Molecular Cloning and Structural Insights into Pectin Lyase Proteins from Different Strains of Fusarium

Abstract

Aim: Molecular cloning and analysis of Pectin Iyase (PNL) genes from different strains of Fusarium for structural predictions and docking studies. Background: PNLs cleave pectin by β-elimination resulting in the formation of 4,5-unsaturated oligogalacturonates, without affecting the ester content of the polymer chain and hence maintaining the specific aroma of fruits. Several PNL lyase genes from Aspergillus and Penicillium have been cloned, but the molecular biology of that from Fusarium has not been explored. Objective: To obtain an insight into the three-dimensional structure of PNL of Fusarium. Methods: PCR amplification-based molecular cloning of PNL genes from Fusarium strains, sequencing, and sequence analysis using bioinformatics tools for homology search, multiple sequence alignment, motif search, physiochemical characterization, phylogenetic tree construction, 3D structure prediction, and molecular docking were conducted. Results: Five PNL genes were cloned from F. oxysporum MTCC1755, F. monoliforme var. subglutinans MTCC2015, F. avenaceum MTCC10572, and F. solani MTCC3004 using the PCR approach. Many conserved amino acids were found at several positions in all the PNL proteins. Phylogenetic analysis of these proteins with other pectinases revealed two major clusters representing members of lyases and hydrolases. In-silico characterization revealed stable PNL proteins. PNL proteins from different Fusarium strains were similar in structural features and biochemical properties owing to their similar primary sequence. Docking studies revealed that electrostatic forces and van der Waal and hydrogen bonds effectuate the interaction between the ligand and the enzyme. Aspartate, tyrosine, and tryptophan residues in the active site of the enzyme are responsible for ligand binding. Conclusion: PNL from different Fusarium species show similarity at structural as well as biochemical level. PNL protein from F. moniliforme and F. solani was similar in properties except for the variation of single amino acid. Docking studies on the enzyme and different ligands provided an insight into the interacting residues and forces as well as the suitability of the substrate for catalysis.