Computational Identification of Conserved microRNAs and Their Targets in Tea (Camellia sinensis)

Akan Das, Tapan Kumar Mondal
DOI: 10.4236/ajps.2010.12010                

Abstract

MicroRNAs (miRNAs) are a class of ~22 nucleotides long non coding RNA molecules which play an important role in gene regulation at the post transcriptional level. The conserved nature of miRNAs provides the basis of new miRNA identification through homology search. In an attempt to identify new conserved miRNAs in tea, previously known plant miRNAs were used for searching their homolog in a tea Expressed Sequence Tags and full length nucleotide sequence database. The sequences showing homolog no more than four mismatches were predicted for their fold back structures and passed through a series of filtration criteria, finally led us to identify 13 conserved miRNAs in tea belonging to 9 miRNA families. A total of 37 potential target genes in Arabidopsis were identified subsequently for 7 miRNA families based on their sequence complementarity which encode transcription factors (8%), enzymes (30%) and transporters (14%) as well as other proteins involved in physiological and metabolic processes (48%). Overall, our findings will accelerate the way for further researches of miRNAs and their functions in tea.

Keywords

Camellia sinensis, Computational Identification, Expressed Sequence Tags, microRNA, Targets

Conflicts of Interest

The authors declare no conflicts of interest.

References

[1]	B. Zhang, X. Pan and A. T. Anderson, “Identification of 188 Conserved Maize microRNAs and Their Targets”, FEBS Letters, Vol. 580, No. 15, June 2006, pp. 3753-3762.
[2]	X. Zhou, J. Ruan, G. Wang and W. Zhang, “Characterization and Identification of MicroRNA Core Promoters in Four Model Species,” PLoS Computational Biology, Vol. 3, No. 3, January 2007, pp. e37.
[3]	J. Singh and J. Nagaraju, “In silico Prediction and Characterization of microRNAs from Red Flour Beetle (Tribolium castaneum),” Insect Molecular Biology, Vol. 17, No. 4, August 2008, pp. 427-436.
[4]	B. Zhang, X. Pan, G. P. Cobb and T. A. Anderson, “Plant microRNA: A Small Regulatory Molecule with Big Impact,” Developmental Biology, Vol. 289, No. 1, January 2006, pp. 3-16.
[5]	C. A. Mallory and H. Vaucheret, “Functions of microRNAs and Related Small RNAs in Plants,” Nature Genetics, Vol. 38, May 2006, pp. S31-S36.
[6]	R. Sunkar, V. Chinnusamy, J. Zhu and K. J. Zhu, “Small RNAs as Big Players in Plant Abiotic Stress Responses and Nutrient Deprivation,” Trends in Plant Science, Vol. 12, No. 7, July 2007, pp. 301-309.
[7]	B. Zhang, X. Pan, C. H. Cannon, G. P. Cobb and A. T. Anderson, “Conservation and Divergence of Plant microRNA Genes,” Plant Journal, Vol. 46, No. 2, April 2006, pp. 243-259.
[8]	A. N. Eckardt, “MicroRNAs Regulate Auxin Homeostasis and Plant Development,” The Plant Cell, Vol. 17, May 2005, pp. 1335-1338.
[9]	S. H. Guo, Q. Xie, F. J. Fei and H. N. Chua, “MicroRNA Directs mRNA Cleavage of the Transcription Factor NAC1 to Downregulate Auxin Signals for Arabidopsis Lateral Root Development,” The Plant Cell, Vol. 17, May 2005, pp. 1376-1386.
[10]	M. W. Jones-Rhoades and P. D. Bartel, “Computtional Identification of Plant microRNAs and Their Targets, Including a Stress-Induced miRNA,” Molecular Cell, Vol. 14, June 2004, pp. 787-799.
[11]	R. Sunkar and J. K. Zhu, “Novel and Stress-Regulated microRNAs and Other Small RNAs from Arabidopsis”, The Plant Cell, Vol. 16, No. 8, August 2004, pp. 2001-2019.
[12]	Y. Lu, Q. Gan, X. Chi and S. Qin, “Roles of microRNA in Plant Defense and Virus Offense Interaction,” Plant Cell Reports, Vol. 27, No. 10, October 2008, pp. 1571-1579.
[13]	R. Alba, Z. Fei, P. Payton, Y. Liu, L. S. Moore, P. Debbie, J. Cohn and M. D’Ascenzo, “ESTs, cDNA Microarrays, and Gene Expression Profiling: Tools for Dissecting Plant Physiology and Development,” The Plant Journal, Vol. 39, No. 5, September 2004, pp. 697-714.
[14]	B. H. Zhang, X. P. Pan, Q. L. Wang, G. P. Cobb and T. A. Anderson, “Identification and Characterization of New Plant microRNAs Using EST Analysis,” Cell Research, Vol. 15, No. 5, May 2005, pp. 336-360.
