Sains Malaysiana 49(6)(2020): 1245-1272

http://dx.doi.org/10.17576/jsm-2020-4906-04

 

Identification and Analysis of microRNAs Responsive to Abscisic Acid and Methyl Jasmonate Treatments in Persicaria minor

(Pengenalpastian dan Analisis Gerak Balas mikroRNA kepada Rawatan Asid Absisik dan Metil Jasmonat dalam Persicaria minor)

 

ABDUL FATAH A. SAMAD1,2, NAZARUDDIN NAZARUDDIN3, JAEYRES JANI3 & ISMANIZAN ISMAIL1,4*

 

1Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor Darul Ehsan, Malaysia

 

2Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310 UTM Skudai, Johor Darul Takzim, Malaysia

 

3Department of Chemistry, Faculty of Mathematics and Natural Sciences, Syiah Kuala University

Darussalam, 23111 Banda Aceh, Indonesia

 

4Centre for Biotechnology and Functional Food, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor Darul Ehsan, Malaysia

 

Received: 9 August 2019/Accepted: 14 February 2020

 

ABSTRACT

Persicaria minor has been recognised as a plant with high content of volatile organic compounds (VOC) especially terpenoid and green leaf volatile (GLV). Previous finding had showed signaling molecules such as abscisic acid (ABA) and methyl jasmonate (MeJA) can increase the VOC content in plant. In this study, we performed next generation sequencing (NGS) of small RNA to uncover miRNAs roles and their response to both phytohormones (ABA and MeJA) in P. minor. For both ABA and MeJA treated P. minor, small RNA libraries containing 17,253,566 and 40,437,576 reads were generated, respectively. In addition, 18,634,904 reads were generated in plant treated with sterile distilled water which served as control. In these libraries, a total of 88 miRNAs were identified, comprising 41 known and 47 novel miRNAs. It was observed that 21 and 38 miRNAs were significantly regulated in ABA and MeJA libraries, respectively. Four selected miRNAs related to VOC pathways were subjected to RT-qPCR analysis and found to display diverse expression patterns with their targets. This study provides the initial framework for further exploration of miRNA roles in ABA and MeJA responses.

 

Keywords: Abscisic acid; methyl jasmonate; microRNA; Persicaria minor; volatile organic compound

 

ABSTRAK

Persicaria minor telah dikenal pasti sebagai tumbuhan yang mempunyai kandungan sebatian organik meruap (VOC) yang tinggi terutama terpenoid dan sebatian daun hijau meruap (GLV). Kajian lepas menunjukkan molekul pengisyaratan seperti asid absisik (ABA) dan metil jasmonat (MeJA) boleh meningkatkan kandungan VOC dalam tumbuhan. Dalam kajian ini, kami menjalankan penjujukan generasi terkini (NGS) RNA kecil untuk merungkai peranan miRNA dan tindak balasnya terhadap kedua-dua fitohormon (ABA dan MeJA) dalam P. minor. Bagi kedua-dua rawatan ABA dan MeJA terhadap P. minor, perpustakaan kecil RNA masing-masing telah menjana sejumlah 17,253,566 dan 40,437,576 bacaan. Tambahan lagi, sejumlah 18,634,904 bacaan telah dijana daripada tumbuhan terawat air suling steril yang bertindak sebagai kawalan. Dalam perpustakaan tersebut, sejumlah 88 miRNA telah dikenal pasti yang terdiri daripada 41 miRNA yang telah diketahui fungsinya dan 47 miRNA novel. Sejumlah 21 dan 38 miRNA masing-masing telah dicerap dikawal atur secara signifikan dalam perpustakaan ABA dan MeJA. Sebanyak empat miRNA yang berkait dengan tapak jalan VOC telah dikaji melalui analisis RT-qPCR dan didapati menunjukkan corak pengekspresan yang pelbagai terhadap transkrip sasaran masing-masing. Kajian ini menyediakan rangka kerja awal untuk penerokaan selanjutnya mengenai peranan miRNA dalam tindak balas ABA dan MeJA.

