Molecular cloning, expression and Insilco analysis of drought stress inducible MYB transcription factor encoding gene from C4 plant Eleusine coracana
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Abstract
Drought is one of the key abiotic stresses that critically influences the crops by restraining their growth and yield potential. Being sessile, plant tackle the detrimental effects of drought stress by modulating the cellular state by changing the gene expression. The transcriptional syndicate essentially drives such alteration of gene expression. Transcription factors (TF) are the key regulatory protein that controls the expression of their target gene by binding to the cis-regulatory elements present in the promoter region. Myb-TF, ubiquitously present in all eukaryotes belong to one of the largest TF family, and play a wide array of biological functions in plants, including anthocyanin biosynthesis, vasculature system, cell signalling, seed maturation and abiotc stress responses. The present performed isolation and molecular cloning of full length Myb TF from Eleusine corocana. The isolated full-length coding sequence has 1053 bp and 350 aa was submitted to NCBI (Accession number MT312253). The transcript level of EcMYB increases under different abiotic stress treatments including dehydration, salinity, and high-temperature stress. The promoter region of EcMyb1 was found to be enriched in stress-responsive cis-regulatory elements such as DRE, HSE, ABRE etc. In phylogenetic analysis, EcMyb1 appeared to have high homology with its monocot orthologs particularly Sateria italica, Hordeum vulgare, Saccharum barberi and Oryza sativa. The three-dimension protein structure was generated based on homology modeling and structural aspects were discussed. Further, Insilco analysis was conducted to explore the physiological properties, subcellular localization, potential posttranslational modification sites (phosphorylation and glycosylation sites), and molecular and biological function of the full-length protein. Overall, the expression profiling and Insilco analysis of EcMyb1 strongly indicated its potential role in abiotic stress response in Eleusine corocana.
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Keywords
Abiotic stress, cis-regulatory elements, finger millet , In- silico analysis, MYB-transcription factor, Transcriptional regulation
References
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Bailey TL (2011). DREME: motif discovery in transcription factor ChIP-seq data. Bioinformatics, 27(12),1653-1659. doi: 10.1093/bioinformatics/btr261.
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Banu SA, Huda KM, & Tuteja N. (2014). Isolation and functional characterization of the promoter of a DEAD-box helicase Psp68 using Agrpobacterium-mediated transient assay. Plant Signalling & amp: Behavior, 91, (1)8-9.doi: 10.4161/psb.28992.
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Gui J, Luo L, Zhong Y, Sun J, UmezawaT & Li L. (2019). Phosphorylation of LTF1, an MYB Transcription Factor in Populus, Acts as a Sensory Switch Regulating Lignin Biosynthesis in Wood Cells. Molecular Plant, 12, 1325–1337. DOI: 10.1016/j.molp.2019.05.008.
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Katiyar A, Smita S, Lenka SK, Rajwanshi R, Chinnusamy V & Bansal K. (2012). Genome-wide classification and expression analysis of MYB transcription factor families in rice and Arabidopsis. BMC genomics, 13(1), 544.
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Allan, AC, Hellens, RP & Laing, WA (2008).MYB transcription factors that colour our fruit. Trends in Plant Science, 13, 99–102. doi: 10.1016/j.tplants.2007.11.012.
Ambawat S, Sharma P, Yadav NR & Yadav RC (2013).MYB transcription factor genes as regulators for plant responses: an overview. Physiology and Molecular Biology of Plants, 19 ,3307-21.doi: 10.1007/s12298-013-0179-1.
Ardito F, Giuliani M, Perrone D, Troiano G& Muzio LL (2017). The crucial role of protein phosphorylation in cell signaling and its use as targeted therapy. International Journal of Molecular Medicine, 40, 271-280.doi: 10.3892/ijmm.2017.3036.
Bailey TL (2011). DREME: motif discovery in transcription factor ChIP-seq data. Bioinformatics, 27(12),1653-1659. doi: 10.1093/bioinformatics/btr261.
