In Silico Analysis of Osa-miR164 Gene Family in Rice (Oryza Sativa)
Main Article Content
Abstract
MicroRNA (miRNA) is a small non-coding RNA molecule containing about 22- 24 nucleotides, which functions in post-transcriptional regulation of gene expression. Previous reports have shown that miRNA plays an important role on the resistance ability of plants to adverse conditions. Rice (Oryza sativa) is a major food crop. Climate change makes the situation of salinity and drought in Vietnam worse, significantly affects rice cultivation area, leading to the decrease of the quantity and the quality of rice grains. In this research, we focused on miR164 family in rice. By using bioinformatics approach, we analyzed sequences of all osa-miR164 belonging to rice miR164 family, evaluated the expression profile of osa-miR164 under different stress conditions, predicted cis-regulatory elements on osa-miR164 gene promoters, and simultaneously predicted miR164-targeted genes and their expressions. The results showed the high conserve in mature osa-miR164 sequences but not in the precursor sequences, different expression pattern of osa-miR164 gene members under stress conditions and various cis-regulatory elements present in osa-miR164 gene promoters which may explain for diverse expression pattern of osa-miR164 genes. Some potential target genes of osa-miR164 were identified and their expressions under different stress conditions were analyzed.
Keywords:
MiR164, microRNA, non-coding RNA, rice, Oryza sativa.
References
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[23] X. Y. Yang, Z. H. Zeng, J. Y. Yan, W. Fan, H. W. Bian, M. Y. Zhu, J. L. Yang, S. J. Zheng, Association of Specific Pectin Methylesterases with Al-induced Root Elongation Inhibition in Rice, Physiol, Plant, Vol. 148, 2013, pp. 502-511, https://doi.org/10.1111/PPL.12005.
[2] R. C. Lee, R. L. Feinbaum, V. Ambros, The C. Elegans Heterochronic Gene Lin-4 Encodes Small RNAs with Antisense Complementarity to Lin-14, Cell, Vol. 75, 1993, pp. 843-854, https://doi.org/10.1016/0092-8674(93)90529-Y.
[3] B. J. Reinhart, E. G. Weinstein, M. W. Rhoades, B. Bartel, D. P. Bartel, MicroRNAs in Plants, Genes Dev, Vol. 16, 2002, pp. 1616-1626, https://doi.org/10.1101/GAD.1004402.
[4] J. C. Carrington, V. Ambros, Role of MicroRNAs in Plant and Animal Development, Science, Vol. 80, No. 301, No. 80, 2003, pp. 336-338, https://doi.org/10.1126/SCIENCE.1085242.
[5] R. Simita, G. Thomas, P. Alexis, B. Thomas, L. Patrick, T. Klaus, Interplay of MiR164, Cup-shaped Cotyledon Genes and Lateral Suppressor Controls Axillary Meristem Formation in Arabidopsis Thaliana, J. Plant, Vol. 55, 2008, pp. 65-76, https://doi.org/10.1111/J.1365 313X.2008.03483.X.
[6] G. Hui-Shan, X. Qi, F. Ji-Feng, C. N. Hai, MicroRNA Directs MRNA Cleavage of the Transcription Factor NAC1 to Downregulate Auxin Signals for Arabidopsis Lateral Root Development, Plant Cell, Vol. 17, 2005, pp. 376-1386, https://doi.org/10.1105/TPC.105.030841.
[7] L. Patrick, P. Alexis, M. Halima, T. Jan, MicroRNA Regulation of the CUC Genes is Required for Boundary Size Control in Arabidopsis Meristems, Development, Vol. 131, 2004, pp. 4311-4322, https://doi.org/10.1242/DEV.01320.
[8] K. J. Hee, W. H. Ryun, K. Jeongsik, L. P. Ok, L. I. Chul, C. S. Hee, H. Daehee, N. H. Gil, Trifurcate Feed-forward Regulation of Age-dependent Cell Death Involving MiR164 in Arabidopsis, Science, Vol. 323, 2009, pp. 1053-1057, https://doi.org/10.1126/SCIENCE.1166386.
[9] R. Sunkar, X. Zhou, Y. Zheng, W. Zhang, J. K. Zhu, Identification of Novel and Candidate MiRNAs in Rice by High Throughput Sequencing, BMC Plant Biol, Vol. 8, No. 1, 2008, pp. 25, https://doi.org/10.1186/1471-2229-8-25.
[10] Y. Fang, K. Xie, L. Xiong, Conserved MiR164-Targeted NAC Genes Negatively Regulate Drought Resistance in Rice, J. Exp, Bot, Vol. 65, 2014, pp. 2119, https://doi.org/10.1093/JXB/ERU072.
