Original Article
Identification of stress-induced plant microRNAs and their targets from a true mangrove Rhizophora apiculata – an in silico approach
Year: 2020 | Month: June | Volume 8 | Issue 1
1.Allen, E., Xie, Z., Gustafson, A.M., Sung, G.H., Spatafora, J.W. and Carrington, J.C. 2004. Evolution of microRNA genes by inverted duplication of target gene sequences in Arabidopsis thaliana. Nat. Genet., 36(12), 1282-1290.
View at Google Scholar View at PUBMED2.Altschul, S.F., Gish, W., Miller, W., Myers, E.W. and Lipman, D.J. 1990. Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
View at Google Scholar View at PUBMED3.Asada, K. 1994. Production and action of active oxygen species in photosynthetic tissues. In: Foyer, C.H. and Mullineaux, P.M., editors. Causes of Photo Oxidative Stress and Amelioration of Defense Systems in Plants. CRC Press, Boca Raton. pp. 77-104.
View at Google Scholar4.Asaeda, T. and Barnuevo, A. 2019. Oxidative stress as an indicator of niche-width preference of mangrove Rhizophora stylosa. For. Ecol. Manag., 432, 73-82
View at Google Scholar5.Bartel, D.P. 2004. MicroRNAs: Genomics, biogenesis, mechanism, and function. Cell, 116, 281-297
View at Google Scholar View at PUBMED6.Catalanotto, C., Cogoni, C. and Zardo, G. 2016. MicroRNA in control of gene expression: An overview of nuclear functions. Int. J. Mol. Sci., 17, 1712.
View at Google Scholar View at PUBMED7.Costa, M.D.L., Reis, P.A.B., Valente, M.A.S., Irsigler, A.S.T., Carvalho, C.M., Loureiro, M.E., Aragão, F.J..L., Boston, R.S., Fietto, L.G. and Fontes, E.P.B. 2008. A new branch of endoplasmic reticulum stress signaling and the osmotic signal converge on plant-specific asparagine-rich proteins to promote cell death. J. Biol. Chem., 283, 20209-20219
View at Google Scholar View at PUBMED8.Dai, X. and Zhao, P.X. 2011. psRNATarget: A plant small RNA target analysis server. Nucleic Acids Res., 39, W155-W59.
View at Google Scholar View at PUBMED9.Das, S. 1999. An adaptive feature of some mangroves of Sundarbans, West Bengal. J. Plant Biol., 42, 109-16
View at Google Scholar10.Dasgupta, N., Hazra, A., Bhattacharya, S. and Das, S. 2017. In Silico screening of putative miRNAs and their targets from a common mangrove Bruguiera gymnorrhiza. Int. J. Cell Sci. Mol. Biol., 2, 1-18.
View at Google Scholar11.Dasgupta, N., Nandy, P. and Das, S. 2011. Photosynthesis and antioxidative enzyme activities in five Indian mangroves with respect to their adaptability. Acta Physiol. Plant. 33, 803-810
View at Google Scholar12.Dasgupta, N., Nandy, P., Tiwari, C. and Das, S. 2010. Salinityimposed changes of some isozymes and total leaf protein expression in five mangroves from two different habitats. J. Plant Interact., 5, 211-221.
View at Google Scholar13.Dasgupta, N., Sengupta, C. and Das, S. 2014. Role of secondary metabolites and radical scavenging aptitude for better adaptability of mangroves in varying salinity of Sundarbans, India. Ann. Trop. Res., 36, 1-21.
View at Google Scholar14.de Carvalho, F., Gheysen, G., Kushnir, S., Van Montagu, M., Inze,D. and Castresana, C. 1992. Suppression of beta-1, 3-glucanase transgene expression in homozygous plants. EMBO J., 11, 2595-2602
View at Google Scholar View at PUBMED15.Demiral, T. and Türkan, I. 2005. Comparative lipid peroxidation, antioxidant defense systems and proline content in roots of two rice cultivars differing in salt tolerance. Environ. Exp. Bot., 53, 247-257.
View at Google Scholar16.Ding, Y., Ding, L., Xia, Y., Wang, F. and Zhu, C. 2020. Emerging roles of microRNAs in plant heavy metal tolerance and homeostasis. J. Agric. Food Chem., 68: 1958-1965.
View at Google Scholar17.Dixon, M.S., Jones, D.A., Keddie, J.S., Thomas, C.M., Harrison, K. and Jones, J.D.G. 1996. The tomato Cf-2 disease resistance locus comprises two functional genes encoding leucine-rich repeat proteins. Cell, 84, 451-459.
View at Google Scholar View at PUBMED18.Durand, M., Porcheron, B., Hennion, N., Maurousset, L., Lemoine, R. and Pourtau, N. 2016. Water deficit enhances C export to the roots in Arabidopsis thaliana plants with contribution of sucrose transporters in both shoot and roots. Plant Physiol., 170, 1460-1479.
View at Google Scholar19.Fahlgren, N., Jogdeo, S., Kasschau, K.D., Sullivan, C.M., Chapman, E.J., Laubinger, S., Smith, L.M., Dasenko, M., Givan, S.A. and Weigel, D. 2010. MicroRNA gene evolution in Arabidopsis lyrata and Arabidopsis thaliana. Plant Cell, 22, 1074-1089.
