Skip to main content

Advertisement

SpringerLink
Log in

Tobacco microRNAs prediction and their expression infected with Cucumber mosaic virus and Potato virus X

  • Published:
Molecular Biology Reports Aims and scope Submit manuscript

Abstract

MicroRNAs (miRNAs) are a newly identified class of non-coding small RNAs of about 21–24 nucleotides. They play important roles in multiple biological processes by degrading targeted mRNAs or repressing mRNA translation. To date, a total of 2,043 plant miRNAs are present in the miRNA Registry database (miRBase Release 14.0), and none for tobacco (Nicotiana tabacum). In this research, we used known plant miRNAs against both genomic survey sequence (GSS) and expressed sequence tags (EST) databases to search for potential miRNAs in tobacco. A total of 25 potential miRNAs were identified following a range of strict filtering criteria, and 33 potential targets of miRNAs were predicted by searching the tobacco Unigene database. Most of these miRNA targeting genes were predicted to encode transcription factors which play important roles in tobacco development. Additionally, real-time PCR assays were performed to profile the expression levels of 10 miRNAs after the infection of Cucumber mosaic virus (CMV) and Potato virus X (PVX). The results showed that symptom severity is correlated to the miRNA accumulation, and increased miR168 expression during virus infection is a common, plant- and virus-independent response.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2

Similar content being viewed by others

References

  1. Ambros V (2004) The functions of animal microRNAs. Nature 431:350–355

    Article  CAS  PubMed  Google Scholar 

  2. Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116:281–297

    Article  CAS  PubMed  Google Scholar 

  3. Rhoades MW, Reinhart BJ, Lim LP, Burge CB, Bartel B, Bartel DP (2002) Prediction of plant microRNA targets. Cell 110:513–520

    Article  CAS  PubMed  Google Scholar 

  4. Tang G, Reinhart BJ, Bartel DP, Zamore PD (2003) A biochemical framework for RNA silencing in plants. Genes Dev 17:49–63

    Article  CAS  PubMed  Google Scholar 

  5. Jover-Gil S, Candela H, Ponce MR (2005) Plant microRNAs and development. Int J Dev Biol l49:733–744

    Article  Google Scholar 

  6. Jones-Rhoades MW, Bartel DP, Bartel B (2006) MicroRNAS and their regulatory roles in plants. Annu Rev Plant Biol 57:19–53

    Article  CAS  PubMed  Google Scholar 

  7. Chapman EJ, Prokhnevsky AI, Gopinath K, Dolja VV, Carrington JC (2004) Viral RNA silencing suppressors inhibit the microRNA pathway at an intermediate step. Genes Dev 18:1179–1186

    Article  CAS  PubMed  Google Scholar 

  8. Zhang X, Yuan YR, Pei Y, Lin SS, Tuschl T, Patel DJ, Chua NH (2006) Cucumber mosaic virus-encoded 2b suppressor inhibits Arabidopsis Argonaute1 cleavage activity to counter plant defense. Genes Dev 20:3255–3268

    Article  CAS  PubMed  Google Scholar 

  9. 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 104:12157–12162

    Article  CAS  PubMed  Google Scholar 

  10. Lewsey M, Robertson FC, Canto T, Palukaitis P, Carr JP (2007) Selective targeting of miRNA-regulated plant development by a viral counter-silencing protein. Plant J 50:240–252

    Article  CAS  PubMed  Google Scholar 

  11. Shiboleth YM, Haronsky E, Leibman D, Arazi T, Wassenegger M, Whitham SA, Gaba V, Gal-On A (2007) The conserved FRNK box in HC-Pro, a plant viral suppressor of gene silencing, is required for small RNA binding and mediates symptom development. J Virol l81:13135–13148

    Article  Google Scholar 

  12. 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 14:227–233

    Article  CAS  PubMed  Google Scholar 

  13. Schwab R, Palatnik JF, Riester M, Schommer C, Schmid M, Weigel D (2005) Specific effects of microRNAs on the plant transcriptome. Dev Cell 8:517–527

    Article  CAS  PubMed  Google Scholar 

  14. Alvarez JP, Pekker I, Goldshmidt A, Blum E, Amsellem Z, Eshed Y (2006) Endogenous and synthetic microRNAs stimulate simultaneous, efficient, and localized regulation of multiple targets in diverse species. Plant Cell 18:1134–1151

    Article  CAS  PubMed  Google Scholar 

  15. Reinhart BJ, Weinstein EG, Rhoades MW, Bartel B, Bartel DP (2002) MicroRNAs in plants. Genes Dev 16:1616–1626

    Article  CAS  PubMed  Google Scholar 

  16. Adai A, Johnson C, Mlotshwa S, Archer-Evans S, Manocha V, Vance V, Sundaresan V (2005) Computational prediction of miRNAs in Arabidopsis thaliana. Genome Res 15:78–91

