Abstract
Fungi are ecologically outstanding decomposers of lignocellulose. Fungal lignocellulose degradation is prominent in saprotrophic Ascomycota and Basidiomycota of the subkingdom Dikarya. Despite ascomycetes dominating the Dikarya inventory of aquatic environments, genome and transcriptome data relating to enzymes involved in lignocellulose decay remain limited to terrestrial representatives of these phyla. We sequenced the genome of an exclusively aquatic ascomycete (the aquatic hyphomycete Clavariopsis aquatica), documented the presence of genes for the modification of lignocellulose and its constituents, and compared differential gene expression between C. aquatica cultivated on lignocellulosic and sugar-rich substrates. We identified potential peroxidases, laccases, and cytochrome P450 monooxygenases, several of which were differentially expressed when experimentally grown on different substrates. Additionally, we found indications for the regulation of pathways for cellulose and hemicellulose degradation. Our results suggest that C. aquatica is able to modify lignin to some extent, detoxify aromatic lignin constituents, or both. Such characteristics would be expected to facilitate the use of carbohydrate components of lignocellulose as carbon and energy sources.
Highlights
Besides two other glycoside hydrolase families (GH10 and GH5), which are described as acting on cellulose and hemicellulose main chain bonds, we found upregulation of members of the CE1 family that contains acetyl xylan esterases and of the AA9 family that contains lytic polysaccharide mono-oxygenases (LPMOs)
We identified the upregulation of enzymes involved in the later stages of lignocellulose degradation on both wheat straw and alder leaves, we only detected the upregulation of genes for the initial polymer decomposition when C. aquatica was grown on wheat straw
In particular the enzymes for extracellular depolymerization were more clearly upregulated on the more cellulose rich wheat straw
Summary
The aquatic hyphomycetes (AQH; Ingoldian fungi) are a polyphyletic group of fungi, most of which belong to the phylum Ascomycota and some of which belong to the Basidiomycota, are major decomposers of lignocellulosic plant litter found submerged in aquatic environments but that most likely originated from the terrestrial environment [1,2]. Whereas it is generally accepted that AQHs can degrade and utilize cellulose and hemicellulose from plant litter, the available knowledge about the enzyme systems involved is astonishingly scarce compared with that gathered from terrestrial fungi [1,3]. The potential for AQHs to degrade lignin, the third major component of lignocellulose, and 4.0/). The proportions of the three lignocellulose components vary considerably among plant species, with the highest proportion of lignin occurring in wood [4]. Basidiomycetes causing a white-rot type of lignin degradation (i.e., a substantial mineralization of lignin to CO2 and H2 O) involve wood-rotting and litter-decaying species and employ extracellular lignin-modifying enzymes such as laccases and the class II secretory heme peroxidases (PODs) lignin peroxidase (LiP; EC 1.11.1.14), manganese peroxides
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