Transcriptome study of Talaromyces verruculosus TS63-9 for pectin-degrading CAZymes

ABSTRACT Pectins are a primary structural component of plant cell walls. In a previous study, we isolated a fungal strain, Talaromyces verruculosus TS63-9, which exhibited a high pectinase activity (142.43 U/mL) in a large-scale screening and sequenced its genome (GCA_001305275.1). Here, we further sequenced its transcriptome to study the transcriptional changes of TS63-9 in response to pectin treatment. A total of 1,435 genes were differentially expressed, with 757 upregulated and 678 downregulated. Among the differentially expressed genes, 47 were identified as encoding carbohydrate-active enzymes (CAZymes) for pectin degradation, including 39 upregulated and 8 downregulated genes. Notably, 18 upregulated CAZyme genes (including nine genes from GH28, and the rest from AA7, CE8, CE12, GH35, GH43, GH54, GH78, and PL1 families) contained a signal peptide, suggesting their potential secretion for extracellular pectin degradation. TS63-9 also possesses intracellular pectin catabolic genes (IPCGs) to encode enzymes for the further breakdown of pectin-derived monosaccharides, with 37 genes upregulated by pectins. Key pathways for D-galacturonic acid, L-rhamnose, and D-galactonate are strongly activated, alongside glycolysis and TCA cycle genes. This transcriptional activation demonstrates efficient carbon flux from pectin-derived monosaccharides into the central metabolism. Additionally, the promoters of 15 pectin-degrading CAZyme genes and 11 IPCGs contained a conserved pectin-responsive motif. Furthermore, the heterologous expression of a putative endo-polygalacturonase (endo-PG) gene in Pichia pastoris verified its function for pectin degradation. Our study provides the first insight into the transcriptional basis for the high pectinase activity of T. verruculosus . IMPORTANCE Fungi are primary degraders of plant biomass in various environments by encoding and secreting numerous CAZymes. We previously isolated the fungus Talaromyces verruculosus TS63-9 from tobacco leaves with a high pectinolytic activity and sequenced its genome. In this study, we further sequenced its transcriptomes to identify and characterize pectin-degrading CAZymes. The extracellular pectinolytic CAZymes and the putative pectin-responsive motif identified from TS63-9 have great potential to be harnessed for sustainable bioenergy production and for enhancing various aspects of the agricultural industry.