICON ESCULENTUM; MICRORNAS; PLANT LEAVES; PLANT VIRUSES; RNA, PLANT; TOBACCO;

EID: 84891764349     PISSN: 00320889     EISSN: 15322548     Source Type: Journal    
DOI: 10.1104/pp.113.231100     Document Type: Article

References (63)

1. Allen RS, Li J, Stahle MI, Dubroué A, Gubler F, Millar AA (2007) Genetic analysis reveals functional redundancy and the major target genes of the Arabidopsis miR159 family. Proc Natl Acad Sci USA 104: 16371-16376
2. Ambros V, Bartel B, Bartel DP, Burge CB, Carrington JC, Chen X, Dreyfuss G, Eddy SR, Griffiths-Jones S, Marshall M, et al (2003) A uniform system for microRNA annotation. RNA 9: 277-279
3. An G, Ebert PR, Mitra A, Ha SB (1988) Binary vectors. In SB Gelvin, RA Schilperoort, DP Verma, eds, Plant Molecular Biology Manual. Kluwer Academic Publishers, Dordrecht, The Netherlands, pp A3:1-A3:19
4. Bachan S, Dinesh-Kumar SP (2012) Tobacco rattle virus (TRV)-based virus-induced gene silencing. Methods Mol Biol 894: 83-92
5. Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116: 281-297
6. Chen X (2004) A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development. Science 303: 2022-2025
7. Chuck G, Meeley R, Hake S (2008) Floral meristem initiation and meristem cell fate are regulated by the maize AP2 genes ids1 and sid1. Development 135: 3013-3019
8. Deng X, Kelloniemi J, Haikonen T, Vuorinen AL, Elomaa P, Teeri TH, Valkonen JP (2013) Modification of Tobacco rattle virus RNA1 to serve as a VIGS vector reveals that the 29K movement protein is an RNA silencing suppressor of the virus. Mol Plant Microbe Interact 26: 503-514
9. Ding XS, Schneider WL, Chaluvadi SR, Mian MA, Nelson RS (2006) Characterization of a Brome mosaic virus strain and its use as a vector for gene silencing in monocotyledonous hosts. Mol Plant Microbe Interact 19: 1229-1239
10. Dong Y, Burch-Smith TM, Liu Y, Mamillapalli P, Dinesh-Kumar SP (2007) A ligation-independent cloning tobacco rattle virus vector for high-throughput virus-induced gene silencing identifies roles for NbMADS4-1 and-2 in floral development. Plant Physiol 145: 1161-1170
11. Eamens AL, Agius C, Smith NA, Waterhouse PM, Wang MB (2011) Efficient silencing of endogenous microRNAs using artificial microRNAs in Arabidopsis thaliana. Mol Plant 4: 157-170
12. Eckardt NA (2012) A new tool for investigating small RNA function. Plant Cell 24: 372
13. Franco-Zorrilla JM, Valli A, Todesco M, Mateos I, Puga MI, Rubio-Somoza I, Leyva A, Weigel D, García JA, Paz-Ares J (2007) Target mimicry provides a new mechanism for regulation of microRNA activity. Nat Genet 39: 1033-1037
14. Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ (2008) miRBase: tools for microRNA genomics. Nucleic Acids Res 36: D154-D158
15. HaM, PangM, Agarwal V, Chen ZJ (2008) Interspecies regulation of microRNAs and their targets. Biochim Biophys Acta 1779: 735-742
16. Hanania U, Velcheva M, Or E, Flaishman M, Sahar N, Perl A (2007) Silencing of chaperonin 21, that was differentially expressed in inflorescence of seedless and seeded grapes, promoted seed abortion in tobacco and tomato fruits. Transgenic Res 16: 515-525
17. Hefferon KL (2012) Plant virus expression vectors set the stage as production platforms for biopharmaceutical proteins. Virology 433: 1-6
18. Holzberg S, Brosio P, Gross C, Pogue GP (2002) Barley stripe mosaic virusinduced gene silencing in a monocot plant. Plant J 30: 315-327
19. Igarashi A, Yamagata K, Sugai T, Takahashi Y, Sugawara E, Tamura A, Yaegashi H, Yamagishi N, Takahashi T, Isogai M, et al (2009) Apple latent spherical virus vectors for reliable and effective virusinduced gene silencing among a broad range of plants including tobacco, tomato, Arabidopsis thaliana, cucurbits, and legumes. Virology 386: 407-416