 

Kata kunci: Asid absisik; metil jasmonat; mikroRNA; Persicaria minor; sebatian organik meruap

 

REFERENCES

Abd Hamid, N.A., Zainal, Z. & Ismail, I. 2018. Two members of unassigned type of short-chain dehydrogenase/reductase superfamily (SDR) isolated from Persicaria minor show response towards ABA and drought stress. Journal of Plant Biochemistry and Biotechnology 27(3): 260-271.

Almagro, L., Gómez Ros, L.V., Belchi-Navarro, S., Bru, R., Ros Barceló, A. & Pedreño, M.A. 2009. Class III peroxidases in plant defence reactions. Journal of Experimental Botany 60(2): 377-390.

Audic, S. & Claverie, J.M. 1997. The significance of digital gene expression profiles. Genome Research 7(10): 986-995.

Baggerly, K.A., Deng, L., Morris, J.S. & Aldaz, C.M. 2003. Differential expression in SAGE: Accounting for normal between-library variation. Bioinformatics 19(12): 1477-1483.

Baharum, S.N., Bunawan, H., Ghani, M.A., Mustapha, W.A. & Noor, N.M. 2010. Analysis of the chemical composition of the essential oil of Polygonum minus Huds. using two-dimensional gas chromatography-time-of-flight mass spectrometry (GC-TOF MS). Molecules 15(10): 7006-7015.

Benjamini, Y. & Hochberg, Y. 1995. Controlling the false discovery rate: A practical and powerful approach to multiple testing. Journal of the Royal Statistical Society. Series B (Methodological) 57(1): 289-300.

Chappell, J., VonLanken, C. & Vögeli, U. 1991. Elicitor-inducible 3-Hydroxy-3-Methylglutaryl coenzyme A reductase activity is required for sesquiterpene accumulation in tobacco cell suspension cultures. Plant Physiology 97(2): 693-698.

Christapher, P.V., Parasuraman, S., Christina, J.M., Asmawi, M.Z. & Vikneswaran, M. 2015. Review on Polygonum minus. Huds, a commonly used food additive in Southeast Asia. Pharmacognosy Research 7(1): 1-6.

Ee, S.F., Mohamed-Hussein, Z.A., Othman, R., Shaharuddin, N.A., Ismail, I. & Zainal, Z. 2014. Functional characterization of sesquiterpene synthase from Polygonum minus. The Scientific World Journal 2014: 840592.

El-Sayed, M. & Verpoorte, R. 2004. Growth, metabolic profiling and enzymes activities of Catharanthus roseus seedlings treated with plant growth regulators. Plant Growth Regulation 44(1): 53-58.

Gor, M., Ismail, I., Mustapha, W., Zainal, Z., Noor, N., Othman, R. & Hussein, Z. 2011. Identification of cDNAs for jasmonic acid-responsive genes in Polygonum minus roots by suppression subtractive hybridization. Acta Physiologiae Plantarum 33(2): 283-294.

Huang, H., Liu, B., Liu, L. & Song, S. 2017. Jasmonate action in plant growth and development. Journal of Experimental Botany 68(6): 1349-1359.

Jörnvall, H. 2008. Medium- and short-chain dehydrogenase/reductase gene and protein families: MDR and SDR gene and protein superfamilies. Cellular and Molecular Life Sciences: CMLS 65(24): 3873-3878.

Kondo, K., Uritani, I. & Oba, K. 2003. Induction mechanism of 3-hydroxy-3-methylglutaryl-CoA reductase in potato tuber and sweet potato root tissues. Bioscience, Biotechnology and Biochemistry 67(5): 1007-1017.

Kozomara, A., Birgaoanu, M. & Griffiths-Jones, S. 2019. miRBase: From microRNA sequences to function. Nucleic Acids Research 47(D1): D155-D162.

Lenka, S.K., Nims, N.E., Vongpaseuth, K., Boshar, R.A., Roberts, S.C. & Walker, E.L. 2015. Jasmonate-responsive expression of paclitaxel biosynthesis genes in Taxus cuspidata cultured cells is negatively regulated by the bHLH transcription factors TcJAMYC1, TcJAMYC2, and TcJAMYC4. Frontiers in Plant Science 6: 115-115.

