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Isolation, characterization and expression analysis of stress responsive plant nuclear transcriptional factor subunit (NF-YB2) from commercial Saccharum hybrid and wild relative Erianthus arundinaceus

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Abstract

Plant nuclear factor (NF-Y) is a transcription activating factor, consisting of three subunits, and plays a key regulatory role in many stress-responsive mechanisms including drought and salinity stresses. NF-Ys function both as complex and individual subunits. Considering the importance of sugarcane as a commercial crop with high socio-economic importance and the crop being affected mostly by water deficit stress and salinity stress causing significant yield loss, nuclear transcriptional factor NF-YB2 was focused in this study. Plant nuclear factor subunit B2 from Erianthus arundinaceus (EaNF-YB2), a wild relative of sugarcane which is known for its drought and salinity stress tolerance, and commercial Saccharum hybrid Co 86032 (ShNF-YB2) was isolated and characterized. Both EaNF-YB2 and ShNF-YB2 genes are 543 bp long that encodes for a polypeptide of 180 amino acid residues. Comparison of EaNF-YB2 and ShNF-YB2 gene sequences revealed nucleotide substitutions at nine positions corresponding to three synonymous and six nonsynonymous amino acid substitutions that resulted in variations in physiochemical properties. However, multiple sequence alignment (MSA) of NF-YB2 proteins showed conservation of functionally important amino acid residues. In silico analysis revealed NF-YB2 to be a hydrophilic and intracellular protein, and EaNF-YB2 is thermally more stable than that of ShNF-YB2. Phylogenetic analysis suggested the lower rate of evolution of NF-YB2. Subcellular localization in sugarcane callus revealed NF-YB2 localization at nucleus that further evidenced it to be a transcription activation factor. Comparative RT-qPCR experiments showed a significantly higher level of NF-YB2 expression in E. arundinaceus when compared to that in the commercial Saccharum hybrid Co 86032 under drought and salinity stresses. Hence, EaNF-YB2 could be an ideal candidate gene, and its overexpression in sugarcane through genetic engineering approach might enhance tolerance to drought and salinity stresses.

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All relevant data are within the paper and its supporting information files.

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Acknowledgements

The authors would like to thank the Department of Biotechnology (Grant No. 102/IFD/SAN/1151/2017-2018), New Delhi, Government of India for funding support. We thank the Director, Centre for Plant Molecular Biology and Bioinformatics (CPMB&B) and the Head, Department of Bioinformatics, Tamil Nadu Agricultural University (TNAU), Coimbatore for extending Bioinformatics facility.

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  1. Division of Crop Improvement, ICAR Sugarcane Breeding Institute, Tamil Nadu, Coimbatore, 641007, India

    Swathik Clarancia Peter, Naveenarani Murugan, Manoj Vadakkancherry Mohanan, Sarath Padmanabhan Thelakat Sasikumar, Dharshini Selvarajan, Ashwin Narayan Jayanarayanan, Mahadevaiah Chennappa, Valarmathi Ramanathan, Hemaprabha Govindakurup, Bakshi Ram & Appunu Chinnaswamy

  2. Division of Crop Production, ICAR Sugarcane Breeding Institute, Tamil Nadu, Coimbatore, 641007, India

    Suresha G. Shivalingamurthy

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  1. Swathik Clarancia Peter
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Contributions

SCP: conceptualization, design, methodology, performed the experiments and manuscript drafting. NM: vector construction. MVM, realtime PCR; SPTS, DS, ANJ, MC, VR: writing-review and editing. SGS: localization experiment. HG, BR: review and editing of the manuscript. AC: conceptualization, designed, performed the experiments, supervision, review and editing of the manuscript. All authors read and approved the final manuscript.

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Correspondence to Appunu Chinnaswamy.

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Peter, S.C., Murugan, N., Mohanan, M.V. et al. Isolation, characterization and expression analysis of stress responsive plant nuclear transcriptional factor subunit (NF-YB2) from commercial Saccharum hybrid and wild relative Erianthus arundinaceus. 3 Biotech 10, 304 (2020). https://doi.org/10.1007/s13205-020-02295-1

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