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Received: 2010-07-21

Revision Accepted: 2010-11-05

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Journal of Zhejiang University SCIENCE B 2011 Vol.12 No.2 P.116-125

10.1631/jzus.B1000278


Microarray-based identification of tomato microRNAs and time course analysis of their response to Cucumber mosaic virus infection*#


Author(s):  Qiu-lei Lang, Xiao-chuan Zhou, Xiao-lin Zhang, Rafal Drabek, Zhi-xiang Zuo, Yong-liang Ren, Tong-bin Li, Ji-shuang Chen, Xiao-lian Gao

Affiliation(s):  College of Life Sciences, Zhejiang University, Hangzhou 310058, China; more

Corresponding email(s):   chenjsbio@163.com, xgao@uh.edu

Key Words:  Solanum lycopersicum, Plant miRNA, Cucumber mosaic virus, miRNA array, miRNA response


Qiu-lei Lang, Xiao-chuan Zhou, Xiao-lin Zhang, Rafal Drabek, Zhi-xiang Zuo, Yong-liang Ren, Tong-bin Li, Ji-shuang Chen, Xiao-lian Gao. Microarray-based identification of tomato microRNAs and time course analysis of their response to Cucumber mosaic virus infection*#[J]. Journal of Zhejiang University Science B, 2011, 12(2): 116-125.

@article{title="Microarray-based identification of tomato microRNAs and time course analysis of their response to Cucumber mosaic virus infection*#",
author="Qiu-lei Lang, Xiao-chuan Zhou, Xiao-lin Zhang, Rafal Drabek, Zhi-xiang Zuo, Yong-liang Ren, Tong-bin Li, Ji-shuang Chen, Xiao-lian Gao",
journal="Journal of Zhejiang University Science B",
volume="12",
number="2",
pages="116-125",
year="2011",
publisher="Zhejiang University Press & Springer",
doi="10.1631/jzus.B1000278"
}

%0 Journal Article
%T Microarray-based identification of tomato microRNAs and time course analysis of their response to Cucumber mosaic virus infection*#
%A Qiu-lei Lang
%A Xiao-chuan Zhou
%A Xiao-lin Zhang
%A Rafal Drabek
%A Zhi-xiang Zuo
%A Yong-liang Ren
%A Tong-bin Li
%A Ji-shuang Chen
%A Xiao-lian Gao
%J Journal of Zhejiang University SCIENCE B
%V 12
%N 2
%P 116-125
%@ 1673-1581
%D 2011
%I Zhejiang University Press & Springer
%DOI 10.1631/jzus.B1000278

TY - JOUR
T1 - Microarray-based identification of tomato microRNAs and time course analysis of their response to Cucumber mosaic virus infection*#
A1 - Qiu-lei Lang
A1 - Xiao-chuan Zhou
A1 - Xiao-lin Zhang
A1 - Rafal Drabek
A1 - Zhi-xiang Zuo
A1 - Yong-liang Ren
A1 - Tong-bin Li
A1 - Ji-shuang Chen
A1 - Xiao-lian Gao
J0 - Journal of Zhejiang University Science B
VL - 12
IS - 2
SP - 116
EP - 125
%@ 1673-1581
Y1 - 2011
PB - Zhejiang University Press & Springer
ER -
DOI - 10.1631/jzus.B1000278


Abstract: 
A large number of plant microRNAs (miRNAs) are now documented in the miRBase, among which only 30 are for Solanum lycopersicum (tomato). Clearly, there is a far-reaching need to identify and profile the expression of miRNAs in this important crop under various physiological and pathological conditions. In this study, we used an in situ synthesized custom microarray of plant miRNAs to examine the expression and temporal presence of miRNAs in the leaves of tomato plants infected with Cucumber mosaic virus (CMV). Following computational sequence homology search and hairpin structure prediction, we identified three novel tomato miRNA precursor genes. Our results also show that, in accordance with the phenotype of the developing leaves, the tomato miRNAs are differentially expressed at different stages of plant development and that CMV infection can induce or suppress the expression of miRNAs as well as up-regulate some star miRNAs (miRNA*s) which are normally present at much lower levels. The results indicate that developmental anomalies elicited by virus infection may be caused by more complex biological processes.

