In silico analysis and gene expression patterns of lignin peroxidase isozymes in Phanerochaete chrysosporium

Phanerochaete chrysosporium (Pc), is a prominent lignin-degrading fungus which serves as an important source for lignin-degrading enzymes (LDEs). The present study was focused on a detailed in silico analysis and gene expression patterns of lignin peroxidases (PcLiPs), which is a significant class of LDEs. In spite of extensive research on P. chrysosporium enzymes, the number of PcLiP isozymes remains unexplored. In the present study, ten PcLiP sequences were identified by the RedoXiBase and BLAST survey, displaying putative glycosylated extracellular protein which was approximately 38 to 39 kDa. Different domains of the protein included putative binding sites for stress, nutrient components, metal ions, peroxidase motifs, ligninase motifs, and also secretory signal peptides. Molecular docking analysis of all the PcLiPs, showed that the PcLiP4 had strong binding affinity towards hydrogen peroxide (H₂O₂), manganese (II) sulfate (MnSO₄), and veratryl alcohol (VA) as compared to other PcLiPs. In order to analyze the PcLiPs gene expression, the fungus was incubated in potato dextrose broth medium (PDB). Notably, high expression levels of PcLiPs were observed during the 48-h growth stage of the fungus and there was variable gene expression under conditions of incubation with different stress factors and co-factors, such as H₂O₂, MnSO₄, VA, and heat stress. Among the ten PcLiPs characterized, isozymes, such as, PcLiP4, PcLiP9, PcLiP10, and PcLiP8 exhibited varying concentrations of nutritional elements and stress levels together with high expression. Present study employing in silico analysis, molecular docking studies, and gene expression analysis demonstrated that the PcLiP4 could be an ideal candidate for lignin biodegradation. Results showed the operation of specific regulatory mechanisms which govern PcLiPs expression. As an outcome, regulatory factors towards obtaining high yield of PcLiPs and the best isozyme for heterologous gene expression were identified. These findings would contribute to enhancing the efficiency of biodegradation of lignocelluloses and related recalcitrant waste products.