Significant levels of extracellular reactive oxygen species produced by brown rot basidiomycetes on cellulose

Biomimetic triggered release from hydroxyethyl cellulose @ Prussian blue microparticles for tri-modality biofilm removal

Human health is under growing threat from the increasing incidence of bacterial infections. Through their antimicrobial mechanisms, bacteria use appropriate strategies to overcome the antimicrobial effects of antibiotics. The enhanced effects of synergistic strategies on drug-resistant bacteria and biofilms have led to increasing interest in these approaches in recent years. Herein, biomimetic hydroxyethyl cellulose @ Prussian blue microparticles (HEC@PB MPs) generated by the gas-shearing method show a synergistic antibacterial property induced by antibiotic-, photothermal- and photodynamic- effect. MPs, as tri-modality antibacterial agents, exhibit ideal antibacterial activity and biofilm removal effect, and their mode of action on bacteria was investigated. Additionally, a drug release concept encouraged by the ROS-driven breakdown of cellulose, as seen in brown-rot fungi, was introduced. It combines ROS-responsive HEC and photodynamic PB and is likely to fit a niche in many applications.

Lignin Biodegradation and Its Valorization

Lignin, a rigid polymer composed of phenolic subunits with high molecular weight and complex structure, ranks behind only cellulose in the contribution to the biomass of plants. Therefore, lignin can be used as a new environmentally friendly resource for the industrial production of a variety of polymers, dyes and adhesives. Since laccase was found to be able to degrade lignin, increasing attention had been paid to the valorization of lignin. Research has mainly focused on the identification of lignin-degrading enzymes, which play a key role in lignin biodegradation, and the potential application of lignin degradation products. In this review, we describe the source, catalytic specificity and enzyme reaction mechanism of the four classes of the lignin-degrading enzymes so far discovered. In addition, the major pathways of lignin biodegradation and the applications of the degradative products are also discussed. Lignin-degrading bacteria or enzymes can be used in combination with chemical pretreatment for the production of value-added chemicals from lignin, providing a promising strategy for lignin valorization.

Capturing an Early Gene Induction Event during Wood Decay by the Brown Rot Fungus Rhodonia placenta

Brown rot fungi dominate wood decomposition in coniferous forests, and their carbohydrate-selective mechanisms are of commercial interest. Brown rot was recently described as a two-step, sequential mechanism orchestrated by fungi using differentially expressed genes (DEGs) and consisting of oxidation via reactive oxygen species (ROS) followed by enzymatic saccharification. There have been indications, however, that the initial oxidation step itself might require induction. To capture this early gene regulation event, here, we integrated fine-scale cryosectioning with whole-transcriptome sequencing to dissect gene expression at the single-hyphal-cell scale (tens of micrometers). This improved the spatial resolution 50-fold, relative to previous work, and we were able to capture the activity of the first 100 μm of hyphal front growth by Rhodonia placenta in aspen wood. This early decay period was dominated by delayed gene expression patterns as the fungus ramped up its mechanism. These delayed DEGs included many genes implicated in ROS pathways (lignocellulose oxidation [LOX]) that were previously and incorrectly assumed to be constitutively expressed. These delayed DEGs, which include those with and without predicted functions, also create a focused subset of target genes for functional genomics. However, this delayed pattern was not universal, with a few genes being upregulated immediately at the hyphal front. Most notably, this included a gene commonly implicated in hydroquinone and iron redox cycling: benzoquinone reductase. IMPORTANCE Earth's aboveground terrestrial biomass is primarily wood, and fungi dominate wood decomposition. Here, we studied these fungal pathways in a common "brown rot"-type fungus, Rhodonia placenta, that selectively extracts sugars from carbohydrates embedded within wood lignin. Using a space-for-time design to map fungal gene expression at the extreme hyphal front in wood, we made two discoveries. First, we found that many genes long assumed to be "on" (constitutively expressed) from the very beginning of decay were instead "off" before being upregulated, when mapped (via transcriptome sequencing [RNA-seq]) at a high resolution. Second, we found that the gene encoding benzoquinone reductase was "on" in incipient decay and quickly downregulated, implying a key role in "kick-starting" brown rot.

