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Characterization and 3D structure prediction of chitinase induced in sugarcane during pathogenesis of Colletotrichum falcatum

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Abstract

Chitinases are known to play an important role in many host-pathogen interactions. To reveal the defense associated role of chitinases in sugarcane during interaction with Colletotrichum falcatum causing red rot, detailed studies were conducted on the expression of chitinases in sugarcane cultivars varying in disease resistance, their characterization and theoretical 3D structure prediction through transcriptomic and bioinformatics tools. Partial mRNA sequences of chitinase corresponding to 782 bp were amplified from red rot resistant (Co 93009) and susceptible (CoC 671) cultivars. The relative expression of chitinase gene in both the cultivars by qRT-PCR showed a high level of expression only in the resistant cultivar. Consequently, the full length chitinase sequence ScChiB1 corresponding to 840 bp fragment was isolated from the red rot resistant cv Co 93009. Translated amino acid sequence of the full length sugarcane chitinase gene ScChiB1 from sugarcane cv Co 93009 revealed the typical characteristics of classes I/IV chitinase starting with a signal peptide and ending with a signature domain. Phylogenetic analysis grouped ScChiB1 in class IV, based upon major deletions in catalytic domain. Protein structure modeling (3D) using rice class I chitinase (2DKV) as a template also clearly revealed structural differences due to the presence of three deletions in the catalytic domains of sugarcane class IV chitinase. This concluded that the predicted structure of sugarcane chitinase ScChiB1 belongs to class IV of family 19 glycosyl hydrolases.

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Abbreviations

ScChiB:

Sugarcane chitinase B

ScChiB1:

840 bp full length chitinase B mRNA of red rot resistant cultivar Co 93009

C. falcatum :

Colletotrichum falcatum

cTP:

Chloroplast transit peptide

mTP:

Mitochondrial targeting peptide

SP:

Signal peptide

Loc:

Prediction of localization

S:

Secretory pathway

RC:

Reliability class

TPlen:

Predicted presequence length

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Acknowledgments

The authors are grateful to Dr. N. Vijayan Nair, Director of the institute for providing facilities and encouragement. The financial support received from the Department of Biotechnology, New Delhi and ICAR as Outreach grant under ALCOERA is gratefully acknowledged.

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Correspondence to R. Viswanathan.

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Rahul, P.R., Kumar, V.G., Sathyabhama, M. et al. Characterization and 3D structure prediction of chitinase induced in sugarcane during pathogenesis of Colletotrichum falcatum . J. Plant Biochem. Biotechnol. 24, 1–8 (2015). https://doi.org/10.1007/s13562-013-0226-6

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  • DOI: https://doi.org/10.1007/s13562-013-0226-6

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