Research Article | Volume: 4, Issue: 6, Nov-Dec, 2016

Identification and profiling of high temperature responsive miRNAs in French bean (Phaseolus vulgaris L)

M. N. Jyothi S. Usha B. Suchithra N. Sharadamma D. V. Rai V. R. Devaraj R. Nagesh Babu   

Open Access   

Published:  Nov 05, 2016

DOI: 10.7324/JABB.2016.40607

MicroRNAs (miRNAs) are group of small, non-coding RNAs that play important roles in plant growth, development and stress response. There have been an increasing number of investigations aimed at discovering miRNAs and analyzing their functions in model plants. In this study, we constructed high temperature stress induced small RNA libraries and characterized 26 potential miRNAs belonging to 21 families in French bean. A total of 140 annotated potential targets were found, of which majority were transcription factors (MYB, bHLH, GRF1, bZIP, NAC etc.,) which may play an important role in stress resistance. RT-qPCR and Northern blot analysis revealed differential expressions of candidate miRNAs and their target genes. The observed induction of miRNA expression is correlated with the down regulation of their targets. Investigation of gene ontology linked with targets of miRNAs forecasted their involvement in various biological functions. We anticipate the further studies may offer new avenues in developing stress tolerant variety of French bean.

Keyword:     miRNA MYB quantitative PCR Transcription factors


Jyothi MN, Usha S, Suchithra B, Sharadamma N, Rai DV, Devaraj VR, Nagesh babu R. Identification and profiling of high temperature responsive miRNAs in French bean (Phaseolus vulgaris L). J App Biol Biotech. 2016; 4 (06): 038-058. DOI: 10.7324/JABB.2016.40607

Copyright: Author(s). This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial-ShareAlike license.

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1. Hasanuzzaman M, Nahar K, Alam MM, Roychowdhury R, Fujita M. Physiological, biochemical, and molecular mechanisms of heat stress tolerance in plants. Int J Mol Sci 2013; 14:9643-84.

2. Sunkar R, Zhu J. Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. Plant Cell 2004; 16:2001-2019.

3. Khraiwesh B, Zhua JK, Zhuc J. Role of miRNAs and siRNAs in biotic and abiotic stress responses of plants. Biochemica et Biophysica Acta 2012; 1819:137-148.

4. Kruszka K, Pieczynski M, Windels D, Bielewicz D, Jarmolowski A, Szweykowska-Kulinska Z, Vazquez F. Role of microRNAs and other sRNAs of plants in their changing environments. Journal of Plant Physiology 2012; 169:1664-1672.

5. Ruiz-Ferrer V, Voinnet O. Roles of plant small RNAs in biotic stress responses. Annual Review of Plant Biology 2009; 60:485-510.

6. Katiyar-Agarwal S, Jin H. Role of small RNAs in host-microbe interactions. Annual Review of Phytopathology 2010; 48:225-246.

7. Lv DK, Bai X, Li Y, Ding XD, Ge Y, Cai H, Ji W, Wu N, Zhu YM. Profiling of cold-stress-responsive miRNAs in rice by microarrays. Gene 2010; 459:39-47.

8. Jian X, Zhang L, Li G, Zhang L, Wang X, Cao X, Fang X, Chen F. Identification of novel stress regulated microRNAs from Oryza sativa L. Genomics 2010; 95:47-55.

9. Bartels D, Sunkar R. Drought and salt tolerance in plants. Critical Reviews in Plant Sciences 2005; 24:23-58.

10. Xin M, Wang Y, Yao Y, Xie C, Peng H, Ni Z, Sun Q. Diverse set of microRNAs are responsive to powdery mildew infection and heat stress in wheat (Triticum aestivum L.). BMC Plant Biology 2010; 10:123-36.

11. Yu X, Wang H, Lu Y, de Ruiter M, Cariaso M, Prins M, van Tunen A, He Y. Identification of conserved and novel microRNAs that are responsive to heat stress in Brassica rapa. J Exp Bot 2012; 63:1025-38.

12. Kruszka K, Pacak A, Swida-Barteczka A, Nuc P, Alaba S, Wroblewska Z, Karlowski W, Jarmolowski A, Szweykowska-Kulinska Z. Transcriptionally and post-transcriptionally regulated microRNAs in heat stress response in barley. J Exp Bot 2014; 65:6123-6135.

13. Arenas-Huertero CB, Rabanal F, Blanco-Melo D, De la Rosa C, Estrada-Navarrete G, Sanchez F, Covarrubias AA, Reyes JL. Conserved and novel miRNAs in the legume Phaseolus vulgaris in response to stress. Plant Mol Biol 2009; 70:385-401.

14. Valdes-Lopez O, Yang SS, Aparicio-Fabre R, Graham PH, Reyes JL, Vance CP, Hernandez G. MicroRNA expression profile in common bean (Phaseolus vulgaris) under nutrient deficiency stresses and manganese toxicity. New Phytol 2010; 187:805-818.

15. Pelaez P, Trejo MS, Iniguez LP, Estrada-Navarrete G, Covarrubias AA, Reyes JL, Sanchez F. Identification and characterization of microRNAs in Phaseolus vulgaris by high-throughput sequencing. BMC Genomics 2012; 13:83.