Baldoni, E., Genga, A. & Cominelli, E. (2015). Plant MYB transcription factors: their role in drought response mechanisms. International Journal of Molecular Sciences, 16(7),15811-15851.doi: 10.3390/ijms160715811.
Banu SA, Huda KM, & Tuteja N. (2014). Isolation and functional characterization of the promoter of a DEAD-box helicase Psp68 using Agrpobacterium-mediated transient assay. Plant Signalling & amp: Behavior, 91, (1)8-9.doi: 10.4161/psb.28992.
Benkert P, Biasini M & Schwede T. (2011). Toward the estimation of the absolute quality of individualprotein structure models. Bioinformatics., 27(3) , 343-350.DOI: 10.1093/bioinformatics/btq662.
Bhatt, M., Salvi, P.& Lohani, P. (2021). Gateway cloning and in-planta transformation of drought stress responsive Ecmyb1 gene isolated from Eleusine coracana var.PRM 6107. Environment Conservation Journal, 22(1&2), 205–211. https://doi.org/10.36953/ECJ.2021.221229.
Biedenkapp H, Borgmeyer U, Sippel AE & Klempnauer KH. (1988). Viralmyb oncogene encodes a sequence-specific DNA-binding activity. Nature, 335,835-837.doi: 10.1093/nar/29.17.3546.
BiłasR, Szafran K, Hnatuszko-Konka K &Kononowicz AK. (2016). Cis-regulatory elements used to control gene expression in plants. Plant Cell, Tissue and Organ Culture(PCTOC), 127, 2269-87.
Bjellqvist B, Hughes GJ, Pasquali C, Paquet N, Ravier F & Sanchez JC. (1993). The focusing positions of polypeptides in immobilized pH gradients can be predicted from their amino acid sequences. Electrophoresis, 14, 1023-1031.doi: 10.1002/elps.11501401163.
Burkle A & Uversky VN. (2013). Posttranslational Modification. Elsevier, 3,425-430.doi: 10.1021/pr060394e.
Chen VB, Arendall WB, Headd JJ, Keedy DA, Immormino RM, Kapral GJ, Murray LW, Richardson JS& Richardson DC. (2010). MolProbity: all-atom structure validation for macromolecular crystallography. ActaCrystallographica Section D: Biological Crystallography, 66(1), 12-21.doi: 10.1107/S0907444909042073.
Chinnusamy V, Schumaker K & Zhu JK. (2004). Molecular genetic perspectives on cross-talk and specificity in abiotic stress signalling in plants. Journal of Experimental Botany, 55, 225-236.https://doi.org/10.1093/jxb/erh005.
Chow C, Zheng H, Wu N, Chien C, Huang H., Tzong-Yi& Lee T. (2015). PlantPAN 2.0: an update of plant promoter analysis navigator for reconstructing transcriptional regulatory networks in plants. Nucl Acids Res, 44,1154–1160.doi: 10.1093/nar/gkv1035.
Deaton AM & Bird A. (2011). CpG islands and the regulation of transcription. Genes & Development, 25,101010-22.doi: 10.1101/gad.2037511.
Dubos C, Stracke R, Grotewold E, Weisshaar B, Martin C & Lepiniec L. (2010). MYBtranscription factors in ArabidopsisTrends in Plant. Science,15,10573-81.doi: 10.1016/j.tplants.2010.06.005.
Elango N &Soojin VY. (2011). Functional relevance of CpG island length for regulation of gene expression.Genetics, 187,4 1077-83. doi: 10.1534/genetics.110.126094.
Fernando, V.D. & Schroeder, D.F., 2016.Role of ABA in Arabidopsis salt, drought and desiccation tolerance.In Abiotic and biotic stress in plants-recent advances and future perspectives.IntechOpen, 507-524.
