Fermentation medium optimization, molecular modelling and docking analysis of the alginate lyase of a novel Pseudomonas sp. LB56 isolated from seaweed waste

Abstract

Alginate lyase has the potential for the ecofriendly depolymerization of alginate and generation of value-added products important in agriculture, bioenergy, food processing, medical diagnostic and pharmaceutical industries. Substantial research has focused on the cost-effective production of alginate lyase via screening of potent microbial isolates for use as biocatalysts and the optimization of fermentation media with low-cost feedstocks. This study evaluated the alginate lyase-producing efficacy of a novel Pseudomonas sp. LB56 (GenBank accession no. MT176182) isolated from Sargassum seaweed waste. The feedstock for solid-state fermentation (SSF) was decomposed Sargassum biomass amended with cow dung. The production of alginate lyase was maximal using 9.5 g Sargassum, 14 g cow dung and at pH 8 after optimization via a 23–factorial central composite design. Comparative modelling and molecular docking studies were conducted to elucidate the 3D structure of the alginate lyase of this novel isolate, as well as to investigate its catalytic interactions with different polymeric sizes of alginate [polymannuronate (mannuronate disaccharide and mannuronate trisaccharide), polyguluronate (guluronate disaccharide and guluronate trisaccharide) and alginate]. The overall results suggest that biowaste (Sargassum seaweed amended with cow dung) can be used as a feedstock for economical production of alginate lyase. Additionally, the identified active site residues of alginate lyase, which were shared by different polymers of alginate, can be tailored via rational and/or combinatorial approaches for efficient biotransformation of alginate-enriched wastes into biologically active alginate oligomers and third generation biofuels.