Identification of microRNAs in ecological model plant Mimulus

Muhammad Younas Khan Barozai, Muhammad Din, Iftikhar Ahmed Baloch

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Department of Botany, University of Baluchistan, Sariab Road Quetta. Pakistan.

DOI: 10.4236/jbpc.2011.23037                

Abstract

MicroRNAs (miRNAs) are small, non-coding and regulatory RNAs about 20 to 24 nucleotides long. Their conserved nature among the various organisms makes them a good source of new miRNAs discovery by comparative genomics approach. This study resulted in 34 miRNAs belonging to 21 families in ecological model plant Mimulus. All the miRNA families (mir 156, 157, 159, 160, 164, 172, 319, 393, 395, 397, 399, 400, 403, 417, 419, 472, 782, 854, 858, 867 and 2112) are found for the first time in Mimulus. The MIR-399 is found as precursor miRNA cluster with 4 mature sequences. All 34 miRNA precursors form stable minimum free energy stem loop structure as their orthologues form and the mature miRNAs reside in the stem portion of the stem loop structure. Twenty eight are from Mimulus guttatus and six miRNAs belong to Mimulus lewisii. Their targets consist of dihy-droflavonol-4-reductase, cycloidea-like protein, DNA-directed RNA polymerase II, maturase (matR) and transcription factors like; squamosa-promoter binding, MYB, palmate-like pentafoliata 1.

Keywords

Keywords: Comparative Genomics; MicroRNAs; Mimulus

Conflicts of Interest

The authors declare no conflicts of interest.

