Characterization of Seaweed Polysaccharide-Degrading Enzymes Using In Silico Analysis towards Application of Marine Macroalgal Biomass in Biorefinery

Seaweed polysaccharides and their hydrolyzed products deliver an increasingly important role in the field of medicine, cosmetics, functional foods, and agriculture due to biological activities. For effective utilization of seaweeds, the biomass has to be processed using physical, chemical, or biological methods. Enzymes that degrade these polysaccharides find application in the bioconversion of macroalgae or seaweeds into biofuels and biochemicals. In this study, in silico characterization of seaweed polysaccharide-degrading enzymes such as carrageenase, agarase, laminarinase, and fucoidanase was carried out. A total of 7 sequences of carrageenase, 10 sequences of agarase, 6 sequences of laminarinase and 4 sequences of fucoidanase produced by different microorganisms were retrieved from the Protein Data Bank and subjected to in silico analysis. Multiple sequence alignment and phylogenetic analysis were performed using the Clustal Omega and MEGA 11 software. Motif analysis of these seaweed polysaccharide-degrading enzymes were carried out using the MEME server. The biochemical parameters of these enzymes were analyzed using Protparam. Multiple sequence alignment showed that the sequences of carrageenase, agarase, laminarinase, and fucoidanase had conserved regions. The biochemical parameters such as the number of amino acids, pI values, aliphatic index, instability index, and GRAVY values were compared for each enzyme sequence. Phylogenetic analysis showed their homology. The active site for the different reported polysaccharide-degrading enzymes was predicted using the CASTp web server. This study will help to analyze the polysaccharide-depolymerizing enzymes concerning enzyme engineering for improved catalytic functions and stability that may find application in bioconversion and biorefinery.