20. Ivashuta S, Banks IR, Wiggins BE, Zhang Y, Ziegler TE, Roberts JK, Heck GR (2011) Regulation of gene expression in plants through miRNA inactivation. PLoS ONE 6: e21330
21. Jia HF, Chai YM, Li CL, Lu D, Luo JJ, Qin L, Shen YY (2011) Abscisic acid plays an important role in the regulation of strawberry fruit ripening. Plant Physiol 157: 188-199
22. Jin H (2008) Endogenous small RNAs and antibacterial immunity in plants. FEBS Lett 582: 2679-2684
23. Jones-Rhoades MW, Bartel DP, Bartel B (2006) MicroRNAS and their regulatory roles in plants. Annu Rev Plant Biol 57: 19-53
24. Jung JH, Park CM (2007) MIR166/165 genes exhibit dynamic expression patterns in regulating shoot apical meristem and floral development in Arabidopsis. Planta 225: 1327-1338
25. Kaloshian I (2007) Virus-induced gene silencing in plant roots. Methods Mol Biol 354: 173-181
26. Kim J, Jung JH, Reyes JL, Kim YS, Kim SY, Chung KS, Kim JA, Lee M, Lee Y, Narry Kim V, et al (2005) MicroRNA-directed cleavage of ATHB15 mRNA regulates vascular development in Arabidopsis inflorescence stems. Plant J 42: 84-94
27. Larsen JS, Curtis WR (2012) RNA viral vectors for improved Agrobacteriummediated transient expression of heterologous proteins in Nicotiana benthamiana cell suspensions and hairy roots. BMC Biotechnol 12: 21
28. Li F, Pignatta D, Bendix C, Brunkard JO, Cohn MM, Tung J, Sun H, Kumar P, Baker B (2012) MicroRNA regulation of plant innate immune receptors. Proc Natl Acad Sci USA 109: 1790-1795
29. Liu Y, Schiff M, Dinesh-Kumar SP (2002a) Virus-induced gene silencing in tomato. Plant J 31: 777-786
30. Liu Y, Schiff M, Marathe R, Dinesh-Kumar SP (2002b) Tobacco Rar1, EDS1 and NPR1/NIM1 like genes are required for N-mediated resistance to tobacco mosaic virus. Plant J 30: 415-429
31. Lu R, Martin-Hernandez AM, Peart JR, Malcuit I, Baulcombe DC (2003) Virus-induced gene silencing in plants. Methods 30: 296-303
32. Lu S, Sun YH, Chiang VL (2008) Stress-responsive microRNAs in Populus. Plant J 55: 131-151
33. MacFarlane SA, Popovich AH (2000) Efficient expression of foreign proteins in roots from tobravirus vectors. Virology 267: 29-35
34. MacFarlane SA, Vassilakos N, Brown DJ (1999) Similarities in the genome organization of tobacco rattle virus and pea early-browning virus isolates that are transmitted by the same vector nematode. J Gen Virol 80: 273-276
35. Mallory AC, Reinhart BJ, Jones-Rhoades MW, Tang G, Zamore PD, Barton MK, Bartel DP (2004) MicroRNA control of PHABULOSA in leaf development: importance of pairing to the microRNA 5 region. EMBO J 23: 3356-3364
36. Martínez-Priego L, Donaire L, Barajas D, Llave C (2008) Silencing suppressor activity of the Tobacco rattle virus-encoded 16-kDa protein and interference with endogenous small RNA-guided regulatory pathways. Virology 376: 346-356
37. Martín-Hernández AM, Baulcombe DC (2008) Tobacco rattle virus 16-kilodalton protein encodes a suppressor of RNA silencing that allows transient viral entry in meristems. J Virol 82: 4064-4071
38. McConnell JR, Barton MK (1998) Leaf polarity and meristem formation in Arabidopsis. Development 125: 2935-2942
39. McHale NA, Koning RE (2004) MicroRNA-directed cleavage of Nicotiana sylvestris PHAVOLUTA mRNA regulates the vascular cambium and structure of apical meristems. Plant Cell 16: 1730-1740
40. Mlotshwa S, Yang Z, Kim Y, Chen X (2006) Floral patterning defects induced by Arabidopsis APETALA2 and microRNA172 expression in Nicotiana benthamiana. Plant Mol Biol 61: 781-793
41. Ori N, Cohen AR, Etzioni A, Brand A, Yanai O, Shleizer S, Menda N, Amsellem Z, Efroni I, Pekker I, et al (2007) Regulation of LANCEOLATE by miR319 is required for compound-leaf development in tomato. Nat Genet 39: 787-791
42. Phillips JR, Dalmay T, Bartels D (2007) The role of small RNAs in abiotic stress. FEBS Lett 581: 3592-3597
