Identification of miRNAs and their target genes in Papaver somniferum

Document Type : Research Paper


1 University of tehran

2 University of Tehran


MicroRNAs (miRNAs) are A group of 17_22 nucleotides that derived from its precursor sequence and show an enormous role in various biological and metabolic processes in both animals and plants. There are several ways to identify miRNAs. One of the easiest and cheapest way to identify miRNAs is bioinformatics methods. In this study، a bioinformatics approach was used to identify potential miRNAs in Papaver somniferum. We blasted publicly available EST sequences obtained from NCBI GenBank against previously known plant miRNAs and ultimately distinguished seven potential miRNA in Papaver somniferum. Target genes predicted miRNA are a protein serine / threonine kinase (signal transduction)، PPR protein family (Edit and stability of RNA) and globulins 7 S (hydration and dehydration cells), phototropin (response phototropism), protein of serine / threonine phosphatase (glycogen metabolism), TIR protein family (defense against bacteria). These genes play an important role in growth and development، metabolism، morphology and determine flowering time and response to biotic and abiotic stresses.


Main Subjects

  1. Akana, J., Fedorov, A. A., Fedorov, E., Novak, W.R., Babbitt, P.C., Almo, S.C. & Gerlt, J.A. (2006). D-Ribulose 5-phosphate 3-epimerase: functional and structural relationships to members of the ribulose-phosphate binding (beta/alpha) 8-barrel superfamily. Biochemistry, 45 (8), 2493–503.
  2. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., Lipman, D.J. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389–3402.
  3. Barratt, D.P., Derbyshire, P., Findlay, K., Pike, M., Wellner, N., Lunn, J. & Smith, A. M. (2009). Normal growth of Arabidopsis requires cytosolic invertase but not sucrose synthase. Proceedings of the National Academy of Sciences, 106(31), 13124-13129.
  4. Beam, C. E., Saveson, C. J. & Lovett, S. T. (2002). Role for radA/sms in recombination intermediate processing in Escherichia coli. Journal of Bacteriology184(24), 6836-6844.
  5. Bertini, I. (2007). Biological inorganic chemistry: structure and reactivity. University Science Books.
  6. Bonnet, E., Wuyts, J., Rouze, P. & Peer, Y.V. (2004). Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences. Bioinformatics 20, 2911–2917.
  7. Mitcham, J. L., Parnet, P., Bonnert, T. P., Garka, K. E., Gerhart, M. J., Slack, J. L. & Sims, J. E. (1996). T1/ST2 signaling establishes it as a member of an expanding interleukin-1 receptor family. Journal of Biological Chemistry271(10), 5777-5783.
  8. Dai, X., Zhao, P.X. (2011). PsRNATarget: a plant small RNA target analysis s erver. Nucleic Acids Res. 39, W155–W159.
  9. DiDonato, R. J., Arbuckle, E., Buker, S., Sheets, J., Tobar, J., Totong, R. & Celenza, J. L. (2004). Arabidopsis ALF4 encodes a nuclear‐localized protein required for lateral root formation. The Plant Journal37(3), 340-353.
  10. Hagel, J. M. & Facchini, P. J. (2013). Benzylisoquinoline alkaloid metabolism–a century of discovery and a brave new world. Plant and Cell Physiology, pct020.
  11. Hagen, G. & Guilfoyle, T. (2002). Auxin-responsive gene expression: genes, promoters and regulatory factors. Plant Molecular Biology49(3-4), 373-385.
  12. He, G. H., Helbing, C. C., Wagner, M. J., Sensen, C. W. & Riabowol, K. (2005). Phylogenetic analysis of the ING family of PHD finger proteins. Molecular biology and evolution22(1), 104-116.
  13. Jin, J. B., Kim, Y. A., Kim, S. J., Lee, S. H., Kim, D. H., Cheong, G. W. & Hwang, I. (2001). A new dynamin-like protein, ADL6, is involved in trafficking from the trans-Golgi network to the central vacuole in Arabidopsis. The Plant Cell, 13(7), 1511-1526.
