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Molecular Cloning and Expression Analysis of MYB-Related Transcription Factor Gene, ScMYB76 from Sugarcane (Saccharum Hybrid)
Background/Objectives: In grass family, sugarcane has been gaining importance due to its role in sugar and biofuel production. We previously reported MYB Transcription Factor (TF) family of genes that regulates almost all biological, physical and biochemical functions in sugarcane. Thus, the present study aimed to characterize an MYB-related Transcription Factor (TF) gene, of ScMYB76 from sugarcane and its expression during water-deficit and salt stress induced condition. Methods: ScMYB76 gene specific primers were designed and used to isolate by PCR from sugarcane leaf tissue. The isolated gene was cloned and sequenced for sequence-structure analysis using various computational tools. To analyze the sequence-to-structure-to-function paradigm, comparative modeling, docking and validation were performed using I-TASSER, TFmodeller and 3D footprint platforms, respectively. The expression pattern during the induced stress condition was analyzed by quantitative RT-PCR. Findings: A cDNA encloding a putative MYB-related TF, ScMYB76 was cloned from sugarcane leaves and consisted of 636 bp Open Reading Frame (ORF) which encodes 212 amino acid length protein with the calculated molecular mass of 23.49 KDa and a pI of 10.2. The deduced ScMYB76 protein was predicted to consist of a single helix-turn-helix MYB-like motif and other residues which are highly conserved among other MYB-related TFs. Comparative modeling and docking of ScMYB76 with MYBCORE cis-motif was generated and evaluated by structure quality assessment parameters. Analysis of expression pattern of ScMYB76 indicates an important function of this gene during abiotic stress in sugarcane. Applications/Improvements: The isolated and analyzed TF gene, ScMYB76 from sugarcane will add a valuable gene resource for crop improvement in regard to abiotic stress.
Docking, Expression, MYB-Related, Stress, Sugarcane, Transcription Factor.
- Hotta CT, et al. The biotechnology roadmap for sugarcane improvement. Tropical Plant Biology. 2010; 3(2):75–87.
- Osakabe Y, Osakabe K, Shinozaki K, Tran LP. Response of plants to water stress. Front Plant Sci. 2014; 5:86.
- Wang H, Wang H, Shao H, Tang X. Recent advances in utilizing transcription factors to improve plant abiotic stress tolerance by transgenic technology. Plant Sci. 2016; 7:67.
- Roy S. Function of MYB domain transcription factors in abiotic stress and epigenetic control of stress response in plant genome, Plant Signal Behav. 2016; 11(1):23.
- Riechmann JL, Ratcliffe OJ. A genomic perspective on plant transcription factors. Current Opinion in Plant Biology. 2000; 3(5):423–34.
- Cheng L, Li X, Huang X, Ma T, Liang Y, Ma X, Peng X, Jia J, Chen S, Chen Y, Deng B, Liu G. Over expression of sheepgrass R1-MYB transcription factor LcMYB1 confers salt tolerance in transgenic Arabidopsis. Plant Physiol Biochem. 2013; 70:252–60.
- Baldoni E, Genga A, Cominell E. Plant MYB transcription factors: Their role in drought response mechanisms. Int J Mol Sci. 2016; 16(7):15811–51.
- Geethalakshmi S, Barathkumar S, Prabu GR. The MYB transcription factor family genes in sugarcane (Saccharum sp). Plant Molecular Biology Reporter. 2015; 33(3):512–31.
- Roy A, Kucukural A, Zhang Y. ITASSER: A unified platform for automated protein structure and function prediction. Nat Protocol. 2010; 5(4):725–38.
- Laskowski RA, MacArthur MW, Moss DS, Thornton JM. PROCHECK: A program to check the stereochemical quality of protein structures. Journal of Applied Crystallography. 1993; 26:283–91.
- Eisenberg D, Lüthy R, Bowie JU. VERIFY3D: Assessment of protein models with three-dimensional profiles. Methods Enzymol. 1997; 277:396–404.
- Wiederstein M, Sippl MJ. ProSA-web: Interactive web service for the recognition of errors in three dimensional structures of proteins. Nucleic Acids Res. 2007; 35:407–10.
- Moreira BC, Branger PA, Vides JC. TFmodeller: Comparative modelling of protein–DNA complexes. Bioinformatics. 2007; 23(13):1694–96.
- Bower MJ, Cohen FE, Dunbrack RL. Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: A homology modeling tool. Journal of Molecular Biology. 1997; 267(5):1268–82.
- Moreira BC. 3D-footprint: A database for the structural analysis of protein–DNA complexes. Nucleic Acids Res. 2010; 38:91–7.
- Morozov AV, Siggia ED. Connecting protein structure with predictions of regulatory sites. Proc Natl Acad Sci USA. 2007; 104(17):7068–73.
- Mahony S, Benos PV. STAMP: A web tool for exploring DNA-binding motif similarities. Nucleic Acids Res. 2007; 35:253–8.
- Stracke R, Werber M, Weisshaar B. The R2R3-MYB gene family in Arabidopsis thaliana. Current Opin Plant Biol. 2001; 4(5):447–56.
- Du H, Feng BR, Yang SS, Huang YB, Tang YX. The R2R3-MYB transcription factor gene family in maize. PLoS One. 2012; 7(6):63.
- Myrset AH, Bostad A, Jamin N, Lirsac PN, Toma F, Gabrielsen OS. DNA and redox state induced conformational changes in the DNA-binding domain of the Myb oncoprotein. EMBO J. 1993; 12(12):4625–33.
- Ogata K, Hojo H, Aimoto S, Nakai T, Nakamura H, Sarai A, Ishii S, Nishimura Y. Solution structure of a DNA-binding unit of Myb: A helix-turn-helix-related motif with conserved tryptophans forming a hydrophobic core. Proc Natl Acad Sci USA. 1992; 89(14):6428–32.
- Murzin AG, Brenner SE, Hubbard T, Chothia C. SCOP: A structural classification of proteins database for the investigation of sequences and structures. J Mol Biol. 1995; 247(4):536–40.
- Finn RD, Tate J, Mistry J, Coggill PC, Sammut SJ, Hotz HR, Ceric G, Forslund K, Eddy SR, Sonnhammer ELL, Bateman A. The Pfam protein families database. Nucleic Acids Res. 2008; 36:281–8.
- Angarica VE, Pérez AG, Vasconcelos AT, Collado-Vides J, Contreras-Moreira B. Prediction of TF target sites based on atomistic models of protein-DNA complexes. BMC Bioinform. 2008; 9:436.
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