Small RNA profiling of virus-infected grapevines: Evidences for virus infection-associated and variety-specific miRNAs

Functional and Integrative Genomics

Volumn 12, Issue 4, 2012, Pages 659-669

  Singh, Kashmir ^a,b   Talla, Aarthi ^a   Qiu, Wenping ^a  

^a MISSOURI STATE UNIVERSITY   (United States)

^b PANJAB UNIVERSITY   (India)

Author keywords

Grapevine; miRNAs; siRNAs; Small RNAs; Virus infection

Indexed keywords

MICRORNA; MICRORNA 17; MICRORNA 18; MICRORNA 19; MICRORNA 20; MICRORNA 21; MICRORNA 22; MIR169; MIR398; MIRNA168; MIRNA319; MIRNA3623; MIRNA395; MIRNA396; RNA; SMALL RNA; UNCLASSIFIED DRUG; PLANT RNA; SMALL INTERFERING RNA; TRANSCRIPTION FACTOR; TRANSCRIPTOME; VEGETABLE PROTEIN;

ABIOTIC STRESS; ARTICLE; CONTROLLED STUDY; GENE EXPRESSION REGULATION; GENE FUNCTION; GRAPE; GRAPEVINE; NONHUMAN; PLANT DEFENSE; PRIORITY JOURNAL; RNA ANALYSIS; VIRUS INFECTION; VITIS; CAULIMOVIRIDAE; CELL CYCLE; GENETICS; METABOLISM; PATHOGENICITY; PHYSIOLOGICAL STRESS; PLANT DISEASE; VIROLOGY;

BADNAVIRUS; CAULIMOVIRIDAE; DNA VIRUSES; VITIS;

CAULIMOVIRIDAE; CELL CYCLE; GENE EXPRESSION REGULATION, PLANT; MICRORNAS; PLANT DISEASES; PLANT PROTEINS; RNA, PLANT; RNA, SMALL INTERFERING; STRESS, PHYSIOLOGICAL; TRANSCRIPTION FACTORS; TRANSCRIPTOME; VITIS;

EID: 84877082243     PISSN: 1438793X     EISSN: 14387948     Source Type: Journal    
DOI: 10.1007/s10142-012-0292-1     Document Type: Article

References (43)

