In silico analysis of the germinlike protein multigene family members of tomato with predicted oxalate oxidase activity

Germins and germin like proteins (GLPs) have been reported as plant glycoproteins belonging to the ‘cupin’ superfamily. They have been documented to possess enzymatic activities leading to the generation of H₂O₂, a reactive oxygen species (ROS). Hence, members of the GLP family have been proposed to play major role in plant disease resistance through ROS-mediated signaling. Interestingly, the functional characterization of GLP(s) in terms of their suitability as a key player in plant disease resistance has remained under-explored in case of tomato (Solanumlycopersicum L.). In the present study, 15 tomato GLPs, predicted to have oxalate oxidase activity, have been investigated in silico. Deduced multiple amino acid sequence alignment-based clustering of these proteins was carried out to classify them into 3 sub-families. All the proteins were found to contain the conserved amino acid stretches, representing the BoxA, B and C, and an inter-motif region of variable length. It was observed through homology modeling and structural alignment that the active sites of all except 3 of these proteins have Mn²⁺ bound at the active site involving the three conserved histidine and one conserved glutamate residue(s). The active site architecture was analyzed with a comparative view in order to examine the metal binding capacity of tomato GLPs. Thus the present work makes a platform for further genetic, molecular biological and functional genomics studies in the field of tomato GLPs, the possible key players for conferring biotic and/or abiotic stress tolerance, in future.

In tomato, 15 genes encoding germin like proteins (GLPs) with predicted oxalate oxidase activity were found to be distributed in 5 different chromosomes.

The 15 tomato GLPs were found to have structural distinctness with a basic conserved ‘jelly roll’ structure.

Three out of the 15 proteins were predicted not to bind Mn²⁺.

The distinct active site architecture of the tomato GLPs might explain the differential Mn²⁺ binding.