    Article  CAS  PubMed  Google Scholar 

  17. 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

    Article  CAS  PubMed  Google Scholar 

  18. Griffiths-Jones S (2004) The microRNA registry. Nucleic Acids Res 32:D109–D111

    Article  CAS  PubMed  Google Scholar 

  19. Griffiths-Jones S (2006) miRBase: the microRNA sequence database. Methods Mol Biol l342:129–138

    Google Scholar 

  20. Griffiths-Jones S, Grocock RJ, van Dongen S, Bateman A, Enright AJ (2006) miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res 34:D140–D144

    Article  CAS  PubMed  Google Scholar 

  21. Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ (2008) miRBase: tools for microRNA genomics. Nucleic Acids Res 36:D154–D158

    Article  CAS  PubMed  Google Scholar 

  22. Yang W, Liu X, Zhang J, Feng J, Li C, Chen J (2009) Prediction and validation of conservative microRNAs of Solanum tuberosum L. Mol Biol Rep. doi:10.1007/s11033-009-9881-z

  23. Huang Y, Zou Q, Tang SM, Wang LG, Shen XJ (2009) Computational identification and characteristics of novel microRNAs from the silkworm (Bombyx mori L.). Mol Biol Rep. doi:10.1007/s11033-009-9897-4

  24. Sheng X, Song X, Yu Y, Niu L, Li S, Li H, Wei C, Liu T, Zhang L, Du L (2010) Characterization of microRNAs from sheep (Ovis aries) using computational and experimental analyses. Mol Biol Rep. doi:10.1007/s11033-010-9987-3

  25. Liu G, Fang Y, Zhang H, Li Y, Li X, Yu J, Wang X (2010) Computational identification and microarray-based validation of microRNAs in Oryctolagus cuniculus. Mol Biol Rep. doi:10.1007/s11033-010-0006-5

  26. Wang XJ, Reyes JL, Chua NH, Gaasterland T (2004) Prediction and identification of Arabidopsis thaliana microRNAs and their mRNA targets. Genome Biol l5:R65

    Article  Google Scholar 

  27. Saunders JW, Bush LP (1979) Nicotine biosynthetic enzyme activities in Nicotiana tabacum L. genotypes with different alkaloid levels. Plant Physiol l64:236–240

    Article  Google Scholar 

  28. Zhang K, Letham DS, John PC (1996) Cytokinin controls the cell cycle at mitosis by stimulating the tyrosine dephosphorylation and activation of p34cdc2-like H1 histone kinase. Planta 200:2–12

    Article  CAS  PubMed  Google Scholar 

  29. Mäder M, Ungemach J, Schloß P (1980) The role of peroxidase isoenzyme groups of Nicotiana tabacum in hydrogen peroxide formation. Planta 147:467–470

    Article  Google Scholar 

  30. Sunderland N, Wicks FM (1971) Embryoid formation in pollen grains of Nicotiana tabacum. J Exp Bot 22:213–226

    Article  Google Scholar 

  31. Ward ER, Uknes SJ, Williams SC, Dincher SS, Wiederhold DL, Alexander DC, Ahl-Goy P, Metraux JP, Ryals JA (1991) Coordinate gene activity in response to agents that induce systemic acquired resistance. Plant Cell 3:1085–1094

    Article  CAS  PubMed  Google Scholar 

  32. Billoud B, De Paepe R, Baulcombe D, Boccara M (2005) Identification of new small non-coding RNAs from tobacco and Arabidopsis. Biochimie 87:905–910

    Article  CAS  PubMed  Google Scholar 

  33. Zhang B, Pan X, Anderson TA (2006) Identification of 188 conserved maize microRNAs and their targets. FEBS Lett 580:3753–3762

    Article  CAS  PubMed  Google Scholar 

  34. Zhang Y (2005) miRU: an automated plant miRNA target prediction server. Nucleic Acids Res 33:W701–W704

    Article  CAS  PubMed  Google Scholar 

  35. Feng J, Zeng R, Chen J (2008) Accurate and efficient data processing for quantitative real-time PCR using a tripartite plant virus as a model. Biotechniques 44:901–912

    Article  CAS  PubMed  Google Scholar 

  36. Chen C, Ridzon DA, Broomer AJ, Zhou Z, Lee DH, Nguyen JT, Barbisin M, Xu NL, Mahuvakar VR, Andersen MR, Lao KQ, Livak KJ, Guegler KJ (2005) Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Res 33:e179

    Article  PubMed  Google Scholar 

  37. Zhang B, Pan X, Cannon CH, Cobb GP, Anderson TA (2006) Conservation and divergence of plant microRNA genes. Plant J 46:243–259

    Article  CAS  PubMed  Google Scholar 

  38. Guddeti S, Zhang DC, Li AL, Leseberg CH, Kang H, Li XG, Zhai WX, Johns MA, Mao L (2005) Molecular evolution of the rice miR395 gene family. Cell Res 15:631–638