Liang, Z., Ma, Y., Xu, T., Cui, B., Liu, Y., Guo, Z. & Yang, D. 2013. Effects of abscisic acid, gibberellin, ethylene and their interactions on production of phenolic acids in Salvia miltiorrhiza bunge hairy roots. PLoS ONE 8(9): e72806.

Liu, Z., Zhang, S., Sun, N., Liu, H., Zhao, Y., Liang, Y., Zhang, L. & Han, Y. 2015. Functional diversity of jasmonates in rice. Rice (N Y) 8(1): 42.

Livak, K.J. & Schmittgen, T.D. 2001. Analysis of relative gene expression data using real-time quantitative PCR and the 2− ΔΔCT method. Methods 25(4): 402-408.

Loke, K.K., Rahnamaie-Tajadod, R., Yeoh, C.C., Goh, H.H., Mohamed-Hussein, Z.A., Mohd Noor, N., Zainal, Z. & Ismail, I. 2016. RNA-seq analysis for secondary metabolite pathway gene discovery in Polygonum minus. Genomics Data 7: 12-13.

Loreti, E., Povero, G., Novi, G., Solfanelli, C., Alpi, A. & Perata, P. 2008. Gibberellins, jasmonate and abscisic acid modulate the sucrose-induced expression of anthocyanin biosynthetic genes in Arabidopsis. New Phytologist 179(4): 1004-1016.

Markham, N.R. & Zuker, M. 2008. UNAFold: Software for nucleic acid folding and hybridization. Methods in Molecular Biology 453: 3-31.

Nazaruddin, N., Samad, A.F.A., Sajad, M., Jani, J., Zainal, Z. & Ismail, I. 2017. Small RNA-seq analysis in response to methyl jasmonate and abscisic acid treatment in Persicaria minor. Genomics Data 12: 157-158.

Ohyama, K., Suzuki, M., Masuda, K., Yoshida, S. & Muranaka, T. 2007. Chemical phenotypes of the hmg1 and hmg2 mutants of Arabidopsis demonstrate the In-planta role of HMG-CoA reductase in triterpene biosynthesis. Chemical and Pharmaceutical Bulletin (Tokyo) 55(10): 1518-1521.

Pontes, O., Costa-Nunes, P., Vithayathil, P. & Pikaard, C.S. 2009. RNA polymerase V functions in Arabidopsis interphase heterochromatin organization independently of the 24-nt siRNA-directed DNA methylation pathway. Molecular Plant 2(4): 700-710.

Rahnamaie-Tajadod, R., Loke, K.K., Goh, H.H. & Mohd Noor, N. 2017. Differential gene expression analysis in Polygonum minus leaf upon 24 hours of methyl jasmonate elicitation. Frontiers in Plant Science 8(109). doi: 10.3389/fpls.2017.00109.

Rai, M.K., Shekhawat, N.S., Harish, Gupta, A.K., Phulwaria, M., Ram, K. & Jaiswal, U. 2011. The role of abscisic acid in plant tissue culture: a review of recent progress. Plant Cell, Tissue and Organ Culture (PCTOC) 106(2): 179-190.

Riemann, M., Dhakarey, R., Hazman, M., Miro, B., Kohli, A. & Nick, P. 2015. Exploring jasmonates in the hormonal network of drought and salinity responses. Frontiers in Plant Science 6: 1077.

Roslan, N.D., Yusop, J.M., Baharum, S.N., Othman, R., Mohamed-Hussein, Z.A., Ismail, I., Noor, N.M. & Zainal, Z. 2012. Flavonoid biosynthesis genes putatively identified in the aromatic plant Polygonum minus via Expressed Sequences Tag (EST) analysis. International Journal of Molecular Sciences 13(3): 2692-2706.

Rusdi, N.A., Goh, H.H., Sabri, S., Ramzi, A.B., Mohd Noor, N. & Baharum, S.N. 2018. Functional characterisation of new sesquiterpene synthase from the Malaysian herbal plant, Polygonum minus. Molecules (Basel, Switzerland) 23(6): 1370.

