Unravelling cadmium induced noncoding RNAS and their validations from finger millet
Автор: Suresh Kumar C., Nagesh Babu R., Shafia Hoor F.
Журнал: Журнал стресс-физиологии и биохимии @jspb
Статья в выпуске: 3 т.19, 2023 года.
Бесплатный доступ
MicroRNAs (miRNAs) play important roles in plant responses to abiotic stress. Numerous studies have been increasing in respect to miRNA identification under stress conditions. In this study we analysed the expression patterns of seven miRNAs (miR156, 159, 169, 396, 397, 398 and 399) from cadmium stressed seedlings of Finger millet by RT-qPCR. Further these miRNAs were cloned and sequenced, which conformed its presence. Predicted targets and GO analysis of the miRNAs were found to be involved in diverse cellular processes in plants, development, apoptosis, detoxification, catalysis, protein modification. Cis-regulatory elements identification suggested their involvement in regulatory networks. This is the first study to demonstrate differentially expressed miRNA in Finger millet under cadmium stress. Findings in the present study prominence the role played by miRNAs in Finger millet under cadmium stress.
Cis-regulatory element, go analysis, nb-arc domain, rt-qpcr
Короткий адрес: https://sciup.org/143180564
IDR: 143180564
Список литературы Unravelling cadmium induced noncoding RNAS and their validations from finger millet
- Barrera-Figueroa BE, Gao L, Wu Z, Zhou X, Zhu J, Jin H, Liu R, Zhu JK (2012) High throughput sequencing reveals novel and abiotic stressregulated microRNAs in the inflorescences of rice. BMC Plant Biol 12:132
- Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116(2): 281-297
- Bonnet E, Wuyts J, Rouze P Van de Peer Y (2004) Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences. Bioinformatics 20:29112917
- Dai X, Zhao PX (2011) psRNATarget: a plant small RNA target analysis Server. Nucleic Acids Res 39: W155-W159
- Ding Y, Chen Z, Zhu C (2011) Microarray-based analysis of cadmium-responsive microRNAs in rice (Oryza sativa). J Exp Bot 62: 3563-3573
- Ding YF, Zhu C (2009) The role of microRNAs in copper and cadmium homeostasis. Biochem Biophys Res Commun 386: 6-10
- Fang X, Zhao Y, Ma Q, Huang Y, Wang P, Zhang J, Nian H, Yang C (2013) Identification and Comparative Analysis of Cadmium Tolerance-Associated miRNAs and Their Targets in Two Soybean Genotypes. PLoS ONE 8(12): e81471
- Gielen H, Remans T, Vangronsveld J, Cuypers A (2012) MicroRNAs in metal stress: specific roles or secondary responses. Int J Mol Sci 13: 1582615847
- Hossain MA, Hasanuzzaman M, Fujita M (2010) Up-regulation of antioxidant and glyoxalase systems by exogenous glycine betaine and proline in mung bean confer tolerance to cadmium stress. Physiol Mol Biol Plants 16(3): 259-272
- Huang SQ, Xiang AL, Che LL, Chen S, Li H, Song JB, Yang ZM (2010) A set of miRNAs from Brassica napus in response to sulphate deficiency and cadmium stress. Plant Biotechnol Journal 8: 887899
- Lee Y, Jeon K, Lee JT, Kim S, Kim VN (2002) MicroRNA maturation: stepwise processing and subcellular localization. EMBO Journal 21: 4663-4670
- Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real time quantitative PCR and the 2-ÄACT method. Methods 25: 402-408
- Lu S, Li L, Yi X, Joshi CP, Chiang VL (2008a) Differential expression of three eucalyptus secondary cell wall-related cellulose synthase genes in response to tension stress. J Exp Bot 59: 681-695
- Lu S, Sun YH, Shi R, Clark C, Li L, Chiang VL (2005) Novel and mechanical stress-responsive MicroRNAs in Populus trichocarpa that are absent from Arabidopsis. Plant Cell 17: 2186-2203
- Macovei A, Tuteja N (2012) microRNAs targeting DEAD-box helicases are involved in salinity stress response in rice (Oryza sativa L.). BMC Plant Biol 12: 183
- McLaughlin MJ, Parker DR, Clarke JM (1999) Metals and micronutrients- food safety issues. Field Crop Res 60: 143-163
- Meyers BC, Axtell MJ, Bartel B, Bartel DP, Baulcombe D, Bowman JL, Cao X, Carrington JC, Chen X, Green PJ, Griffiths S, Jacobsen SE, Mallory AC, Martienssen RA, Poethig RS, Qi Y, Vaucheret H, Voinnet O, Watanabe Y, Weigel D, Zhu JK (2008) Criteria for annotation of plant microRNAs. Plant Cell 20: 3186-3190
- Mousavi SA, Chauvin A, Pascaud F, Kellenberger S, Farmer EE (2013) GLUTAMATE RECEPTOR-LIKE genes mediate leaf-to-leaf wound signalling. Nature 500: 422-426
- Pinto AP, Mota AM, de Varennes A, Pinto FC (2004) Influence of organic matter on the uptake of cadmium, zinc, copper and iron by sorghum plants. Sci Total Environ 326: 239-247
