Computational Analysis of Alginate Lyases Produced by Different Microorganisms
Keywords:Alginate Lyase, Multiple Sequence Alignment, Phylogenetic Analysis, Motif, Homology Modeling, CASTp
Alginates are considered as the major structural material present in the cell-wall of brown seaweeds and are produced by bacterial species like Azotobacter and Pseudomonas. Alginate lyase depolymerizes alginate into alginate oligosaccharides. Alginate lyase (AL) can be classified into two groups such as G block and M block-specific lyase as well as endolytic and exolytic enzymes based on their substrate specificities and mode of action respectively. Oligosaccharides derived from alginate have innumerable biological activities including immune regulation, anticoagulation, anti-oxidant, anti-cancer and health-promoting activities. In the present study, in silico characterization of the different reported alginate lyases was performed. A total of 50 protein sequences of alginate lyase produced by different microorganisms were retrieved from UniProt database and characterized. Multiple sequence alignment was executed using Clustal Omega. ProtParam tool was used to evaluate physicochemical parameters analyses. Phylogenetic tree was constructed by Neighbor-Joining method using MEGA-X. Motif analysis of alginate lyase sequences was carried out by MEME server. 45 structures of alginate lyase were modelled using SWISSMODEL. Multiple sequence alignment validates that sequences are highly variable among various alginate lyases reported in different species. Alginate lyase from different species possesses different molecular weights with amino acid residues ranging from 320 to 1059. The pI ranged between 4.42 and 9.59. The variation within these alginate lyases along with other physicochemical parameters was also examined. The active site for the different reported alginate lyases were predicted through CASTp server.