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

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.IMPORTANCEFungi 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.