[15]	Q. Guo, A. Xiang, Q. Yang and Z. Y. Yang, “Bioinformatic Identification of microRNAs and Their Target Genes from Solanum tuberosum Expressed Sequence Tags,” Chinese Science Bulletin, Vol. 52, No. 17, September 2007, pp. 2380-2389.
[16]	M. N. Nasaruddin, K. Harikrishna, Y. R. Othman, S. L. Hoon and A. J. Harikrishna, “Computational Prediction of microRNAs from Oil Palm (Elaeis guineensis Jacq.) Expressed Sequence Tags,” Asian Pacific Journal of Molecular Biology and Biotechnology, Vol. 15, No. 3, October 2007, pp. 107-113.
[17]	W. Jin, N. Li, B. Zhang, F. Wu, W. Li, A. Guo and Z. Deng, “Identification and Verification of microRNA in Wheat (Triticum aestivum),” Journal of Plant Research, Vol. 121, No. 3, March 2008, pp. 351-355.
[18]	B. Billoud, D. R. Paepe, D. Baulcombe and M. Boccara, “Identification of New Small non-coding RNAs from Tobacco and Arabidopsis,” Biochimie, Vol. 87, No. 9, September 2005, pp. 905-910.
[19]	R. Sunkar and G. Jagadeeswaran, “In silico Identification of Conserved microRNAs in Large Number of Diverse Plant Species,” BMC Plant Biology, Vol. 8, No. 37, 2008, p. 13.
[20]	S. Griffiths-Jones, H. K. Saini, D. S. Van and A. J. Enright, “MiRBase: Tools for microRNA Genomics,” Nucleic Acids Research, Vol. 36, November 2008, pp. D154-D158.
[21]	N. Rajewsky and D. N. Socci, “Computational Identification of microRNA Targets,” Developmental Biology, Vol. 267, No. 2, March 2004, pp. 529-535.
[22]	L. Zhang, M. J. Chia, S. Kumari, C. J. Stein, Z. Liu, A. Narechania, A. C. Maher, K. Guill, D. M. McMullen and D. Ware, “A Genome-Wide Characterization of microRNA Genes in Maize,” PLoS Genetics, Vol. 5, No. 11, November 2009, pp. 5e1000716.
[23]	S. F. Altschul, T. L. Madden, A. A. Sch?ffer, J. Zhang, Z. Zhang, W. Miller and D. J. Lipman, “Gapped BLAST and PSI-BLAST: A New Generation of Protein Database Search Programs,” Nucleic Acids Research, Vol. 25, No. 17, September 1997, pp. 3389-3402.
[24]	M. Zuker, “Mfold Web Server for Nucleic Acid Folding and Hybridization Prediction,” Nucleic Acids Research, Vol. 31, No. 13, July 2003, pp. 3406-3415.
[25]	J. D. Thompson, D. G. Higgins and T. J. Gibson, “CLUSTAL W: Improving the Sensitivity of Progressive Multiple Sequence Alignments through Sequence Weighting, Position Specific Gap Penalties and Weight Matrix Choice,” Nucleic Acids Research, Vol. 22, No. 22, November 1994, pp. 4673-4680.
[26]	K. Tamura and M. Nei, “Estimation of the Number of Nucleotide Substitutions in the Control Region of Mitochondrial DNA in Humans and Chimpanzees,” Molecular Biology and Evolution, Vol. 10, No. 3, May 1993, pp. 512-526.
[27]	K. Tamura, J. Dudley, M. Nei and S. Kumar, “MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0.,” Molecular Biology and Evolution, Vol. 24, No. 8, August 2007, pp. 1596-1599.
[28]	S. Griffiths-Jones, R. J. Grocock, D. S. Van, A. Bateman and A. J. Enright, “miRBase: microRNA Sequences, Targets and Gene Nomenclature,” Nucleic Acids Research, Vol. 34, November 2006, pp. D140-D144.
[29]	E. Bonnet, J. Wuyts, P. Rouze and Y. V. de Peer, “Evidence that microRNA Precursors, unlike Other Non-Coding RNAs, Have Lower Folding Free Energies than Random Sequences,” Bioinformatics, Vol. 20, No. 17, November 2004, pp. 2911-2917.
[30]	P. D. Bartel, “MicroRNAs: Genomics, Biogenesis, Mechanism and Function,” Cell, Vol. 116, No. 2, January 2004, pp. 281-297.
[31]	V. Ambros, “The Functions of Animal microRNAs,” Nature, Vol. 431, September 2004, pp. 350-355.
[32]	M. Y. Khan-Barozai, M. Irfan, R. Yousaf, I. Ali, U. Qaisar, A. Maqbool, M. Zahoor, B. Rashid, T. Hussnain and S. Riazuddin, “Identification of microRNA in Cotton,” Plant Physiology and Biochemistry, Vol. 46, No. 8, August 2008, pp. 739-751.
[33]	C. X. Qiu, F. L. Xie, Y. Y. Zhu, K. Guo, S. Q. Huang, L. Nie and Z. M. Yang, “Computational Identification of microRNAs and Their Targets in Gossypium hirsutum Expressed Sequence Tags,” Gene, Vol. 395, No. 1, June 2007, pp. 49-61.
[34]	G. R. Prabu and A. K. A. Mandal, “Computational Identification of miRNAs and Their Target Genes from Expressed Sequence Tags of Tea (Camellia sinensis),” Genomics Proteomics and Bioinformatics, Vol. 8, No. 2, June 2010, pp. 113-121.