Finn RD, Coggill P, Eberhardt RY, Eddy SR., Mistry J& Mitchell AL. (2015). The Pfam protein families database: towards a more sustainable future. Nucleic Acids Res, 44, D279-D285.DOI: 10.1093/nar/gkv1344.
Geourjon C & Deleage G (1995) SOPMA: Significant improvements in proteinsecondary structure prediction by consensusprediction from multiple alignments. Oxford University Press 11, 681-684.doi: 10.1093/bioinformatics/11.6.681.
Gui J, Luo L, Zhong Y, Sun J, UmezawaT & Li L. (2019). Phosphorylation of LTF1, an MYB Transcription Factor in Populus, Acts as a Sensory Switch Regulating Lignin Biosynthesis in Wood Cells. Molecular Plant, 12, 1325–1337. DOI: 10.1016/j.molp.2019.05.008.
Gupta SM, Arora S, Mirza N, Pande A, Lata C, Puranik S, Kumar J & Kumar A. (2017). Finger Millet: A“Certain” Crop for an “Uncertain” Future and a Solution to Food Insecurity and Hidden Hunger under Stressful Environments. Frontiers in plant science, 8,643. https://doi.org/10.3389/fpls.2017.00643.
Higo K, Ugawa Y, Iwamoto M & KorenagaT.(1999). Plant cis-acting regulatory DNA elements (PLACE) database. Nucl Acids Res, 27,1297-300.doi: 10.1093/nar/27.1.297.
Hsiao, T.C., 1973. Plant responses to water stress. Annual Review of Plant Physiology. 24(1),519-570.
Jackson SP & Tjian R. (1988). O-glycosylation of eukaryotic transcription factors: Implications for mechanisms of transcriptional regulation. Cell, 55,125-133. doi: 10.1016/0092-8674(88)90015-3.
JadhavP, Salvi P, Bhatt M & Lohani P. (2018). Expression ofEcMYB Transcription Factor Gene Under Different Abiotic Stress Conditions in Eleusine coracana. International Journal of Agriculture,Environment and Biotechnology, 11,5 799-806.doi: 10.30954/0974-1712.10.2018.12.
Katiyar A, Smita S, Lenka SK, Rajwanshi R, Chinnusamy V & Bansal K. (2012). Genome-wide classification and expression analysis of MYB transcription factor families in rice and Arabidopsis. BMC genomics, 13(1), 544.
Kirchler T, Briesemeister S, Singer M, Schutze K, Keinath M, Kohlbacher O, Carbajosa JV, Teige M, Harter K & Chaban C. (2010). The role of phosphorylatable serine residues in the DNA-binding domain of Arabidopsis bZIP transcription factors. European Journal of Cell Biology, 89,175–183.doi: 10.1016/j.ejcb.2009.11.023.
Kreynes AE. (2018). Phosphorylation of MYB75 Transcription Factor by MAP Kinases in Arabidopsis thaliana. PhD Thesis. The University of British Columbia.
Kumar S, StecherG&Tamura K. (2016). MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular BiologyEvolution, 33,1870-1874.doi: 10.1093/molbev/msw054.
Kyte J, Russell F & Doolittle A. (1982). Simple Method for Displaying the Hydropathic Character of a Protein. Journal of Molecular Biology, 157, 105-132.doi: 10.1016/0022-2836(82)90515-0.
Laskowski RA, MacArthur MW, Moss DS & Thornton JM. (1993). PROCHECK: a program to check the stereochemical quality of protein structures. Journal of applied crystallography, 26(2), 283-291. https://doi.org/10.1107/S0021889892009944.
Les-cot M, Dhais P, Thijs G, Marchal K & Moreau Y.(2002). PlantCARE a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. NucleicAcids Res, 30,1325-327.doi: 10.1093/nar/30.1.325.
