Weighted Gene Co-expression Network Analysis Identifies Critical Genes for the Production of Cellulase and Xylanase in Penicillium oxalicum

Abstract

Genes involved in cellular processes undergo environment-dependent co-regulation, but the co-expression patterns of fungal cellulase and xylanase-encoding genes remain unclear. Here, we identified two novel carbon sources, methylcellulose and 2-hydroxyethyl cellulose, which efficiently induced the secretion of cellulases and xylanases in Penicillium oxalicum. Comparative transcriptomic analyses identified carbon source-specific transcriptional patterns, mainly including major cellulase and xylanase-encoding genes, genes involved in glycolysis/gluconeogenesis and the tricarboxylic acid cycle, and genes encoding transcription factors, transporters and G protein-coupled receptors. Moreover, the weighted correlation network analysis of time-course transcriptomes, generated 17 highly connected modules. Module MEivory, comprising 120 members, included major cellulase and xylanase-encoding genes, genes encoding the key regulators PoxClrB and PoxXlnR, and a cellodextrin transporter POX06051/CdtC, which were tightly correlated with the filter-paper cellulase, carboxymethylcellulase and xylanase activities in P. oxalicum. An expression kinetic analysis indicated that members in MEivory were activated integrally by carbon sources, but their expressional levels were carbon source-and/or induction duration-dependent. Three uncharacterized regulatory genes in MEivory were identified, which regulate the production of cellulases and xylanases in P. oxalicum. These findings provide insights into the mechanisms associated with the synthesis and secretion of fungal cellulases and xylanases, and a guide for P. oxalicum application in biotechnology.

Network Analysis Reveals Different Cellulose Degradation Strategies acrossTrichoderma harzianumStrains Associated with XYR1 and CRE1

“…Recently, WGCNA was used to explore the molecular mechanisms underlying biomass degradation by Penicillium oxalicum [25]. In addition, in a large-scale proteomics study, WGCNA was applied to investigate and compare the enzymatic responses of the filamentous fungi Aspergillus terreus , T. reesei , Myceliophthora thermophila , N. crassa , and Phanerochaete chrysosporium grown in several carbon sources [24].…”

“…Such applications are possible because transcripts sharing the same function or involved in the same regulatory pathway tend to present similar expression profiles and, hence, form modules in the network (Wolfe et al, 2005). In fungi, such methodology has been successfully used to provide insight into the regulatory mechanisms of hydrolysis (Borin et al, 2018;Arntzen et al, 2020;Li et al, 2020a).…”

“…To date, only a few studies have employed WGCNA method in studies on Trichoderma spp. [23] and on other filamentous fungi [24, 25].…”

PoxCbh, a novel CENPB‐type HTH domain protein, regulates cellulase and xylanase gene expression in Penicillium oxalicum

“…Eight were previously confirmed to be involved in cellulase and/or xylanase production in P . oxalicum : POX00331/FlbC (Yao et al 2016), POX01118 (Li et al 2020), POX01960 / ClrB (Zhao et al. 2016), POX02484 , POX01184 , POX04420 / CxrB (Yan et al.…”

“…Most proteins encoded by these 31 putative TF genes contained zinc finger domains (Zn2Cys6-, C2H2-, DHHC-, and NF-X1-type) and winged helix repressor DNA-binding domains (Table S1). Eight were previously confirmed to be involved in cellulase and/or xylanase production in P. oxalicum: POX00331/FlbC (Yao et al 2016), POX01118 (Li et al 2020), POX01960/ClrB (Zhao et al 2016), POX02484, POX01184, POX04420/CxrB (Yan et al 2017), POX08292/MBF1 (Zhao et al 2019), and POX07254/CreA (Li et al 2015). Additionally, three genes, POX01183, POX02944, and POX05436, were unrelated to filter paper cellulase production in P. oxalicum (Yan et al 2017).…”