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OJBTM
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,
ABSTRACT
Prabhakaran S, Srividya V, Bharathi N, Jayakanthan M, Manikanda Boopathi N., Use of computational and structural Bioinformatic
strategies in controlling Fusarium wilt in cotton., Online J Bioinformatics, 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