Genome-wide Identification and Comparative Analysis of polygalacturonases in different fungal species

Abstract

Pectinases, an enzyme family with many varied uses, which also include polygalacturonases having major industrial applications. These enzymes are employed in the textile sector for bioscoring cotton, the food industry for softening of fruits , in degumming of plant rough fiber and wastewater treatment. Polygalacturonases catalyze the breakdown of glycosidic linkages between two non-esterified galacturonic acid units. There were diverse sources of polygalacturonases however the potential of better catalyzing ability of fungal polygalacturonases were not explored. Therefore, the goal of the current work was to use bioinformatics tools and techniques to discover the fungal strains that have greater catalytic activity. A total of 4 different fungal species were considered for this research including A. oryzae, A. flavus, N. crassa and R. solani. The isolates mentioned were known to produce polygalacturonase. All proteins (44 sequences) shared the GH28 domain. Phylogenetic study confirmed the evolutionary relationship between A. flavus and A. oryzae. Later, chromosomal mapping of 44 sequences were done and these protein sequences were distributed on chromosome number 1, 2, 3, 4, 6, 7, 8, 9, 10, 11, 13 and 16. Subcellular localization predicted the extracellular nature of the enzyme. The Robetta server identified the four best enzyme models of polygalacturonase. The gene structure display server indicates the presence of only one exon in Af1 and Ao1 and one intron in NSc1. Five motifs were conserved in all the sequences predicted by motif analysis. The gene ontology analysis was performed to provide information about molecular cellular and biological functions of these proteins. Molecular functions indicated the major role of polygalacturonase in hydrolase activity. Biological functions indicated their key role in cell wall organization .Gene expression analysis of polygalacturonase revealed that only one gene of N. crassa downregulated under provided growth condition. The downregulation of gene indicated the inability of polygalacturonase to break pectin due to the xviii absence of transcriptional factor pdr1. Hence the gene expression analysis reveals the mechanism of action of polygalacturonase and mechanisms action of transcriptional factor pdr1. To verify the enzyme activity assay, a laboratory evaluation of one of the identified fungus species A.flavus was also optimized for polygalacturonase production