Sah, S.K., Reddy, K.R. & Li, J. 2016. Abscisic acid and abiotic stress tolerance in crop plants. Frontiers in Plant Science 7: 571-571.

Samad, A.F.A., Rahnamaie-Tajadod, R., Sajad, M., Jani, J., Murad, A.M.A., Noor, N.M. & Ismail, I. 2019. Regulation of terpenoid biosynthesis by miRNA in Persicaria minor induced by Fusarium oxysporum. BMC Genomics 20(1): 586.

Samad, A.F.A., Nazaruddin, N., Murad, A.M.A., Jani, J., Zainal, Z. & Ismail, I. 2018. Deep sequencing and in silico analysis of small RNA library reveals novel miRNA from leaf Persicaria minor transcriptome. 3 Biotech 8(3): 136.

Samad, A.F.A., Sajad, M., Nazaruddin, N., Fauzi, I.A., Murad, A.M.A., Zainal, Z. & Ismail, I. 2017. MicroRNA and transcription factor: Key players in plant regulatory network. Frontiers in Plant Science 8: 565.

Shigeto, J. & Tsutsumi, Y. 2016. Diverse functions and reactions of class III peroxidases. New Phytologist 209(4): 1395-1402.

Suzuki, M., Kamide, Y., Nagata, N., Seki, H., Ohyama, K., Kato, H., Masuda, K., Sato, S., Kato, T., Tabata, S., Yoshida, S. & Muranaka, T. 2004. Loss of function of 3-hydroxy-3-methylglutaryl coenzyme A reductase 1 (HMG1) in Arabidopsis leads to dwarfing, early senescence and male sterility, and reduced sterol levels. The Plant Journal 37(5): 750-761.

Tholl, D. 2015. Biosynthesis and biological functions of terpenoids in plants. Advances in Biochemical Engineering/Biotechnology 148: 63-106.

Ul Hassan, M.N., Zainal, Z. & Ismail, I. 2015. Green leaf volatiles: Biosynthesis, biological functions and their applications in biotechnology. Plant Biotechnology Journal 13(6): 727-739.

War, A.R., Sharma, H.C., Paulraj, M.G., War, M.Y. & Ignacimuthu, S. 2011. Herbivore induced plant volatiles: Their role in plant defense for pest management. Plant Signaling & Behavior 6(12): 1973-1978.

Wu, H.J., Ma, Y.K., Chen, T., Wang, M. & Wang, X.J. 2012. PsRobot: A web-based plant small RNA meta-analysis toolbox. Nucleic Acids Research 40: 22-28.

Yan, C. & Xie, D. 2015. Jasmonate in plant defence: Sentinel or double agent? Plant Biotechnology Journal 13(9): 1233-1240.

Yang, D., Ma, P., Liang, X., Wei, Z., Liang, Z., Liu, Y. & Liu, F. 2012. PEG and ABA trigger methyl jasmonate accumulation to induce the MEP pathway and increase tanshinone production in Salvia miltiorrhiza hairy roots. Physiologia Plantarum 146(2): 173-183.

Ye, J., Zhang, Y., Cui, H., Liu, J., Wu, Y., Cheng, Y., Xu, H., Huang, X., Li, S., Zhou, A., Zhang, X., Bolund, L., Chen, Q., Wang, J., Yang, H., Fang, L. & Shi, C. 2018. WEGO 2.0: A web tool for analyzing and plotting GO annotations, 2018 update. Nucleic Acids Research 46(W1): W71-W75.

Zhang, B.H., Pan, X.P., Cox, S.B., Cobb, G.P. & Anderson, T.A. 2006. Evidence that miRNAs are different from other RNAs. Cellular and Molecular Life Sciences CMLS 63(2): 246-254.

Zhang, B., Pan, X. & Stellwag, E.J. 2008. Identification of soybean microRNAs and their targets. Planta 229(1): 161-182.

 

*Corresponding author; email: maniz@ukm.edu.my

 

 

 

 

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