1. Amin I, Patil B, Briddon R, Mansoor S, Fauquet C (2011) Comparison of phenotypes produced in response to transient expression of genes encoded by four distinct begomoviruses in Nicotiana benthamiana and their correlation with the levels of developmental miRNAs. Virol J 8(1):238
2. Bartel DP (2009) MicroRNAs: target recognition and regulatory functions. Cell 136(2):215-233
3. Bazzini AA, Hopp HE, Beachy RN, Asurmendi S (2007) Infection and coaccumulation of tobacco mosaic virus proteins alter microRNA levels, correlating with symptom and plant development. Proc Natl Acad Sci USA 104(29):12157-12162
4. Bazzini A, Almasia N, Manacorda C, Mongelli V, Conti G, Maroniche G, Rodriguez M, Distefano A, Hopp HE, del Vas M et al (2009) Virus infection elevates transcriptional activity of miR164a promoter in plants. BMC Plant Biol 9(1):152
5. Buhtz A, Pieritz J, Springer F, Kehr J (2010) Phloem small RNAs, nutrient stress responses, and systemic mobility. BMC Plant Biol 10(1):64
6. Carra A, Mica E, Gambino G, Pindo M, Moser C, Pè ME, Schubert A (2009) Cloning and characterization of small non-coding RNAs from grape. Plant J 59:750-763
7. Carthew RW, Sontheimer EJ (2009) Origins and mechanisms of miRNAs and siRNAs. Cell 136(4):642-655
8. Dunoyer P, Schott G, Himber C, Meyer D, Takeda A, Carrington JC, Voinnet O (2010) Small RNA duplexes function as mobile silencing signals between plant cells. Science 328(5980):912-916
9. Fahlgren N, Howell MD, Kasschau KD, Chapman EJ, Sullivan CM, Cumbie JS, Givan SA, Law TF, Grant SR, Dangl JL et al (2007) High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of MIRNA genes. PLoS One 2(2):e219
10. Fahlgren N, Jogdeo S, Kasschau KD, Sullivan CM, Chapman EJ, Laubinger S, Smith LM, Dasenko M, Givan SA, Weigel D et al (2010) MicroRNA gene evolution in Arabidopsis lyrata and Arabidopsis thaliana. Plant Cell 22(4):1074-1089
11. Feng J, Lai L, Lin R, Jin C, Chen J (2012) Differential effects of Cucumber mosaic virus satellite RNAs in the perturbation of microRNA-regulated gene expression in tomato. Mol Biol Rep 39:775-784
12. Fung RWM, Gonzalo M, Fekete C, Kovacs LG, He Y, Marsh E, McIntyre LM, Schachtman DP, Qiu WP (2008) Powdery mildew induces defense-oriented reprogramming of the transcriptome in a susceptible but not in a resistant grapevine. Plant Physiol 146:236-249
13. Gournas C, Papageorgiou I, Diallinas G (2008) The nucleobase- ascorbatetransporter (NAT) family: genomics, evolution, structure-function relationships and physiological role. Mol Biosyst 4:404-416
14. Hu Q, Hollunder J, Niehl A, Karner CJ, Gereige D, Windels D, Arnold A, Kuiper M, Vazquez F, Pooggin M et al (2011) Specific impact of Tobamovirus infection on the Arabidopsis small RNA profile. PLoS One 6(5):e19549
15. Jaillon O, Aury J, Noel B, Policriti A, Clepet C, Casagrande A, Choisne N, Aubourg S, Vitulo N, Jubin C et al (2007) The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449:463-467
16. Katiyar-Agarwal S, Jin H (2010) Role of small RNAs in host-microbe interactions. Annu Rev Phytopathol 48:225-246
17. Kawashima CG, Matthewman CA, Huang S, Lee B-R, Yoshimoto N, Koprivova A, Rubio-Somoza I, Todesco M, Rathjen T, Saito K et al (2011) Interplay of SLIM1 and miR395 in the regulation of sulfate assimilation in Arabidopsis. Plant J 66(5):863-876
18. Liang G, Yang F, Yu D (2010) MicroRNA395 mediates regulation of sulfate accumulation and allocation in Arabidopsis thaliana. Plant J 62(6):1046-1057
19. Meyers BC, Axtell MJ, Bartel B, Bartel DP, Baulcombe D, Bowman JL, Cao X, Carrington JC, Chen X, Green PJ et al (2008) Criteria for annotation of plant microRNAs. Plant Cell 20(12):3186-3190
20. Mica E, Piccolo V, Delledonne M, Ferrarini A, Pezzotti M, Casati C, Del Fabbro C, Valle G, Policriti A, Morgante M et al (2010) Correction: high throughput approaches reveal splicing of primary microRNA transcripts and tissue specific expression of mature microRNAs in Vitis vinifera. BMC Genomics 11(1):109
