Abstract
BackgroundThe basidiomycete Phanerochaete carnosa is a white-rot species that has been mainly isolated from coniferous softwood. Given the particular recalcitrance of softwoods to bioconversion, we conducted a comparative transcriptomic analysis of P. carnosa following growth on wood powder from one softwood (spruce; Picea glauca) and one hardwood (aspen; Populus tremuloides). P. carnosa was grown on each substrate for over one month, and mycelia were harvested at five time points for total RNA sequencing. Residual wood powder was also analyzed for total sugar and lignin composition.ResultsFollowing a slightly longer lag phase of growth on spruce, radial expansion of the P. carnosa colony was similar on spruce and aspen. Consistent with this observation, the pattern of gene expression by P. carnosa on each substrate converged following the initial adaptation. On both substrates, highest transcript abundances were attributed to genes predicted to encode manganese peroxidases (MnP), along with auxiliary activities from carbohydrate-active enzyme (CAZy) families AA3 and AA5. In addition, a lytic polysaccharide monooxygenase from family AA9 was steadily expressed throughout growth on both substrates. P450 sequences from clans CPY52 and CYP64 accounted for 50% or more of the most highly expressed P450s, which were also the P450 clans that were expanded in the P. carnosa genome relative to other white-rot fungi.ConclusionsThe inclusion of five growth points and two wood substrates was important to revealing differences in the expression profiles of specific sequences within large glycoside hydrolase families (e.g., GH5 and GH16), and permitted co-expression analyses that identified new targets for study, including non-catalytic proteins and proteins with unknown function.
Highlights
The basidiomycete Phanerochaete carnosa is a white-rot species that has been mainly isolated from coniferous softwood
Considering the profile of transcripts encoding P450 monooxygenases, co-expression analysis underscored the transition over time from sequences belonging to many P450 clans to sequences predominately from clan CYP52 and clan CYP64, which are expanded in the P. carnosa genome
While this approach was expected to reduce the requirement for low molecular weight molecules thought to promote incipient stages of fungal growth on intact wood samples [32,33,34], the overall transcriptome patterns generated by P. carnosa during growth on spruce and aspen were similar despite differences in hemicellulose, lignin, and extractive contents in these wood substrates
Summary
The basidiomycete Phanerochaete carnosa is a white-rot species that has been mainly isolated from coniferous softwood. White-rot fungi of the orders Agaricales and Polyporales are especially adept wood-degraders Corresponding studies show high expression of lignolytic enzymes (e.g., lignin peroxidases (LiPs) and manganese peroxidases (MnPs)) and lytic polysaccharide monooxygenases (LPMOs); comparatively high expression of glycoside hydrolases (GHs) from families GH5, GH6, GH7, GH10, GH12, GH28, GH43, and GH131 have been repeatedly reported. Such comparative analyses mainly consider either multiple substrates or multiple time points on a single wood species. Time and substrate dependent influences on the expression of lignocellulose degrading activities remain unclear
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