Abstract
In the current study, a MYB (Myeloblastosis) Transcription Factor (TF) gene sequence (WsMYB46) has been retrieved from the transcriptome repertoire of the medicinal plant Withania somnifera and it has been structurally and functionally characterised using different bioinformatics tools. Amino acid sequence comparison of WsMYB46 and MYB TFs from 30 medicinal plants and the model plant Arabidopsis thaliana provided information about the conserved DNA binding domains of WsMYB46. The analysis suggests that WsMYB46 belongs to the R2R3 family of MYB TFs. The in silico prediction of the physicochemical properties of WsMYB46 and the MYB TFs show that they are localized in the nucleus, contain 312–438 amino acid residues, and are hydrophilic and acidic in nature, with a theoretical pI between 5.15 and 6.65. A 3-D model of the WsMYB46 protein has been constructed, and the functional annotation indicates that the WsMYB46 gene is involved in mRNA and cellular processing. The high degree of structural similarity of WsMYB46 with AtMYB46/AtMYB83, which are known to have important roles in the regulation of secondary cell wall biosynthesis, indicates the possible functional role of WsMYB46 in the regulation of secondary cell wall biosynthesis. The in silico gene expression analysis showed its low expression during salt stress. 427 miRNA sequences from A. thaliana were selected to identify the possible miRNA targets in WsMYB46. Six miRNAs with target sites in WsMYB46 were identified. This comprehensive in silico study of WsMYB46 and other MYB TFs from medicinal plants would be helpful to gain a deeper understanding of MYB TFs and their roles in medicinal plants.
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Data availability
WsMYB sequence is retrieved from the transcriptome datasets assembled by Tripathi and colleagues (Tripathi et al. 2017). The remaining sequences were retrieved from the BLASTP results of WsMYB46 (https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Proteins).
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Acknowledgements
ST is grateful to the Department of Biotechnology under Ministry of Science and Technology, Govt. of India for providing financial assistance through DBT-JRF Fellowship. ST is also grateful to Dr. Ashutosh K. Shukla for providing important suggestions for the improvement of the research work. The authors are thankful to Prof. Neelam Singh Sangwan for sharing the transcriptome datasets of Withania Somnifera, and the Director, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow for providing the facilities. This manuscript has the institutional communication number CIMAP/PUB/2023/152.
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The research was conducted by in house facilities of CSIR-Central Institute of Medicinal and Aromatic Plants (CIMAP), Lucknow, India. The student was provided financial assistance through fellowships provided by Department of Biotechnology (DBT) under Ministry of Science and Technology, Govt. of India.
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Thakur, S., Vasudev, P.G. In silico characterization of a MYB TF (WsMYB46) from the medicinal plant Withania somnifera L. predicting its probable role in secondary cell wall biosynthesis. Genet Resour Crop Evol (2024). https://doi.org/10.1007/s10722-024-01951-2
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DOI: https://doi.org/10.1007/s10722-024-01951-2