In vitro cell composition identification of wood decay fungi by Fourier transform infrared spectroscopy

Decay pathogens follow dissimilar metabolic mechanisms to cause irreversible damage to woody tissues. The objective of this study is to perform inter- and intra-species microbial cell structural comparison using attenuated total reflectance Fourier transform infrared spectroscopy. Representative fungi species, causing brown rot and white rot, namely, Postia placenta and Trametes versicolor, respectively, were cultured in laboratory conditions. In vitro spectral measurements were performed at periodic two week intervals of fungal growth. The study shows structural differences for both species of fungi. The prominent presence of protein amide, carbohydrate and carboxyl bands was of interest. Spectral deconvolution of the infrared broadband around approximately 3300 cm-1 produced peaks at four different wavenumbers. The hydrogen bond energy obtained at the four wavenumbers, from deconvolution, varied from approximately 41 kJ mol-1 to approximately 7 kJ mol-1, indicating the presence of strong and weak forces in microbial cell structure. The hydrogen bond distance, obtained at the deconvoluted wavenumbers, varied between 2.7 Å-2.8 Å, indicating the presence of short and long-distance forces within microbial cells. Microscopic observation showed mycelium colonization, hyphal tip and lateral branching.

Retracted and Republished from: "Substrate-Specific Differential Gene Expression and RNA Editing in the Brown Rot Fungus Fomitopsis pinicola"

Wood-decaying fungi tend to have characteristic substrate ranges that partly define their ecological niche. Fomitopsis pinicola is a brown rot species of Polyporales that is reported on 82 species of softwoods and 42 species of hardwoods. We analyzed gene expression levels of F. pinicola from submerged cultures with ground wood powder (sampled at 5 days) or solid wood wafers (sampled at 10 and 30 days), using aspen, pine, and spruce substrates (aspen was used only in submerged cultures). Fomitopsis pinicola expressed similar sets of wood-degrading enzymes typical of brown rot fungi across all culture conditions and time points. Nevertheless, differential gene expression was observed across all pairwise comparisons of substrates and time points. Genes exhibiting differential expression encode diverse enzymes with known or potential function in brown rot decay, including laccase, benzoquinone reductase, aryl alcohol oxidase, cytochrome P450s, and various glycoside hydrolases. Comparing transcriptomes from submerged cultures and wood wafers, we found that culture conditions had a greater impact on global expression profiles than substrate wood species. These findings highlight the need for standardization of culture conditions in studies of gene expression in wood-decaying fungi. IMPORTANCE All species of wood-decaying fungi occur on a characteristic range of substrates (host plants), which may be broad or narrow. Understanding the mechanisms that allow fungi to grow on particular substrates is important for both fungal ecology and applied uses of different feedstocks in industrial processes. We grew the wood-decaying polypore Fomitopsis pinicola on three different wood species—aspen, pine, and spruce—under various culture conditions. We found that F. pinicola is able to modify gene expression (transcription levels) across different substrate species and culture conditions. Many of the genes involved encode enzymes with known or predicted functions in wood decay. This study provides clues to how wood-decaying fungi may adjust their arsenal of decay enzymes to accommodate different host substrates.