- Qiu D, Xiao J, Ding X, Xiong M, Cai M, Cao Y, Li X, Xu C, Wang S (2007) OsWRKY13 mediates rice disease resistance by regulating defense-related genes in salicylate- and jasmonate-dependent signalling. Mol Plant Microbe Interact 20(5): 492-9
- Rajagopalan R, Vaucheret H, Trejo J, Bartel DP (2006) A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. Genes 20(24): 3407-3425
- Rascio N, Navari-Izzo F (2011) Heavy metal hyperaccumulating plants: how and why do they do it? And what makes them so interesting? Plant Science 180(2): 169-181
- Sunkar R, Chinnusamy V, Zhu J, Zhu JK (2007) Small RNAs as bi players in plant abiotic stress responses and nutrient deprivation. Trends Plant Science 12: 301-309
- Sunkar R, Kapoor A, Zhu JK (2006) Posttranscriptional induction of two Cu/Zn superoxide dismutase genes in Arabidopsis is mediated by down regulation of miR398 and important for oxidative stress tolerance. Plant Cell 18: 2051-2065
- Tang M, Mao D, Xu L, Li D, Song S, Chen C (2014) Integrated analysis of miRNA and mRNA expression profiles in response to Cd exposure in rice seedlings. BMC Genomics 15(1): 835
- Taylor P, Frazier, Guiling Sun, Caitlin E, Burklew, Baohong Zhang (2011) Salt and Drought Stresses Induce the Aberrant Expression of microRNA Genes in Tobacco. Molecular Biotechnology 49 (2): 159-165
- Villiers F, Ducruix C, Hugouvieux V, Jarno N, Ezan E, Garin J, Junot C, Bourguignon J (2011) Investigating the plant response to cadmium exposure by proteomic and metabolomic approaches. Proteomics 11: 1650-1663
- Wang TZ, Chen L, Zhao MG, Tian QY, Zhang WH (2011) Identification of drought-responsive micro-RNAs in Medicago truncatula by genome-wide high-throughput sequencing. BMC Genomics 12: 367
- Weber H, Bernhardt A, Dieterle M, Hano P, Mutlu A, Estelle M, Genschik P, Hellmann H (2005) Arabidopsis AtCUL3a and AtCUL3b Form Complexes with Members of the BTB/POZ-MATH Protein Family. Plant Physiology 137(1): 83-93
- Liang Xu, Yan Wang, Lulu Zhai, Yuanyuan Xu, Liangju Wang, Xianwen Zhu, Yiqin Gong, Rugang Yu, Cecilia Limera, Liwang Liu (2013) Genome-wide identification and characterization of cadmium-responsive microRNAs and their target genes in radish (Raphanus sativus L.) roots. Journal of Experimental Botany 64(14): 4271-4287
- Yingchun Xu, Lingling Chu, Qijiang Jin, Yanjie Wang, Xian Chen, Hui Zhao, Zeyun Xue (2015) Transcriptome-Wide Identification of miRNAs and
- Their Targets from Typha angustifolia by RNA-Seq and their Response to Cadmium Stress. PLoS ONE 10(4): e0125462 Yadav SK (2010) Heavy metals toxicity in plants: An overview on the role of glutathione and phytochelatins in heavy metal stress tolerance of plants. S Afr J Bot 76: 167-179
- Yamaguchi A, Wu MF, Yang L, Wu G, Poethig RS, Wagner D (2009) The MicroRNA-Regulated SBP-Box Transcription Factor SPL3 Is a Direct Upstream Activator of LEAFY, FRUITFULL, and APETALA1. Developmental Cell 17(2): 268-278
- Yamasaki H, Abdel-Ghany SE, Cohu CM, Kobayashi Y, Shikanai T, Pilon M (2007) Regulation of copper homeostasis by micro-RNA in Arabidopsis. J Biol Chem 282: 16369-16378
- Yanfei Ding, Zhen Chen, Cheng Zhu (2011) Microarray-based analysis of cadmium-responsive microRNAs in rice (Oryza sativa). J. Exp. Bot 1-12
- Yao YY, Guo GG, Ni ZF, Sunkar R, Du JK, Zhu JK, Sun QX (2007) Cloning and characterization of microRNAs from wheat (Triticum aestivum L.). Genome Biol 8(6): R96
- Ye, J., Fang, L., Zheng, H., Zhang, Y., Chen, J., Zhang, Z., Wang, J., Li, S., Li, R., Bolund, L., & Wang, J. (2006). WEGO: a web tool for plotting GO annotations. Nucleic acids research, 34(Web Server issue), W293-W297.
- Zeng QY, Yang CY, Ma QB, Li XP, Dong WW, Nian H (2012) Identification of wild soybean miRNAs and their target genes responsive to aluminum stress. BMC Plant Biol 12: 182 Zhang L, Wong MH (2007) Environmental mercury contamination in China: sources and impacts. Environ Int 33: 108-121
- Zhao JP, Jiang XL, Zhang BY, Su XH (2012) Involvement of microRNA-mediated gene expression regulation in the pathological development of stem canker disease in Populus trichocarpa. PLoS ONE 7:e44968
- Zhao Sheng Zhou, Jian Bo Song, Zhi Min Yang (2012) Genome-wide identification of Brassica napus microRNAs and their targets in response to cadmium. Journal of Experimental Botany 63(12): 4597-4613
- Zuker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31: 3406-3415
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