Early Decay Mechanisms of Brown Rot Wood-Degrading Fungi: Transcriptome Patterns, Cation Dynamics, and Substrate Chemistry Effects

Abstract

Fungi gained the capacity to degrade lignocellulose approximately 295 million years ago when they adapted oxidative enzymes to metabolize lignin – a mechanism still used by white rot fungi. Since then, brown rot fungi have evolved a carbohydrate-selective mechanism that uses reactive oxygen species (ROS) to cause extensive, nonspecific depolymerization in plant cell walls, thus solubilizing the carbohydrates and avoiding lignin removal. Brown rot fungi differentially express genes to create a sequence of decay starting with lignocellulose oxidation via ROS, followed by hemicellulose side chain cleavage and main chain degradation, then cellulose degradation via endoglucanases. It is still unclear how brown rot fungi regulate this elaborate mechanism and avoid subjecting their own enzymes and hyphae to ROS damage. Specifically, the process that turns ROS pathways on at the beginning of brown rot decay has not yet been identified, despite assumptions of an inducible mechanism. Many studies have suggested that the presence of either lignin or hemicellulose may initiate brown rot decay, but this has not been clearly shown experimentally.To address this knowledge gap, I captured the earliest stages of brown rot decay by Rhodonia placenta and analyzed the whole transcriptome at the incipient stage of decay to confirm delayed upregulation of the lignocellulose oxidation genes involved in ROS generation. I also examined the interactions between R. placenta and its lignocellulose substrate in two ways. First, I created a fine-resolution map of the cation translocation dynamics in R. placenta and white rot fungus Pleurotus ostreatus for comparison. Second, to examine the effects of lignin and hemicellulose on brown rot gene expression, I used mutant strains of model plant Arabidopsis thaliana with changes in cell wall chemistry as a substrate for R. placenta and examined the whole transcriptome response of the fungus to these modified lignocellulose substrates. This dissertation contributes more clarity to the transcriptomic details of early brown rot as well as the effects of substrate chemistry on brown rot decay. Understanding brown rot decay mechanisms offers potential to harness these pathways for biotechnology applications as well as to make better predictions about the fate of carbon stored in wood.