Study on the Anti-Biodegradation Property of Tunicate Cellulose

Tunicate is a kind of marine animal, and its outer sheath consists of almost pure Iβ crystalline cellulose. Due to its high aspect ratio, tunicate cellulose has excellent physical properties. It draws extensive attention in the construction of robust functional materials. However, there is little research on its biological activity. In this study, cellulose enzymatic hydrolysis was conducted on tunicate cellulose. During the hydrolysis, the crystalline behaviors, i.e., crystallinity index (CrI), crystalline size and degree of polymerization (DP), were analyzed on the tunicate cellulose. As comparisons, similar hydrolyses were performed on cellulose samples with relatively low CrI, namely α-cellulose and amorphous cellulose. The results showed that the CrI of tunicate cellulose and α-cellulose was 93.9% and 70.9%, respectively; and after 96 h of hydrolysis, the crystallinity, crystalline size and DP remained constant on the tunicate cellulose, and the cellulose conversion rate was below 7.8%. While the crystalline structure of α-cellulose was significantly damaged and the cellulose conversion rate exceeded 83.8% at the end of 72 h hydrolysis, the amorphous cellulose was completely converted to glucose after 7 h hydrolysis, and the DP decreased about 27.9%. In addition, tunicate cellulose has high anti-mold abilities, owing to its highly crystalized Iβ lattice. It can be concluded that tunicate cellulose has significant resistance to enzymatic hydrolysis and could be potentially applied as anti-biodegradation materials.

Evidence for ligninolytic activity of the ascomycete fungus Podospora anserina

BACKGROUND

The ascomycete fungus Podospora anserina has been appreciated for its targeted carbohydrate-active enzymatic arsenal. As a late colonizer of herbivorous dung, the fungus acts specifically on the more recalcitrant fraction of lignocellulose and this lignin-rich biotope might have resulted in the evolution of ligninolytic activities. However, the lignin-degrading abilities of the fungus have not been demonstrated by chemical analyses at the molecular level and are, thus far, solely based on genome and secretome predictions. To evaluate whether P. anserina might provide a novel source of lignin-active enzymes to tap into for potential biotechnological applications, we comprehensively mapped wheat straw lignin during fungal growth and characterized the fungal secretome.

RESULTS

Quantitative 13C lignin internal standard py-GC-MS analysis showed substantial lignin removal during the 7 days of fungal growth (24% w/w), though carbohydrates were preferably targeted (58% w/w removal). Structural characterization of residual lignin by using py-GC-MS and HSQC NMR analyses demonstrated that Cα-oxidized substructures significantly increased through fungal action, while intact β-O-4' aryl ether linkages, p-coumarate and ferulate moieties decreased, albeit to lesser extents than observed for the action of basidiomycetes. Proteomic analysis indicated that the presence of lignin induced considerable changes in the secretome of P. anserina. This was particularly reflected in a strong reduction of cellulases and galactomannanases, while H2O2-producing enzymes clearly increased. The latter enzymes, together with laccases, were likely involved in the observed ligninolysis.

CONCLUSIONS

For the first time, we provide unambiguous evidence for the ligninolytic activity of the ascomycete fungus P. anserina and expand the view on its enzymatic repertoire beyond carbohydrate degradation. Our results can be of significance for the development of biological lignin conversion technologies by contributing to the quest for novel lignin-active enzymes and organisms.

Salmonella and Reactive Oxygen Species: A Love-Hate Relationship

Salmonella enterica represents an enterobacterial species including numerous serovars that cause infections at, or initiated at, the intestinal epithelium. Many serovars also act as facultative intracellular pathogens with a tropism for phagocytic cells. These bacteria not only survive in phagocytes but also undergo de facto replication therein. Phagocytes, through the activities of phagocyte NADPH-dependent oxidase and inducible nitric oxide synthase, are very proficient in converting molecular oxygen to reactive oxygen (ROS) and nitrogen species (RNS). These compounds represent highly efficient effectors of the innate immune defense. Salmonella is by no means resistant to these effectors, which may stand in contrast to the host niches chosen. To cope with this paradox, these bacteria rely on an array of detoxification and repair systems. Combination these systems allows for a high enough tolerance to ROS and RNS to enable establishment of infection. In addition, salmonella possesses protein factors that have the potential to dampen the infection-associated inflammation, which evidently results in a reduced exposure to ROS and RNS. This review attempts to summarize the activities and strategies by which salmonella tries to cope with ROS and RNS and how the bacterium can make use of these innate defense factors.