Darkslateblue:Affiliate; Royal Blue:Author; Turquoise:Article

Reference

[1]Axtell, M.J., Bartel, D.P., 2005. Antiquity of microRNAs and their targets in land plants. Plant Cell, 17(6):1658-1673.

[2]Barkoulas, M., Hay, A., Kougioumoutzi, E., Tsiantis, M., 2008. A developmental framework for dissected leaf formation in the Arabidopsis relative Cardamine hirsuta. Nat. Genet., 40(9):1136-1141.

[3]Bazzini, A., Almasia, N., Manacorda, C., Mongelli, V., Conti, G., Maroniche, G., Rodriguez, M., Distefano, A., Hopp, H.E., del Vas, M., et al., 2009. Virus infection elevates transcriptional activity of miR164a promoter in plants. BMC Plant Biol., 9(1):152.

[4]Bolstad, B.M., Irizarry, R.A., Astrand, M., Speed, T.P., 2003. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics, 19(2):185-193.

[5]Chapman, E.J., Prokhnevsky, A.I., Gopinath, K., Dolja, V.V., Carrington, J.C., 2004. Viral RNA silencing suppressors inhibit the microRNA pathway at an intermediate step. Genes Dev., 18(10):1179-1186.

[6]Cillo, F., Mascia, T., Pasciuto, M.M., Gallitelli, D., 2009. Differential effects of mild and severe cucumber mosaic virus strains in the perturbation of microRNA-regulated gene expression in tomato map to the 3( sequence of RNA 2. Mol. Plant-Microbe Interact., 22(10):1239-1249.

[7]Feng, J., Wang, K., Liu, X., Chen, S., Chen, J., 2009. The quantification of tomato microRNAs response to viral infection by stem-loop real-time RT-PCR. Gene, 437(1-2):14-21.

[8]Gao, X., Gulari, E., Zhou, X., 2004. In situ synthesis of oligonucleotide microarrays. Biopolymers, 73(5):579-596.

[9]García-Arenal, F., Escriu, F., Aranda, M.A., Alonso-Prados, J.L., Malpica, J.M., Fraile, A., 2000. Molecular epidemiology of Cucumber mosaic virus and its satellite RNA. Virus Res., 71(1-2):1-8.

[10]Guo, H.S., Ding, S.W., 2002. A viral protein inhibits the long range signaling activity of the gene silencing signal. EMBO J., 21(3):398-407.

[11]Hay, A., Tsiantis, M., 2006. The genetic basis for differences in leaf form between Arabidopsis thaliana and its wild relative Cardamine hirsuta. Nat. Genet., 38(8):942-947.

[12]He, P.A., Nie, Z., Chen, J., Lv, Z., Sheng, Q., Zhou, S., Gao, X., Kong, L., Wu, X., Jin, Y., et al., 2008. Identification and characteristics of microRNAs from Bombyx mori. BMC Genom., 9(1):248.

[13]Hofacker, I.L., 2003. Vienna RNA secondary structure server. Nucleic Acids Res., 31(13):3429-3431.

[14]Itaya, A., Bundschuh, R., Archual, A.J., Joung, J.G., Fei, Z., Dai, X., Zhao, P.X., Tang, Y., Nelson, R.S., Ding, B., 2008. Small RNAs in tomato fruit and leaf development. Biochim. Biophys. Acta, 1779(2):99-107.

[15]Jones-Rhoades, M.W., Bartel, D.P., Bartel, B., 2006. MicroRNAs and their regulatory roles in plants. Ann. Rev. Plant Biol., 57(1):19-53.

