Gene Expression Patterns of Wood Decay Fungi Postia placenta and Phanerochaete chrysosporium Are Influenced by Wood Substrate Composition during Degradation

Abstract

Identification of the specific genes and enzymes involved in the fungal degradation of lignocellulosic biomass derived from feedstocks with various compositions is essential to the development of improved bioenergy processes. In order to elucidate the effect of substrate composition on gene expression in wood-rotting fungi, we employed microarrays based on the annotated genomes of the brown-and white-rot fungi, Rhodonia placenta (formerly Postia placenta) and Phanerochaete chrysosporium, respectively. We monitored the expression of genes involved in the enzymatic deconstruction of the cell walls of three 4-year-old Populus trichocarpa (poplar) trees of genotypes with distinct cell wall chemistries, selected from a population of several hundred trees grown in a common garden. The woody substrates were incubated with wood decay fungi for 10, 20, and 30 days. An analysis of transcript abundance in all pairwise comparisons highlighted 64 and 84 differentially expressed genes (>2-fold, P < 0.05) in P. chrysosporium and P. placenta, respectively. Cross-fungal comparisons also revealed an array of highly differentially expressed genes (>4-fold, P < 0.01) across different substrates and time points. These results clearly demonstrate that gene expression profiles of P. chrysosporium and P. placenta are influenced by wood substrate composition and the duration of incubation. Many of the significantly expressed genes encode "proteins of unknown function," and determining their role in lignocellulose degradation presents opportunities and challenges for future research. IMPORTANCEThis study describes the variation in expression patterns of two wood-degrading fungi (brown-and white-rot fungi) during colonization and incubation on three different naturally occurring poplar substrates of differing chemical compositions, over time. The results clearly show that the two fungi respond differentially to their substrates and that several known and, more interestingly, currently unknown genes are highly misregulated in response to various substrate compositions. These findings highlight the need to characterize several unknown proteins for catalytic function but also as potential candidate proteins to improve the efficiency of enzymatic cocktails to degrade lignocellulosic substrates in industrial applications, such as in a biochemically based bioenergy platform. In an attempt to reduce societal dependence on fossil fuels and consequently aid in the alleviation of associated economic and environmental concerns regarding the exploitation of petroleum reserves, biofuels derived from renewable and domestic sources have received extensive interest in recent years (1). The lignocellulosic biomass derived from plant cell walls is the most abundant global renewable carbon source (2), stemming from either agricultural or forestry residuals or from dedicated energy crops. While improvement in lignocellulosic feedstock for biofuel applications via advanced breeding or genetic engineering appears feasible and is critical for the future...

Transcriptome and Secretome Analyses of the Wood Decay Fungus Wolfiporia cocos Support Alternative Mechanisms of Lignocellulose Conversion

“…Further progress will be made through the integration of transcript patterns over time along with compositional analysis as recently demonstrated with P. placenta colonization of biochemically distinct poplar lines (47). Such profiles could be complemented by simultaneous examination of the fungal secretomes and microscopic assessments of decay.…”

Metadata Analysis of Phanerochaete chrysosporium Gene Expression Data Identified Common CAZymes Encoding Gene Expression Profiles Involved in Cellulose and Hemicellulose Degradation

“…Till date there are 6 Microarray, 1 RNA sequencing and 1 Long-SAGE (Serial Analysis for Gene Expression) studies based on P. chrysosporium, out of which we have analyzed the microarray and RNA sequencing studies to understand the cellulolytic and hemicellulolytic degradation mechanisms. Accession IDs of microarray datasets retrieved from NCBI GEO are GSE14734 23, 24, GSE14735 23, 24 GSE54542 25, GSE2794126, GSE52922 27, GSE69008 28 GSE6946129 details of these gene expression datasets were shown in the Table 1.…”

“…GSE54542 medium contained Oak heartwood fine powdered samples extracted using acetone and resuspended further in DMSO followed by a set of extraction processes 25. Finally, GSE69008 growth medium consisted of chemically distinct Populus trichocarpa wood substrates, which can be divided in to A (high lignin-low glucose) B (low lignin-high glucose) and C (average lignin-average glucose) conditions 28.…”

Cellulase from the fruiting bodies and mycelia of edible mushrooms: A review

“…Measured by whole-transcriptome shotgun sequencing (RNA-seq) and assayed relevant enzyme activities, up-regulation of GH5 endoglucanases and many other GHs clearly occurred with the notable exceptions of two likely expansins and a GH28 pectinase (Zhang et al, 2016). The gene expression of P. placenta and Phanerochaete chrysosporium was monitored by microarrays based on their annotated genomes to elucidate the enzymatic deconstruction of cell walls with different substrate compositions, revealing many of significantly expressed genes encode "proteins of unknown function" (Skyba et al, 2016).…”