GSE119714
Regulatory mechanisms of brown rot genes for responding to environmental carbon signals in Postia placenta
Brown rot fungi evolved the unique strategy to efficiently decay wood structures and selectively extract carbohydrates, and this involved the sophistical regulation of functional genes (Zhang et al., PNAS, 2016, 113: 10968-). However, the regulatory mechanisms of brown rot genes were not well known, impeding the implication and application of brown rot machinery in biomass conversions. In this work, we systematically studied the roles of environmental carbon signals (e.g., aspen, cellobiose, glucose and no-carbon) in regulating gene expression in model brown rot fungus Postia placenta by RNA-seq. We found the complex substrate aspen (Populus sp.), but not the commonly recognized disaccharide cellobiose, was the universal inducer for Carbohydrate Active Enzymes (CAZYs) expression. Even though, cellobiose clearly induced the expression of cellulase (GH5 and GH12, endoglucanase) and xylanase (GH10, endoxylanase) (cellobiose vs. no-carbon, fold change > 4), as we reported previously (Zhang and Schilling, FGB, 2017, 106: 1-). When response to easy to use carbons, P. placenta lost the CCR effect on the main-chain cleaving CAZYs expression, but kept this repressing effect on side-chain cleaving CAZYs and AAs, which indicated a clear adaption relative to that in saprotrophic ascomycete ancestors. This “loss of CCR effect” was independent of the glucose concentrations. To explore the distinctive brown rot regulatory machinery, the gene modules subjected to inducing or CCR effects were then used to predict the regulatory motifs and transcriptional factors to build the regulatory network in P. placenta. Together, these findings will facilitate us to understand the adaptions of regulatory elements in brown rot fungi, as well as the efficient brown rot strategy. Overall design: We sequenced mRNA from 24 samples, including treatments of four carbon souces (e.g., no carbon, glucose, cellobiose and aspen) mutiply two time points (e.g., 15 h and 72 h), to compare the gene regulations in response to variable carbon sources. Three bioreplicates were included for each treatment.