  14. Lamb, D. C., Lei, L., Warrilow, A. G., Lepesheva, G. I., Mullins, J. G., Waterman, M. R. & Kelly, S. L. (2009). The first virally encoded cytochrome p450. Journal of virology83(16), 8266-8269.
  15. Li, C. & Zhang, B. (2016). MicroRNAs in control of plant development. Journal of cellular physiology, 231(2), 303-313.
  16. Lin, S. L., Chang, D. & Ying, S. Y. (2005). Asymmetry of intronic pre-miRNA structures in functional RISC assembly. Gene356, 32-38.
  17. Manna, S. (2015). An overview of pentatricopeptide repeat proteins and their applications. Biochimie, 113, 93-99.
  18. Müntz, K. (1998). Globulins from legume seeds: Structure and function during storage and reactivation. In Plant Proteins from European Crops (pp. 3-12). Springer Berlin Heidelberg.
  19. Park, W., Li, J., Song, R., Messing, J. & Chen, X. (2002). CARPEL FACTORY, a Dicer homolog, and HEN1, a novel protein, act in microRNA metabolism in Arabidopsis thalianaCurrent Biology12(17), 1484-1495.
  20. Qiu, X. B., Shao, Y. M., Miao, S. & Wang, L. (2006). The diversity of the DnaJ/Hsp40 family, the crucial partners for Hsp70 chaperones. Cellular and molecular life sciences63(22), 2560-2570.
  21. Sedlacek, Z., Munstermann, E., Mincheva, A., Lichter, P. & Poustka, A. (1998). The human rab GDI β gene with long retroposon-rich introns maps to 10p15 and its pseudogene to 7p11-p13. Mammalian genome9(1), 78-80.
  22. Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., Kumar, S. (2011). MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 28, 2731–2739.
  23. Unver, T., Budak, H. (2009) Conserved microRNAs and their targets in model grass species Brachypodium distachyon. Planta 230:659–669.
  24. Vincent, S. & Settleman, J. (1997). The PRK2 kinase is a potential effector target of both Rho and Rac GTPases and regulates actin cytoskeletal organization. Molecular and Cellular Biology17(4), 2247-2256.
  25. Wiemer, E. A. (2007). The role of microRNAs in cancer: no small matter. European journal of cancer, 43(10), 1529-1544.
  26. Yin, Z., Li, C., Han, X. & Shen, F. (2008). Identification of conserved microRNAs and their target genes in tomato (Lycopersicon esculentum). Gene414(1), 60-66.
  27. Wera, S. & Hemmings, B. A. (1995). Serine/threonine protein phosphatases. Biochemical Journal311(Pt 1), 17.
  28. Zhang, Y. (2005). miRU: an automated  plant miRNA target  prediction server. Nucleic Acids Res. 33(Web Server issue):W701–4.
  29. Zhang, B., Pan, X., Cobb, G. P. & Anderson, T. A. (2006a). Plant microRNA: a small regulatory molecule with big impact. Developmental Biology289(1), 3-16.
  30. Zhang, B., Pan, X., Wang, Q., Cobb, G. P. & Anderson, T. A. (2006b). Computational identification of microRNAs and their targets. Computational Biology and Chemistry30(6), 395-407.
  31. Zhang, B.H., Pan, X.P., Cox, S.B., Cobb, G.P., Anderson, T.A. (2006c). Evidence that miRNAs are different from other RNAs. Cell. Mol. Life Sci. 63, 246.
  32. Zhang, B., Pan, X., Cannon, C. H., Cobb, G. P. & Anderson, T. A. (2006d). Conservation and divergence of plant microRNA genes. The Plant Journal46(2), 243-259.
  33. Zhang, B., Wang, Q., Wang, K., Pan, X., Liu, F., Guo, T., Anderson, T. A. (2007). Identification of cotton microRNAs and their targets. Gene397(1), 26-37.
  34. Zhang, B., Pan, X. & Stellwag, E. J. (2008). Identification of soybean microRNAs and their targets. Planta229(1), 161-182.
  35. Zhang, W., Luo, Y., Gong, X., Zeng, W., Li, S. (2009). Computational identification of 48 potato microRNAs and their targets. Comput Biol Chem 33:84–93.
  36. Zuker, M. (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res, 31:3406–3415.