Genome-wide identification, in-silico characterization, and expression analysis of polygalacturonases in different...

Polygalacturonases (PGs) are key enzymes that hydrolyze pectin, a complex polysaccharide in plant cell walls, with essential roles in biological processes and industrial applications. This study presents a comprehensive genome-wide identification and in-silico characterization of PGs from four fungal species: Aspergillus oryzae, Aspergillus flavus, Neurospora crassa, and Rhizoctonia solani. A total of 44 PG protein sequences were retrieved from the NCBI database, confirming the presence of the Glyco_hydro_28 (GH28) domain, which is essential for pectin hydrolysis. Phylogenetic analysis using the Neighbor-Joining method revealed four major clades (A, B, C, D), with A. flavus and A. oryzae sharing a close evolutionary relationship (bootstrap support = 93%). Gene structure analysis revealed that A. flavus (Af1) and A. oryzae (Ao1) each have one exon, while Neurospora crassa (NSc1) contains one intron. Ten conserved motifs were identified, with Motif 1 present in Rz1, Rz2, and Rz5, and Motif 2 in all sequences except Ao15 and Ao16. Chromosomal mapping indicated species-specific gene distributions, with A. oryzae showing genes spread across five chromosomes. Gene expression analysis of A. oryzae under various growth conditions revealed 20 differentially expressed genes (DEGs), including 10 upregulated (e.g., Gene_Ao1, LFC = 2.50, FDR = 0.00450) and 10 downregulated (e.g., Gene_AO9, LFC = -2.87, FDR = 1.1e-05). Pathway enrichment analysis highlighted significant involvement of PGs in apoptosis (FDR = 1.2e0^-03), cell cycle regulation (FDR = 9.7e^-03), and DNA repair (FDR = 2.3e^-02). Protein-protein interaction (PPI) network analysis revealed 41 nodes and 400 edges, with an average node degree of 19.5. Structural modeling of the expressed protein LOCUS (XP_Ao1820953) with PDB ID: 5ZU2 showed high stability and flexibility, supported by molecular dynamics simulations. These results provide new insights into the evolutionary, structural, and functional roles of fungal PGs, with implications for their applications in biofuel production, food processing, and fiber retting.