43. Ratcliff F, Martin-Hernandez AM, Baulcombe DC (2001) Technical Advance. Tobacco rattle virus as a vector for analysis of gene function by silencing. Plant J 25: 237-245
44. Sakaguchi J, Watanabe Y (2012) miR165/166 and the development of land plants. Dev Growth Differ 54: 93-99
45. Senthil-Kumar M, Mysore KS (2011) New dimensions for VIGS in plant functional genomics. Trends Plant Sci 16: 656-665
46. Shukla LI, Chinnusamy V, Sunkar R (2008) The role of microRNAs and other endogenous small RNAs in plant stress responses. Biochim Biophys Acta 1779: 743-748
47. Spitzer-Rimon B, Cna'ani A, Vainstein A (2013) Virus-aided gene expression and silencing using TRV for functional analysis of floral scentrelated genes. Methods Mol Biol 975: 139-148
48. Spitzer-Rimon B, Farhi M, Albo B, Cna'ani A, Ben Zvi MM, Masci T, Edelbaum O, Yu Y, Shklarman E, Ovadis M, et al (2012) The R2R3-MYB-like regulatory factor EOBI, acting downstream of EOBII, regulates scent production by activating ODO1 and structural scent-related genes in petunia. Plant Cell 24: 5089-5105
49. Spitzer-Rimon B, Marhevka E, Barkai O, Marton I, Edelbaum O, Masci T, Prathapani NK, Shklarman E, Ovadis M, Vainstein A (2010) EOBII, a gene encoding a flower-specific regulator of phenylpropanoid volatiles' biosynthesis in petunia. Plant Cell 22: 1961-1976
50. Sunkar R, Chinnusamy V, Zhu J, Zhu JK (2007) Small RNAs as big players in plant abiotic stress responses and nutrient deprivation. Trends Plant Sci 12: 301-309
51. Tang Y, Wang F, Zhao J, Xie K, Hong Y, Liu Y (2010) Virus-based microRNA expression for gene functional analysis in plants. Plant Physiol 153: 632-641
52. Todesco M, Rubio-Somoza I, Paz-Ares J, Weigel D (2010) A collection of target mimics for comprehensive analysis of microRNA function in Arabidopsis thaliana. PLoS Genet 6: e1001031
53. Vaistij FE, Elias L, George GL, Jones L (2010) Suppression of microRNA accumulation via RNA interference in Arabidopsis thaliana. Plant Mol Biol 73: 391-397
54. Valentine T, Shaw J, Blok VC, Phillips MS, Oparka KJ, Lacomme C (2004) Efficient virus-induced gene silencing in roots using a modified tobacco rattle virus vector. Plant Physiol 136: 3999-4009
55. Varkonyi-Gasic E, Hellens RP (2011) Quantitative stem-loop RT-PCR for detection of microRNAs. Methods Mol Biol 744: 145-157
56. Vaucheret H, Vazquez F, Crété P, Bartel DP (2004) The action of ARGONAUTE1 in the miRNA pathway and its regulation by the miRNA pathway are crucial for plant development. Genes Dev 18: 1187-1197
57. Wang D, MacFarlane SA, Maule AJ (1997) Viral determinants of pea early browning virus seed transmission in pea. Virology 234: 112-117
58. Yamagishi N, Sasaki S, Yamagata K, Komori S, Nagase M, Wada M, Yamamoto T, Yoshikawa N (2011) Promotion of flowering and reduction of a generation time in apple seedlings by ectopical expression of the Arabidopsis thaliana FT gene using the apple latent spherical virus vector. Plant Mol Biol 75: 193-204
59. Yan J, Gu Y, Jia X, Kang W, Pan S, Tang X, Chen X, Tang G (2012) Effective small RNA destruction by the expression of a short tandem target mimic in Arabidopsis. Plant Cell 24: 415-427
60. Zhang B, Pan X, Cobb GP, Anderson TA (2006) Plant microRNA: a small regulatory molecule with big impact. Dev Biol 289: 3-16
61. Zhao L, Kim Y, Dinh TT, Chen X (2007) miR172 regulates stem cell fate and defines the inner boundary of APETALA3 and PISTILLATA expression domain in Arabidopsis floral meristems. Plant J 51: 840-849
62. Zhong R, Ye ZH (2004) amphivasal vascular bundle 1, a gain-of-function mutation of the IFL1/REV gene, is associated with alterations in the polarity of leaves, stems and carpels. Plant Cell Physiol 45: 369-385
63. Zhu QH, Upadhyaya NM, Gubler F, Helliwell CA (2009) Over-expression of miR172 causes loss of spikelet determinacy and floral organ abnormalities in rice (Oryza sativa). BMC Plant Biol 9: 149