21. Molnar A, Melnyk CW, Bassett A, Hardcastle TJ, Dunn R, Baulcombe DC (2010) Small silencing RNAs in plants are mobile and direct epigenetic modification in recipient cells. Science 328(5980):872-875
22. Moxon S, Schwach F, Dalmay T, Maclean D, Studholme DJ, Moulton V (2008) A toolkit for analysing large-scale plant small RNA datasets. Bioinformatics 24:2252-2253
23. Myles S, Boyko AR, Owens CL, Brown PJ, Grassi F, Aradhya MK, Prins B, Reynolds A, Chia J-M, Ware D et al (2011) Genetic structure and domestication history of the grape. Proc Natl Acad Sci USA 108(9):3530-3535
24. Naqvi A, Haq Q, Mukherjee S (2010) MicroRNA profiling of tomato leaf curl new delhi virus (tolcndv) infected tomato leaves indicates that deregulation of mir159/319 and mir172 might be linked with leaf curl disease. Virol J 7(1):281
25. Olsen AN, Ernst HA, Leggio LL, Skriver K (2005) NAC transcription factors: structurally distinct, functionally diverse. Trends Plant Sci 10(2):79-87
26. Pantaleo V, Szittya G, Moxon S, Miozzi L, Moulton V, Dalmay T, Burgyan J (2010) Identification of grapevine microRNAs and their targets using high-throughput sequencing and degradome analysis. Plant J 62(6):960-976
27. Perez-Quintero A, Neme R, Zapata A, Lopez C (2010) Plant microRNAs and their role in defense against viruses: a bioinformatics approach. BMC Plant Biol 10(1):138
28. Rajagopalan R, Vaucheret H, Trejo J, Bartel DP (2006) A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. Genes Dev 20:3407-3425
29. Sunkar R, Zhu J (2004) Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. Plant Cell 16(8):2001-2019
30. Sunkar R, Chinnusamy V, Zhu J, Zhu J-K (2007) Small RNAs as big players in plant abiotic stress responses and nutrient deprivation. Trends Plant Sci 12(7):301-309
31. Tagami Y, Inaba N, Kutsuna N, Kurihara Y, Watanabe Y (2007) Specific enrichment of miRNAs in Arabidopsis thaliana infected with tobacco mosaic virus. DNA Res 14(5):227-233
32. Trindade I, Capitão C, Dalmay T, Fevereiro M, Santos D (2010) miR398 and miR408 are up-regulated in response to water deficit in Medicago truncatula. Planta 231(3):705-716
33. Varallyay E, Valoczi A, Agyi A, Burgyan J, Havelda Z (2010) Plant virus-mediated induction of miR168 is associated with repression of ARGONAUTE1 accumulation. EMBO J 29(20):3507-3519
34. Velasco R, Zharkikh A, Troggio M, Cartwright DA, Cestaro A, Pruss D, Pindo M, FitzGerald LM, Vezzulli S, Reid J et al (2007) A high quality draft consensus sequence of the genome of a heterozygous grapevine variety. PLoS One 2(12):e1326
35. Voinnet O (2009) Origin, biogenesis, and activity of plant microRNAs. Cell 136(4):669-687
36. Wang C, Wang X, Kibet NK, Song C, Zhang C, Li X, Han J, Fang J (2011a) Deep sequencing of grapevine flower and berry short RNA library for discovery of novel microRNAs and validation of precise sequences of grapevine microRNAs deposited in miRBase. Physiol Plant 143:64-81
37. Wang L, Gu X, Xu D, Wang W, Wang H, Zeng M, Chang Z, Huang H, Cui X (2011b) miR396-targeted AtGRF transcription factors are required for coordination of cell division and differentiation during leaf development in Arabidopsis. J Exp Bot 62(2):761-773
38. Yoo SY, Kim Y, Kim SY, Lee JS, Ahn JH (2007) Control of flowering time and cold response by a NAC-domain protein in Arabidopsis. PLoS One 2(7):e642
39. Zhang X, Yuan Y-R, Pei Y, Lin S-S, Tuschl T, Patel DJ, Chua N-H (2006) Cucumber mosaic virus-encoded 2b suppressor inhibits Arabidopsis Argonaute1 cleavage activity to counter plant defense. Genes Dev 20(23):3255-3268
40. Zhang Y, Singh K, Kaur R, Qiu W (2011a) Association of a novel DNA virus with the grapevine vein-clearing and vine decline syndrome. Phytopathology 9:1081-1090
41. Zhang X, Zou Z, Gong P, Zhang J, Ziaf K, Li H, Xiao F, Ye Z (2011b) Over-expression of microRNA169 confers enhanced drought tolerance to tomato. Biotechnol Lett 33(2):403-409
42. Zhao M, Ding H, Zhu J, Zhang F, Li WX (2011) Involvement of miRNA169 in the nitrogen-starvation responses in Arabidopsis. New Phytol 190:906-915
43. Zhu C, Ding Y, Liu H (2011) miRNA398 and plant stress responses. Physiol Plant. doi: 10.1111/j.1399-3054.2011.01477.x