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Online Journal of Bioinformatics


Volume 10 (2):180-190, 2009.

Use of computational and structural bioinformatic strategies in controlling Fusarium wilt in cotton.


Prabhakaran S, Srividya V, Bharathi N, Jayakanthan M, Manikanda Boopathi N.


Department of Plant Molecular Biology and Biotechnology, CPMB, Tamil Nadu Agricultural University, Coimbatore 641003, India




Prabhakaran S, Srividya V, Bharathi N, Jayakanthan M, Manikanda Boopathi N., Use of computational and structural Bioinformatic strategies in controlling Fusarium wilt in cotton., Onl J Bioinform., 10 (2):180-190, 2009. It has been reported that cotton fiber production has declined during the last few decades due to biotic factors, such as Fusarium wilt. Genetic improvement of cotton against Fusarium wilt using conventional breeding approaches has met with limited success due to several reasons including lack of knowledge on the mechanism of wilt resistance. Recent breakthroughs in computational and structural bioinformatics offer solutions to unravel the mechanism of wilt resistance. It has been shown that aquaporin, a transmembrane protein in host cell, was severely affected by the infection of Fusarium oxysporum f. sp. vasinfectum (Fov). Further, several pathogenecity proteins were characterized such as Fusarium oxysporum G-protein β subunit (Fgb1), α subunit (Fga1) and F-box protein required for pathogenecity (Frp1). However, it is not known which one of these proteins initially affect aquaporin. Results of modeling and docking described herein using Discovery Studio and Auto Dock have shown that Fgb1 is the pathogenic protein that interacts most efficiently with aquaporin. Hence, if binding of Fgb1 was limited, disintegration of aquaporin due to Fusarium infection may be avoided.  Identification of a protein or ligand which binds more efficiently with Fgb1 than that of aquaporin may help to design strategies to avoid Fusarium wilt in cotton and thus cotton production could be improved. Docking of two natural antifungal proteins NaD1 (Nicotiana alata Defensin) and MIC-3 (Meloidogyne Induced Cotton protein) and seven different artificial antifungal compounds have shown that NaD1 binds well with Fgb1 when compared with other proteins. Hence, we propose that transgenic cotton with NaD1 gene may have resistance to Fusarium wilt.


Keywords: Bioinformatics, Fusarium, cotton