Liang, YK., Dubos, C., Dodd, IC., Holroyd, GH., Hetherington, AM. & Campbell, MM. (2005). AtMYB61, an R2R3-MYB transcription factor controlling stomatal aperture in Arabidopsis thaliana. Current Biology, 15(13),1201-1206. doi: 10.1016/j.cub.2005.06.041.
Lippold F, Sanchez DH, Musialak M, Schlereth A, Scheible WR, Hincha DK & Udvardi MK. (2009). AtMyb41 regulates transcriptional and metabolic responses to osmotic stress in Arabidopsis. Plant Physiol, 149,1761-72. doi: 10.1104/pp.108.134874.
Mehrotra S, Goel S, Raina SN & Rajpal VR. (2014). Significance of satellite DNA revealed by conservation of a widespread repeat DNA sequence among angiosperms. Applied Biochemistry and Biotechnology, 173, 71790-801.doi: 10.1007/s12010-014-0966-3.
Ogata K, Kanei-Ishii C, Sasaki M, Hatanaka H, Nagadoi A, EnariM,Nakamura H, Nishimura Y, Ishii S & Sarai A. (1996). The cavity in the hydrophobic core of Myb DNA binding domain is reserved for DNA recognition and transactivation. Nat StructBiol, 3,178-818.doi: 10.1038/nsb0296-178.
Oh, J.E., Kwon, Y., Kim, J.H., Noh, H., Hong, S.W. & Lee, H. (2011). A dual role for MYB60 in stomatal regulation and root growth of Arabidopsis thaliana under drought stress. Plant Molecular Biology, 77(1-2),91-103. doi: 10.1007/s11103-011-9796-7.
Peters CWB, Sippel AE Vingron & Klempnauer (1987). MKHDrosophila and vertebrate myb proteins share two conserved regions, one of which functions as a DNA-binding domain. EMBO J, 6, 3085-3090.doi: 10.1002/j.1460-2075.1987.tb02616.x.
Pramanik K, Kundu S, Banerjee S, Ghosh PK & Maiti TK. (2018). Computational-based structural, functional and phylogenetic analysis of Enterobacterphytases. 3 Biotech, 8(6), 262.doi: 10.1007/s13205-018-1287-y.
Richard, V., Brendolise, EC.&Chagné D., 2009. Multiple Repeats of a Promoter Segment Causes Transcription Factor Autoregulation in Red Apples.The Plant Cell, 2(1),168-183.
Salvi,P , Arora A & Lohani P. (2012). Expression of MYB Transcription Factor in Eleusinecoracana: towards making of drought tolerant plants.LAP Lambert Academic Publishing USA.
Sanchita, Blessy BM & Sharma A. (2013). In silico analysis of putative transcription factor binding sites in differentially expressed genes: Study of the turnover of TFBSs under salt stress responsiveness in solanaceae family. Plant Omics Journal, 6,4278-285.
Schroeder JI, KwakJM & Allen GJ. (2001). Guard cell abscisic acid signalling and engineering drought hardiness in plants.Nature, 410, 6826327. doi: 10.1038/35066500.
Segarra G, Vander Ent. S, Trillas I & Pieterse CMJ (2009). MYB72, a node of convergence in induced systemic resistance triggered by a fungal and a bacterial beneficial Microbe. Plant Biol, 11,90-6. doi: 10.1111/j.1438-8677.2008.00162.x.
Shingote, P.R., Kawar, P.G., Pagariya, M.C., Rathod, P.R. & Kharte, S.B (2017). Ectopic Expression of SsMYB18, a Novel MYB Transcription Factor from Saccharum spontaneum Augments Salt and Cold Tolerance in Tobacco. Sugar Tech, 19(3), 270-282.
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How to Cite
Molecular cloning, expression and Insilco analysis of drought stress inducible MYB transcription factor encoding gene from C4 plant Eleusine coracana. (2023). Journal of Applied and Natural Science, 15(4), 1407-1420. https://doi.org/10.31018/jans.v15i4.4891
