Localizing gene regulation reveals a staggered wood decay mechanism for the brown rot fungus Postia placenta

Abstract

Wood-degrading brown rot fungi are essential recyclers of plant biomass in forest ecosystems. Their efficient cellulolytic systems, which have potential biotechnological applications, apparently depend on a combination of two mechanisms: lignocellulose oxidation (LOX) by reactive oxygen species (ROS) and polysaccharide hydrolysis by a limited set of glycoside hydrolases (GHs). Given that ROS are strongly oxidizing and nonselective, these two steps are likely segregated. A common hypothesis has been that brown rot fungi use a concentration gradient of chelated metal ions to confine ROS generation inside wood cell walls before enzymes can infiltrate. We examined an alternative: that LOX components involved in ROS production are differentially expressed by brown rot fungi ahead of GH components. We used spatial mapping to resolve a temporal sequence in Postia placenta, sectioning thin wood wafers colonized directionally. Among sections, we measured gene expression by whole-transcriptome shotgun sequencing (RNA-seq) and assayed relevant enzyme activities. We found a marked pattern of LOX up-regulation in a narrow (5-mm, 48-h) zone at the hyphal front, which included many genes likely involved in ROS generation. Up-regulation of GH5 endoglucanases and many other GHs clearly occurred later, behind the hyphal front, with the notable exceptions of two likely expansins and a GH28 pectinase. Our results support a staggered mechanism for brown rot that is controlled by differential expression rather than microenvironmental gradients. This mechanism likely results in an oxidative pretreatment of lignocellulose, possibly facilitated by expansin-and pectinase-assisted cell wall swelling, before cellulases and hemicellulases are deployed for polysaccharide depolymerization.B rown rot wood-degrading fungi release sequestered carbon from lignocellulose in forests (1) and have the unique ability to accomplish this without significantly removing the recalcitrant lignin that encases the structural polysaccharides. Accordingly, their decay mechanisms may provide a model for new biomass conversion technologies that not only function despite the presence of lignin but also yield lignin as a potentially useful coproduct (1-3). Deviating from their white rot ancestors, brown rot fungi have evolved mechanisms that are generally faster (4, 5) and more polysaccharide-specific because they circumvent lignin (4,(6)(7)(8). This enhanced efficiency is coupled with losses, not expansions, of key white rot genes, including many linked to lignin degradation and processive cellulose hydrolysis. For example, few brown rot fungi produce the cellobiohydrolases that are included in commercial synergistic glycoside hydrolase (GH) mixtures (9-12). These observations imply that brown rot fungi harbor novel pathways to improve saccharification yields.To explain why brown rot fungi are so efficient, despite their minimal toolkit of biodegradative enzymes, low-molecular-weight (LMW) oxidative agents have been proposed to operate in tandem with the enzymes. ...

Fenton reaction facilitates organic nitrogen acquisition by an ectomycorrhizal fungus

“…First, ˙ OH oxidation of proteins may render the proteins more susceptible to proteolytic degradation. Increased proteolysis following metal‐catalyzed radical oxidation of proteins has been demonstrated for a wide range of proteolytic enzymes and proteins (Zhang et al ., ). In the current study, aspartic protease activity was appreciably higher once BSA had been oxidized by ˙ OH (BSA growth medium) than when BSA was less oxidized (BSA–low Fe; Fig.…”

Moisture in modified wood and its relevance for fungal decay

“…However, as cell wall pores, even in the water-saturated state, are too small for enzymes to enter (Srebotnik et al 1988, Daniel et al 1989, 1990, 2004, fungi break up cell walls by oxidative action (Cragg et al 2015). While fungi classified as white-rot fungi rely on enzymes for this task (Vaaje-Kolstad et al 2010, Hori et al 2013, Riley et al 2014, another class of fungi termed brown-rot fungi have evolved a non-enzymatic strategy based on Fenton chemistry to disrupt cell walls in the initial stage of attack (Goodell et al 1997, Xu & Goodell 2001, Halliwell 2003, Arantes & Milagres 2007, Hastrup et al 2013, Schilling et al 2013, Ringman et al 2014a, Zhang et al 2016. It is speculated that through transportation of chelated iron ions into wood cell walls and reaction of these with hydrogen peroxide, brown-rot fungi create highly reactive free radicals which disrupt chemical bonds of the cell wall constituents.…”

Transcriptome Sequencing and Comparative Analysis of Piptoporus betulinus in Response to Birch Sawdust Induction

“…Although P. betulinus is unable to degrade lignin, it could secrete enzymes which may modify lignin or break lignin seal by the methylation pathway and sufficiently expose cellulose and hemicellulose for enzymatic action. Recently, most of the studies were focused on Postia placenta, such as genome, transcriptome, secretome analysis and nuclear magnetic resonance analysis [27,30]. Martinez et al first reported transcriptional profile of brown-rot fungus P. placenta, and their results revealed that this fungus possessed unique extracellular enzyme systems, including an unusual repertoire of glycoside hydrolases, while exocellobiohydrolases and cellulose-binding domains were absent in this fungus [27].…”