In silico 3D-structure prediction of SsMYB2R: A novel MYB transcription factor from Saccharum spontaneum

• Published in: Indian journal of biotechnology Vol. 13; no. 4; pp. 437 - 447
• Main Authors: Kulkarni, Pranali A, Devarumath, Rachayya M
• Format: Journal Article
• Language: English
• Published: 2014
• Subjects: Amino acids; Cloning; Genes; Mathematical models; Plants (organisms); Proteins; Saccharum spontaneum; Stresses; Three dimensional
• ISSN: 0972-5849

Plant MYB (myeloblastosis) transcription factors play an important role in various biotic and abiotic defense responses. The plant R2R3 MYB proteins are predominantly involved in plant-specific regulatory processes. Saccharum spontaneum is a promising biomass crop because of its high fiber, polymorphism and adaptation to different environmental stresses. Efforts to cross S. spontaneum with sugarcane to introduce its desirable genes into modern cultivars showed minimum conclusive results. In the present study, we exemplify the isolation, cloning and in silico characterization of SsMYB2R gene isolated from S. spontaneum belonging to subfamily of R2R3-MYB transcription factor. The protein showed noteworthy alignments with a SANT/MYB DNA binding domain in members of MYB family proteins from dicotyledons and monocotyledons. The nucleotide sequence of the cloned SsMYB2R revealed a single open reading frame of 1,074 bp coding for 357 amino acids. To comprehend its sequence-to-structure-to-function paradigm, the putative 3D structure of SsMYB2R was generated using I-TASSER server. Further, PROCHECK, PROMOTIF and ProSA programs were used to appraise the stereo chemical quality of the model to conclude scores within the recommended intervals. The secondary and 3D structures thus provided better insight of active sites regarding protein-DNA interacting domains, which help abiding different environmental stress conditions by docking studies.