[16]Meng, Y., Huang, F., Shi, Q., Cao, J., Chen, D., Zhang, J., Ni, J., Wu, P., Chen, M., 2009. Genome-wide survey of rice microRNAs and microRNA-target pairs in the root of a novel auxin-resistant mutant. Planta, 230(5):883-898.

[17]Moxon, S., Jing, R., Szittya, G., Schwach, F., Rusholme Pilcher, R.L., Moulton, V., Dalmay, T., 2008. Deep sequencing of tomato short RNAs identifies microRNAs targeting genes involved in fruit ripening. Genome Res., 18(10):1602-1609.

[18]Palukaitis, P., Roossinck, M.J., Dietzgen, R.G., Francki, R.I., 1992. Cucumber mosaic virus. Adv. Virus Res., 41:281-348.

[19]Pilcher, R.L., Moxon, S., Pakseresht, N., Moulton, V., Manning, K., Seymour, G., Dalmay, T., 2007. Identification of novel small RNAs in tomato (Solanum lycopersicum). Planta, 226(3):709-717.

[20]Shiboleth, Y.M., Haronsky, E., Leibman, D., Arazi, T., Wassenegger, M., Whitham, S.A., 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., 81(23):13135-13148.

[21]Sikora, E.J., Gudauskas, R.T., Murphy, J.F., Porch, D.W., Andrianifahanana, M., Zehnder, G.W., Bauske, E.M., Kemble, J.M., Lester, D.F., 1998. A multivirus epidemic of tomatoes in Alabama. Plant Dis., 82(1):117-120.

[22]Sunkar, R., Zhu, J.K., 2004. Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. Plant Cell, 16(8):2001-2019.

[23]Sunkar, R., Girke, T., Jain, P.K., Zhu, J.K., 2005. Cloning and characterization of microRNAs from rice. Plant Cell, 17(5):1397-1411.

[24]Wang, H., Jones, B., Li, Z., Frasse, P., Delalande, C., Regad, F., Chaabouni, S., Latche, A., Pech, J.C., Bouzayen, M., 2005. The tomato Aux/IAA transcription factor IAA9 is involved in fruit development and leaf morphogenesis. Plant Cell, 17(10):2676-2692.

[25]Wang, Q.L., Li, Z.H., 2007. The functions of microRNAs in plants. Front. Biosci., 12:3975-3982.

[26]Wilson, K.D., Venkatasubrahmanyam, S., Jia, F., Sun, N., Butte, A.J., Wu, J.C., 2009. MicroRNA profiling of human-induced pluripotent stem cells. Stem Cells Devel., 18(5):749-758.

[27]Yin, Z., Li, C., Han, X., Shen, F., 2008. Identification of conserved microRNAs and their target genes in tomato (Lycopersicon esculentum). Gene, 414(1-2):60-66.

[28]Zhang, B., Pan, X., Cannon, C.H., Cobb, G.P., Anderson, T.A., 2006. Conservation and divergence of plant microRNA genes. Plant J., 46(2):243-259.

[29]Zhang, J., Zeng, R., Chen, J., Liu, X., Liao, Q., 2008. Identification of conserved microRNAs and their targets from Solanum lycopersicum Mill. Gene, 423(1):1-7.

[30]Zhang, X., Yuan, Y.R., Pei, Y., Lin, S.S., Tuschl, T., Patel, D.J., Chua, N.H., 2006. Cucumber mosaic virus-encoded 2b suppressor inhibits Arabidopsis Argonaute1 cleavage activity to counter plant defense. Genes Devel., 20(23):3255-3268.

[31]Zhang, Y., 2005. miRU: an automated plant miRNA target prediction server. Nucleic Acids Res., 33:W701-W704.

[32]Zhang, Z., Wei, L., Zou, X., Tao, Y., Liu, Z., Zheng, Y., 2008. Submergence-responsive microRNAs are potentially involved in the regulation of morphological and metabolic adaptations in maize root cells. Ann Bot., 102(4):509-519.

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