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

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.