View at Google Scholar20.Gong, S.M., Ding, Y.F. and Zhu, C. 2015. Role of miRNA in plant seed development. Yi Chuan, 37, 554-560
View at Google Scholar View at PUBMED21.Gu, Q., Chen, Z., Yu, X., Cui, W., Pan, J., Zhao, G., Xu, S., Wang, R. and Shen, W. 2017. Melatonin confers plant tolerance against cadmium stress via the decrease of cadmium accumulation and reestablishment of microRNA-mediated redox homeostasis. Plant Sci., 261, 28-37.
View at Google Scholar22.Hong, J.K., Choi, H.W., Hwang, I.S. and Hwang, B.K. 2007. Role of a novel pathogen-induced pepper C3-H-C4 type RING-finger protein gene, CaRFP1, in disease susceptibility and osmotic stress tolerance. Plant Mol. Biol., 63, 571-588
View at Google Scholar View at PUBMED23.Hossain, M.Z., Hossain, M.D. and Fujita, M. 2006. Induction of pumpkin glutathione S-transferases by different stresses and its possible mechanisms. Biol. Plant., 50, 210-218
View at Google Scholar24.Kumar, R., Mustafiz, A., Sahoo, K.K., Sharma, V., Samanta, S., Sopory, S.K., Pareek, A. and Singla-Pareek, S.L. 2012. Functional screening of cDNA library from a salt tolerant rice genotype pokkali identifies mannose-1-phosphate guanyl transferase gene (OsMPG1) as a key member of salinity stress response. Plant Mol. Biol., 79, 555-568
View at Google Scholar25.Kumar, S. and Trivedi, P.K. 2018. Glutathione S-transferases: Role in combating abiotic stresses including arsenic detoxification in plants. Front. Plant Sci., 9, 751.
View at Google Scholar26.Lau, N.C., Lim, L.P., Weinstein, E.G. and Bartel, D.P. 2001. An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science, 294, 858-862.
View at Google Scholar27.Lee, R.C., Feinbaum, R.L. and Ambros. V. 1993. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell, 75, 843-854.
View at Google Scholar28.Liu, H.H., Tian, X., Li, Y.J., Wu, C.A. and Zheng, C.C. 2008. Microarray-based analysis of stress-regulated microRNAs in Arabidopsis thaliana. RNA, 14, 836-843
View at Google Scholar29.Nandy, P., Das, S., Ghose, M. and Spooner-Hart, R. 2007. Effects of salinity on photosynthesis, leaf anatomy, ion accumulation and photosynthetic nitrogen use efficiency in five Indian mangroves. Wetl. Ecol. Manag., 15, 347-357
View at Google Scholar30.Noman, A. and Aqeel, M. 2017. miRNA-based heavy metal homeostasis and plant growth. Environ. Sci. Pollut. Res., 24, 10068-10082.
View at Google Scholar31.Parida, A.K., Das, A.B. and Mohanty, P. 2004. Investigations on the antioxidative defence responses to NaCl stress in a mangrove, Bruguiera parviflora: Differential regulations of isoforms of some antioxidative enzymes. Plant Growth Regul., 42, 213-226
View at Google Scholar32.Reinhart, B.J., Slack, F.J., Basson, M., Pasquinelli, A.E., Bettinger, J.C., Rougvie, A.E., Horvitz, H.R. and Ruvkun, G. 2000. The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature, 403, 901-906
View at Google Scholar33.Romano, N. and Macino, G. 1992. Quelling: Transient inactivation of gene expression in Neurospora crassa by transformation with homologous sequences. Mol. Microbiol., 6, 3343-3353
View at Google Scholar34.Schmieder, R. and Edwards, R. 2011. Quality control and preprocessing of metagenomic datasets. Bioinformatics, 27, 863-864
View at Google Scholar35.Singh, A., Gautam, V., Singh, S., Das, S.S., Verma, S., Mishra, V., Mukherjee, S. and Sarkar, A.K. 2018. Plant small RNAs: Advancement in the understanding of biogenesis and role in plant development. Planta, 248, 545-558
View at Google Scholar36.Sunkar, R., Li, Y.Sunkar, R., Li, Y.F. and Jagadeeswaran, G. 2012. Functions of microRNAs in plant stress responses. Trends Plant Sci., 17, 196-203.F. and Jagadeeswaran, G. 2012. Functions of microRNAs in plant stress responses. Trends Plant Sci., 17, 196-203.
View at Google Scholar37.Twigg, J., Fulton, N., Gomez, E., Irvine, D.S. and Aitken, R.J. 1998. Analysis of the impact of intracellular reactive oxygen species generation on the structural and functional integrity of human spermatozoa: Lipid peroxidation, DNA fragmentation and effectiveness of antioxidants. Hum. Reprod., 13, 1429-1436
View at Google Scholar38.Upadhyay, V.P., Ranjan, R. and Singh, J.S. 2002. Human-mangrove conflicts: The way out. Curr. Sci., 83, 1328-1336
View at Google Scholar39.Wightman, B., Ha, I. and Ruvkun, G. 1993. Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans. Cell, 75, 855-862.
View at Google Scholar40.Zhu, H., Chen, C., Zeng, J., Yun, Z., Liu, Y., Qu, H., Jiang, Y., Duan, X. and Xia, R. 2020. Micro RNA 528, a hub regulator modulating ROS homeostasis via targeting of a diverse set of genes encoding copper-containing proteins in monocots. New Phytol., 225, 385-399.
View at Google Scholar41.Zuker, M. 2003. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res., 31, 3406-3415
View at Google Scholar