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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., 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
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