References

[1]	Beardsley, P.M. and Olmstead, R.G. (2002) Redefining Phrymaceae: The placement of Mimulus, tribe Mimuleae, and Phryma. American Journal of Botany, 89, 1093-1102. doi:10.3732/ajb.89.7.1093
[2]	Fishman, L.A., Kelly, J., Morgan, E. and Willis, J.H. (2001) A genetic map in the Mimulus guttatus species complex reveals transmission ratio distortion due to heterospecific interactions. Genetics, 159, 1701-1716.
[3]	Mica, E., Gianfranceschi, L. and Pe, M.E. (2006) Characterization of five microRNA families in maize. Journal of Experimental Botany, 57, 2601-2612. doi:10.1093/jxb/erl013
[4]	Bonnet, E., Wuyts, J., Rouze, P. and Van-de-Peer, Y. (2004) Detection of 91 potential conserved plant microRNAs in Arabidopsis thaliana and Oryza sativa identifies important target genes. Proceedings of the National Academy of Sciences of the United States of America, 101, 11511-11516. doi:10.1073/pnas.0404025101
[5]	Weber, M.J. (2005) New human and mouse microRNA genes found by homology search. FEBS Journal, 272, 59-73. doi:10.1111/j.1432-1033.2004.04389.x
[6]	Bartel, D.P. (2004) MicroRNAs: Genomics, biogenesis, mechanism, and function. Cell, 116, 281-297. doi:10.1016/S0092-8674(04)00045-5
[7]	Carrington, J.C. and Ambros, V. (2003) Role of microRNAs in plant and animal development. Science, 301, 336-338. doi:10.1126/science.1085242
[8]	Hammond, S.C., Bernstein, E., Beach, D. and Hannon, G.J. (2000) An RNA-directed nuclease mediates posttranscriptional gene silencing in Drosophila cells. Nature, 404, 293-296. doi:10.1038/35005107
[9]	Kurihara, Y. and Watanabe, Y. (2004) Arabidopsis micro-RNA biogenesis through dicer-like 1 protein functions. Proceedings of the National Academy of Sciences of the United States of America, 101, 12753-12758. doi:10.1073/pnas.0403115101
[10]	Aukerman, M.J. and 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. doi:10.1105/tpc.016238
[11]	Tang, G., Reinhart, B.J., Bartel, D.P. and Zamore, P.D. (2003) A biochemical framework for RNA silencing in plants. Genes & Development, 17, 49-63. doi:10.1101/gad.1048103
[12]	Chen, X. (2003) A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development. Science, 303, 2022-2025. doi:10.1126/science.1088060
[13]	Kidner, C.A. and Martienssen, R.A. (2005) The developmental role of microRNA in plants. Current Opinion in Plant Biology, 8, 38-44. doi:10.1016/j.pbi.2004.11.008
[14]	Allen, E., Xie, Z., Gustafson, A.M. and Carrington, J.C. (2005) MicroRNA-directed phasing during transacting siRNA biogenesis in plants. Cell, 121, 207-221. doi:10.1016/j.cell.2005.04.004
[15]	Yoshikawa, M., Peragine, A., Park, M.Y. and Poethig, R.S. (2005) A pathway for the biogenesis of trans-acting siRNAs in Arabidopsis. Genes & Development, 19, 2164- 2175. doi:10.1101/gad.1352605
[16]	Lu, S., Sun, Y.H., Shi, R., Clark, C., Li, L. and Chiang, V.L. (2005) Novel and mechanical stress responsive microRNAs in Populus trichocarpa that are absent from Arabidopsis. The Plant Cell, 17, 2186-2203. doi:10.1105/tpc.105.033456
[17]	Sunkar, R. and Zhu, J.K. (2004) Novel and stress-regulated microRNAs and other small RNAs from Arabidopsi. The Plant Cell, 16, 2001-2019. doi:10.1105/tpc.104.022830
[18]	Johnson, S.M., Grosshansm, H., Shingara, J., Byrom, M., Jarvis, R., Cheng, A., Labourier, E., Reinert, K.L., Brown, D. and Slack, F.J. (2005) RAS is regulated by the let-7 microRNA family. Cell, 120, 635-647. doi:10.1016/j.cell.2005.01.014
[19]	Bennasser, Y., Le, S.Y., Yeung, M.L. and Jeang, K.T. (2004) HIV-1 encoded candidate micro-RNAs and their cellular targets. Retroviro, 1, 43. doi:10.1186/1742-4690-1-43
[20]	Frazier, T.P, Xie, F., Freistaedter, A., Burklew, C.E., Zhang, B. (2010) Identification and characterization of microRNAs and their target genes in tobacco (Nicotiana tabacum). Planta, 232, 1289-1308. doi:10.1007/s00425-010-1255-1
[21]	Barozai, M.Y.K., Irfan, M., Yousaf, R., Ali, I., Qaisar, U., Maqbool, A., Zahoor, M., Rashid, B., Hussnain, T. and Riazuddin, S. (2008) Identification of micro-RNAs in cotton. Plant Physiology and Biochemistry, 46, 739-751. doi:10.1016/j.plaphy.2008.05.009
[22]	Xie, F, Frazier, T.P. and Zhang, B. (2010) Identification and characterization of microRNAs and their targets in the bioenergy plant switchgrass (Panicum virgatum). Planta, 232, 417-434. doi:10.1007/s00425-010-1182-1
[23]	Griffiths-Jones, S. (2004) The microRNA Registry. Nucleic Acids Research, 32D, 109-111. doi:10.1093/nar/gkh023
[24]	Altschul, S.F., Gish, W., Miller, W., Myers, E.W. and Lipman, D.J. (1990) Basic local alignment search tool. Journal of Molecular Biology, 215, 403-410.
[25]	Stephen, F.A., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W. and Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST, a new generation of protein database search programs. Nucleic Acids Research, 25, 3389-3402. doi:10.1093/nar/25.17.3389
[26]	Zuker, M. (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Research, 31, 3406-3415. doi:10.1093/nar/gkg595
[27]	Li, S.C., Pan, C.U. and Lin, W.C. (2006) Bioinformatic discovery of microRNA precursors from human ESTs and introns. BMC Genomics, 7, 164. doi:10.1186/1471-2164-7-164
[28]	Crooks, G.E., Hon, G., Chandonia, J.M. and Brenner, S.E. (2004) WebLogo: A sequence logo generator. Genome Research, 14, 1188-1190. doi:10.1101/gr.849004
[29]	Larkin, M.A., Blackshields, G., Brown, N.P., Chenna, R., McGettigan, P.A., McWilliam, H., Valentin, F., Wallace, I.M., Wilm, A., Lopez, R., Thompson, J.D., Gibson, T.J. and Higgins, D.G. (2007) ClustalW and ClustalX version 2. Bioinformatics, 23, 2947-2948. doi:10.1093/bioinformatics/btm404
[30]	Kruger, J. and Rehmsmeier, M. (2006) RNAhybrid: MicroRNA target prediction easy, fast and flexible. Nucleic Acids Research, 34(Supplement 2), W451-W454.
[31]	Ambros, V., Bartel, B. and Bartel, D.P. (2003) A uniform system for microRNA annotation. RNA, 9, 277-279. doi:10.1261/rna.2183803
[32]	Meyers, B.C., Axtell, M.J., Bartel, B., et al. (2008) Criteria for annotation of plant MicroRNAs. The Plant Cell, 20, 3186-3190. doi:10.1105/tpc.108.064311
[33]	Reinhart, B.J., Weinstein, E.G., Rhoades, M.W., Bartel, B. and Bartel, D.P. (2002) MicroRNAs in plants. Genes & Development, 16, 1616-1626. doi:10.1101/gad.1004402
[34]	Barozai, M.Y.K., Baloch, I.A. and Din, M. (2011) Computational identification of MicroRNAs and their targets in two species of evergreen Spruce tree (Picea). Waset, 75, 413-418.
[35]	Barozai, M.Y.K., Baloch, I.A. and Din, M. (2011) Identification of MicroRNAs and their targets in Helianthus. Molecular Biology Reports. doi:10.1007/s11033-011-1004-y