[11] A. Kozomara, S. G. Jones, MiRBase: Annotating High Confidence MicroRNAs using Deep Sequencing Data, Nucleic Acids Res, Vol. 42, 2014, pp. D68-D73, https://doi.org/10.1093/NAR/GKT1181.
[12] M. A. Larkin, G. Blackshields, N. P. Brown, R. Chenna, P. A. McGettigan, H. McWilliam, F. Valentin, I. M. Wallace, A. Wilm, R. Lopez, J. D. Thompson, T. J. Gibson, D. G. Higgins, Clustal W and Clustal X version 2.0, Bioinformatics, Vol. 23, 2007, pp. 2947-2948, https://doi.org/10.1093/BIOINFORMATICS/BTM404.
[13] S. Kumar, G. Stecher, K. Tamura, MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets, Mol, Biol, Evol, Vol. 33, 2016, pp. 1870-1874, https://doi.org/10.1093/MOLBEV/MSW054.
[14] X. Ding,, X. Hou, K. Xie, L Xiong, Genome-wide Intification of BURP Domain-containing Genes in Rice Reveals a Gene Family with Diverse Structures and Responses to Abiotic Stresses, Planta, Vol. 230, 2009, pp. 149-163, https://doi.org/10.1007/S00425-009-0929-Z.
[15] H. Morita, K. Wanibuchi, H. Nii, R. Kato, S. Sugio, I. Abe, Structural Basis for the One-pot Formation of the Diarylheptanoid Scaffold by Curcuminoid Synthase from Oryza Sativa, Proc, Natl, Acad, Sci, USA, Vol. 107, 2010, pp. 19778, https://doi.org/10.1073/PNAS.1011499107.
[16] S. Y. Park, J. W. Yu, J. S. Park, J. Li, S. C. Yoo, N. Y. Lee, S. K. Lee, S. W. Jeong, H. S. Seo, H. J. Koh, J. S. Jeon, Y. I. Park, N. C. Paek, The Senescence-induced Staygreen Protein Regulates Chlorophyll Degradation, Plant Cell, Vol. 19, 2007, pp. 1649-1664, https://doi.org/10.1105/TPC.106.044891.
[17] T. Boonburapong, Buaboocha, G. Wide Identification and Analyses of the Rice Calmodulin and Related Potential Calcium Sensor Proteins, BMC Plant Biol, Vol. 7, No. 1, 2007, pp. 4, https://doi.org/10.1186/1471-2229-7-4.
[18] S. Sircar, N. Parekh, Functional Characterization of Drought-responsive Modules and Genes in Oryza Sativa: A Network-based Approach, Front, Genet, Vol. 6, 2015, pp. 256, https://doi.org/10.3389/FGENE.2015.00256.
[19] H. Yang, Y. Matsubayashi, K. Nakamura, Y. Sakagami, Oryza Sativa PSK Gene Encodes a Precursor of Phytosulfokine-alpha, A Sulfated Peptide Growth Factor Found in Plants, Proc, Natl, Acad, Sci, USA, Vol. 96, 1999, pp. 13560-13565, https://doi.org/10.1073/PNAS.96.23.13560.
[20] J. Chen, Y. Ouyang, L. Wang, W. Xie, Q. Zhang, Aspartic Proteases Gene Family in Rice: Gene Structure and Expression, Predicted Protein Features and Phylogenetic Relation, Gene, Vol. 442, 2009, pp. 108-118, https://doi.org/10.1016/J.GENE.2009.04.021.
[21] Z. Tang,, Y. Chen, F. Chen, Y. Ji, OsPTR7 (OsNPF8.1), A Putative Peptide Transporter in Rice, is Involved in Dimethylarsenate Accumulation in Rice Grain, Plant Cell Physiol, Vol. 58, 2017,pp. 904-913, https://doi.org/10.1093/PCP/PCX029.
[22] A. Macovei, N. Tuteja, MicroRNAs Targeting Dead-box Helicases are Involved in Salinity Stress Response in Rice (Oryza sativa L.), BMC Plant Biol, Vol. 12, 2012, https://doi.org/10.1186/1471-2229-12-183.
[23] X. Y. Yang, Z. H. Zeng, J. Y. Yan, W. Fan, H. W. Bian, M. Y. Zhu, J. L. Yang, S. J. Zheng, Association of Specific Pectin Methylesterases with Al-induced Root Elongation Inhibition in Rice, Physiol, Plant, Vol. 148, 2013, pp. 502-511, https://doi.org/10.1111/PPL.12005.