“IN-SILICO CHARACTERIZATION OF PECTATE LYASE GENE FAMILY AND FUNCTIONAL ANALYSIS OF SLPL ASSOCIATED WITH FRUIT SOFTENING IN TOMATO”

Abstract

Pectate lyases (PLs) are cell-wall-modifying enzymes that contribute to pectin disassembly and fruit softening. However, the evolutionary relationships and functional characteristics of the tomato PL gene family remain incompletely resolved. The present study performed an integrated in silico analysis of 22 tomato PL proteins, with particular emphasis on Solyc03g111690 (SlPL), a ripening-associated gene previously implicated in fruit firmness and shelf life. Phylogenetic reconstruction revealed distinct evolutionary clusters and strongly supported paralogous relationships within tomato, while comparative analysis with Arabidopsis thaliana, strawberry and banana indicated conserved evolutionary relationships among plant PLs. Sequence and physicochemical characterization, conserved-domain and motif analyses, and three-dimensional structural modelling supported the classification of SlPL as a pectate lyase. The predicted protein structure exhibited a β-helix-rich architecture with localized flexible regions, consistent with features of this enzyme family. Computational profiling revealed developmental and tissue-dependent expression patterns, including increased SlPL transcript abundance during fruit maturation and ripening. Additionally, the protein association analysis indicated relationships between SlPL and other proteins involved in cell-wall modification, and SlPL could be part of a network of cell wall-modifying proteins. Taken together, these findings support Solyc03g111690 as a candidate gene involved in pectin remodeling during tomato fruit ripening and softening, providing a computational framework for its further functional validation and genome-engineering applications.