    Article  CAS  PubMed  Google Scholar 

  39. Mallory AC, Dugas DV, Bartel DP, Bartel B (2004) MicroRNA regulation of NAC-domain targets is required for proper formation and separation of adjacent embryonic, vegetative, and floral organs. Curr Biol l14:1035–1046

    Article  Google Scholar 

  40. Xie FL, Huang SQ, Guo K, Xiang AL, Zhu YY, Nie L, Yang ZM (2007) Computational identification of novel microRNAs and targets in Brassica napus. FEBS Lett 581:1464–1474

    Article  CAS  PubMed  Google Scholar 

  41. Gusmaroli G, Tonelli C, Mantovani R (2001) Regulation of the CCAAT-Binding NF-Y subunits in Arabidopsis thaliana. Gene 264:173–185

    Article  CAS  PubMed  Google Scholar 

  42. Aukerman MJ, Sakai H (2003) Regulation of flowering time and floral organ identity by a MicroRNA and its APETALA2-like target genes. Plant Cell 15:2730–2741

    Article  CAS  PubMed  Google Scholar 

  43. Chen X (2004) A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development. Science 303:2022–2025

    Article  CAS  PubMed  Google Scholar 

  44. 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 l61:781–793

    Article  Google Scholar 

  45. Emery JF, Floyd SK, Alvarez J, Eshed Y, Hawker NP, Izhaki A, Baum SF, Bowman JL (2003) Radial patterning of Arabidopsis shoots by class III HD-ZIP and KANADI genes. Curr Biol 13:1768–1774

    Article  CAS  PubMed  Google Scholar 

  46. Llave C, Xie Z, Kasschau KD, Carrington JC (2002) Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA. Science 297:2053–2056

    Article  CAS  PubMed  Google Scholar 

  47. Millar AA, Gubler F (2005) The Arabidopsis GAMYB-like genes, MYB33 and MYB65, are microRNA-regulated genes that redundantly facilitate anther development. Plant Cell 17:705–721

    Article  CAS  PubMed  Google Scholar 

  48. Achard P, Herr A, Baulcombe DC, Harberd NP (2004) Modulation of floral development by a gibberellin-regulated microRNA. Development 131:3357–3365

    Article  CAS  PubMed  Google Scholar 

  49. Jakoby M, Weisshaar B, Droge-Laser W, Vicente-Carbajosa J, Tiedemann J, Kroj T, Parcy F (2002) bZIP transcription factors in Arabidopsis. Trends Plant Sci 7:106–111

    Article  CAS  PubMed  Google Scholar 

  50. Okushima Y, Overvoorde PJ, Arima K, Alonso JM, Chan A, Chang C, Ecker JR, Hughes B, Lui A, Nguyen D, Onodera C, Quach H, Smith A, Yu G, Theologis A (2005) Functional genomic analysis of the AUXIN RESPONSE FACTOR gene family members in Arabidopsis thaliana: unique and overlapping functions of ARF7 and ARF19. Plant Cell 17:444–463

    Article  CAS  PubMed  Google Scholar 

  51. Guo HS, Ding SW (2002) A viral protein inhibits the long range signaling activity of the gene silencing signal. EMBO J 21:398–407

    Article  CAS  PubMed  Google Scholar 

  52. Voinnet O, Pinto YM, Baulcombe DC (1999) Suppression of gene silencing: a general strategy used by diverse DNA and RNA viruses of plants. Proc Natl Acad Sci USA 96:14147–14152

    Article  CAS  PubMed  Google Scholar 

  53. Voinnet O, Lederer C, Baulcombe DC (2000) A viral movement protein prevents spread of the gene silencing signal in Nicotiana benthamiana. Cell 103:157–167

    Article  CAS  PubMed  Google Scholar 

  54. Mallory AC, Vaucheret H (2006) Functions of microRNAs and related small RNAs in plants. Nat Genet 38(Suppl):S31–367

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgment

This research was supported by National Key Project for International Cooperation, China (2004DFA05000) and Zhejiang Natural Science Fundation (Y307466).

Author information

Authors and Affiliations

  1. College of Life Sciences, Zhejiang University, Hangzhou, China

    Qiulei Lang & Jishuang Chen

  2. Institute of Bioengineering, Zhejiang Sci-Tech University, Hangzhou, China

    Qiulei Lang, ChunZhi Jin, Leiyu Lai, Junli Feng, Shaoning Chen & Jishuang Chen

Authors
  1. Qiulei Lang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. ChunZhi Jin
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Leiyu Lai
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Junli Feng
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Shaoning Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Jishuang Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Jishuang Chen.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOC 4837 kb)

Supplementary material 2 (DOC 61 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Lang, Q., Jin, C., Lai, L. et al. Tobacco microRNAs prediction and their expression infected with Cucumber mosaic virus and Potato virus X . Mol Biol Rep 38, 1523–1531 (2011). https://doi.org/10.1007/s11033-010-0260-6

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11033-010-0260-6

Keywords

Search

Navigation