Transcriptome and exoproteome analysis of utilization of plant-derived biomass by Myceliophthora thermophila

Abstract

Myceliophthora thermophila is a thermophilic fungus whose genome encodes a wide range of carbohydrate-active enzymes (CAZymes) involved in plant biomass degradation. Such enzymes have potential applications in turning different kinds of lignocellulosic feedstock into sugar precursors for biofuels and chemicals. The present study examined and compared the transcriptomes and exoproteomes of M. thermophila during cultivation on different types of complex biomass to gain insight into how its secreted enzymatic machinery varies with different sources of lignocellulose. In the transcriptome analysis three monocot (barley, oat, triticale) and three dicot (alfalfa, canola, flax) plants were used whereas in the proteome analysis additional substrates, i.e. wood and corn stover pulps, were included. A core set of 59 genes encoding CAZymes was up-regulated in response to both monocot and dicot straws, including nine polysaccharide monooxygenases and GH10, but not GH11, xylanases. Genes encoding additional xylanolytic enzymes were up-regulated during growth on monocot straws, while genes encoding additional pectinolytic enzymes were up-regulated in response to dicot biomass. Exoproteome analysis was generally consistent with the conclusions drawn from transcriptome analysis, but additional CAZymes that accumulated to high levels were identified. Despite the wide variety of biomass sources tested some CAZy family members were not expressed under any condition. The results of this study provide a comprehensive view from both transcriptome and exoproteome levels, of how M. thermophila responds to a wide range of biomass sources using its genomic resources.

Transcriptional Regulation and Responses in Filamentous Fungi Exposed to Lignocellulose

“…Correspondence was found between the genes that were induced and the differences between the composition of the monocot and dicot straws [71]. The dicot straws induced more genes encoding pectinolytic activity than the monocot straws, which corresponds well with the increased proportion of pectins in dicots [71]. The monocot but not dicot straws induced a carbohydrate esterase 1 (CE1) CAZy family feruloyl esterase which corresponds well with the higher proportion of feruloyl linkages in monocot cell walls as reviewed by Vogel [72].…”

“…They then analysed the expression dataset as if the straws from different monocot or dicot species were replicates of a group. In total, 95 genes encoding CAZymes were induced on the lignocelluloses compared to the glucose control with 59 CAZyme-encoding genes induced on both monocot and dicot straws, 22 CAZyme-encoding genes induced only on the monocot straws and 14 CAZyme-encoding genes induced only on the dicot straws [71]. Correspondence was found between the genes that were induced and the differences between the composition of the monocot and dicot straws [71].…”

“…Kolbusz et al [71] investigated the responses of M. thermophila to three agricultural straws from dicots (alfalfa, flax and canola) and three straws from monocots (barley, triticale and oat). Using a principal component analysis (PCA), Kolbusz et al [71] found that the expression patterns from the monocots clustered separately from the dicots.…”

“…Using a principal component analysis (PCA), Kolbusz et al [71] found that the expression patterns from the monocots clustered separately from the dicots. They then analysed the expression dataset as if the straws from different monocot or dicot species were replicates of a group.…”

“…In total, 95 genes encoding CAZymes were induced on the lignocelluloses compared to the glucose control with 59 CAZyme-encoding genes induced on both monocot and dicot straws, 22 CAZyme-encoding genes induced only on the monocot straws and 14 CAZyme-encoding genes induced only on the dicot straws [71]. Correspondence was found between the genes that were induced and the differences between the composition of the monocot and dicot straws [71]. The dicot straws induced more genes encoding pectinolytic activity than the monocot straws, which corresponds well with the increased proportion of pectins in dicots [71].…”