16. Nagesh babu R, Jyothi MN, Sharadamma N, Rai DV, Devaraj VR. Expression of miRNAs regulates growth and development of French bean (Phaseolus vulgaris) under Salt and Drought Stress conditions. Int. Res. J. Biol Sci 2013; 2:1-6.

17. Nagesh babu R, Jyothi MN, Usha, Sharadamma N, Rai DV, Devaraj VR. Identification of miRNAs from French bean (Phaseolus vulgaris) under low nitrate stress. Turkish Journal of Biochemistry 2014; 39:1-8.

18. Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 2003; 31:3406-3415.

19. 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. Criteria for annotation of plant microRNAs. Plant Cell 2008; 20:3186-3190.

20. Tagami Y, Inaba N, Kutsuna N, Kurihara Y, Watanabe Y. Specific enrichment of miRNAs in Arabidopsis thaliana infected with Tobacco mosaic virus. DNA Res 2007; 14:227-233.

21. Liang G, He H, Yu D. Identification of nitrogen starvation-responsive microRNAs in Arabidopsis thaliana. PLoS One 2012; 7:1-11.

22. Mishra NS, Vikash Kumar, Sopory SK, Mukherjee SK. Cloning and validation of novel miRNA from basmati rice indicates cross talk between abiotic and biotic stresses. Mol Genet Genomics 2009; 282:463-474.

23. Moxon S, Jing R, Szittya G, Schwach F, Rusholme-Pilcher RL, Moulton V, Dalmay T. Deep sequencing of tomato short RNAs identifies microRNAs targeting genes involved in fruit ripening. Genome Res 2008; 18:1602-1609.

24. Zhang N, Yang J, Wang Z, Wen Y, Wang J, He W, Liu B, Si H, Wang D. Identification of novel and conserved microRNAs related to drought stress in Potato by deep sequencing. PLoSOne 2014; 18:1-9.

25. Trindade I, Capitao C, Dalmay T, Fevereiro MP, Santos DM. miR398 and miR408 are up-regulated in response to water deficit in Medicago truncatula. Planta 2010; 231:705-716.

26. Jagadeeswaran G, Zheng Y, Li YF, Shukla LI, Matts J, Hoyt P, Macmil SL, Wiley GB, Roe BA, Zhang W, Sunkar R. Cloning and characterization of small RNAs from Medicago truncatula reveals four novel legume-specific microRNA families. New Phytol 2009; 184:85-98.

27. Khan-Barozai MY, Irfan M, Yousaf R, Ali I, Qaisar U, Maqbool A, Zahoor M, Rashid B, Hussnain T, Riazuddin S. Identification of micro-RNAs in cotton. Plant Physiol Biochem 2008; 46:739- 751.

28. Kumar RR, Pathak H, Sharma SK, Kala YK, Nirjal MK, Singh GP, Goswami S, Rai RD. Novel and conserved heat-responsive microRNAs in wheat (Triticum aestivum L.). Funct Integr Genomics 2014; 10:1-26.

29. Guan Q, Lu X, Zeng H, Zhang Y, Zhu J. Heat stress induction of miR398 triggers a regulatory loop that is critical for thermo-tolerance in Arabidopsis. Plant J 2013; 74:840-51.

30. Mittal D, Madhyastha DA, Grover A. Genome-wide transcriptional profiles during temperature and oxidative stress reveal coordinated expression patterns and overlapping regulons in Rice. PLoS ONE 2012; 7:1-15.

31. Li MY, Wang F, Xu ZS, Jiang Q, Ma J, Tan GF, Xiong AS. High throughput sequencing of two celery varieties small RNAs identifies microRNAs involved in temperature stress response. BMC Genomics 2014; 15:242.

32. Debernardi JM, Rodriguez RE, Mecchia MA, Palatnik JF. Functional Specialization of the Plant miR396 Regulatory Network through Distinct MicroRNA-Target Interactions. PLoS Genet 2012; 8:1-14.

33. Pashkovskiy PP, Ryazansky SS. Biogenesis, Evolution, and Functions of Plant microRNAs. Biochemistry (Moscow) 2013; 78:627-637.

34. Xiong H, Li J, Liu P, Duan J, Zhao Y, Guo X, Li Y, Zhang H, Ali J, Li Z. Over expression of OsMYB48-1, a novel MYB-related transcription factor enhances drought and salinity tolerance in Rice. PLoS ONE 2014; 9:1-13.

35. Yatusevich R, Mugford SG, Matthewman C, Gigolashvili T, Frerigmann H, Delaney S, Koprivova A, Flugge UI, Kopriva S. Genes of primary sulfate assimilation are part of the glucosinolate biosynthetic network in Arabidopsis thaliana. Plant J 2010; 62:1-11.

36. Lu X, Guan Q, Zhu J. Down-regulation of CSD2 by a heat-inducible miR398 is required for thermo-tolerance in Arabidopsis. Plant Signaling & Behavior 2013; 8:1-3.

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