Cellular level chemical changes in Scots pine heartwood during incipient brown rot decay

The heartwoods of many wood species have natural resistance to wood decay due to the accumulation of antifungal heartwood extractives. The natural durability of heartwoods has been extensively investigated, yet very little information is available on the initiation of heartwood decay. This experiment examined the onset of Rhodonia placenta brown rot decay in Scots pine heartwood in order to identify the key changes leading to heartwood decay. An imaging approach based on Raman imaging and multivariate image analysis revealed that the degradation of heartwood began in the innermost cell wall layers and then spread into the remaining cell walls and the middle lamella. Pinosylvins were extensively degraded in the cell walls, middle lamella and extractive deposits, while unidentified material most likely consisting of hemicelluloses and/or lipophilic extractives was removed from the inner cell wall layers. Changes similar to inner cell wall degradation were seen in the remaining cell walls in more advanced decay. The results indicate that the key change in incipient heartwood decay is the degradation of antifungal heartwood extractives. The inner cell wall degradation seen in this experiment may serve a nutritive purpose or facilitate the penetration of degradative agents into the cell walls and middle lamella.

High energy oxidation and organosolv solubilization for high yield isolation of cellulose nanocrystals (CNC) from Eucalyptus hardwood

Cellulose nanocrystals (CNC) have been widely used as responsive materials, chiral templates, and tough nano-composites due to its unparalleled properties. Acid and enzyme hydrolyses are extensively employed to prepare CNC. These traditional approaches exhibit inherent limitations of corrosion hazards, time-consuming process, and/or low yield. Herein, irradiation oxidation and organosolv solubilization are conducted to cause rapid degradation with simultaneous crystallization of cellulose to achieve approx. 87% yield of CNC. The morphology, spectroscopic, and stability properties of the as-prepared CNC are characterized through UV-vis spectroscopy, zetal potential, XRD, TEM, DLS, GPC, FT-IR and TGA techniques. The resultant CNC suspension presents unique property with high stability after 9 months storage at 4 °C. Moreover, CNC liquid crystal phase is successfully generated by addition of anions or cations solution to the CNC aqueous dispersion without stirring. The innovative approach in this work opens an avenue to obtain CNC directly from lignocellulosic biomass through irradiation oxidation and organosolv solubilization without acid hydrolysis and washing procedure.

Substrate-Specific Differential Gene Expression and RNA Editing in the Brown Rot Fungus Fomitopsis pinicola

Wood-decaying fungi tend to have characteristic substrate ranges that partly define their ecological niche. Fomitopsis pinicola is a brown rot species of Polyporales that is reported on 82 species of softwoods and 42 species of hardwoods. We analyzed the gene expression levels and RNA editing profiles of F. pinicola from submerged cultures with ground wood powder (sampled at 5 days) or solid wood wafers (sampled at 10 and 30 days), using aspen, pine, and spruce substrates (aspen was used only in submerged cultures). Fomitopsis pinicola expressed similar sets of wood-degrading enzymes typical of brown rot fungi across all culture conditions and time points. Nevertheless, differential gene expression and RNA editing were observed across all pairwise comparisons of substrates and time points. Genes exhibiting differential expression and RNA editing encode diverse enzymes with known or potential function in brown rot decay, including laccase, benzoquinone reductase, aryl alcohol oxidase, cytochrome P450s, and various glycoside hydrolases. There was no overlap between differentially expressed and differentially edited genes, suggesting that these may provide F. pinicola with independent mechanisms for responding to different conditions. Comparing transcriptomes from submerged cultures and wood wafers, we found that culture conditions had a greater impact on global expression profiles than substrate wood species. In contrast, the suites of genes subject to RNA editing were much less affected by culture conditions. These findings highlight the need for standardization of culture conditions in studies of gene expression in wood-decaying fungi.IMPORTANCE All species of wood-decaying fungi occur on a characteristic range of substrates (host plants), which may be broad or narrow. Understanding the mechanisms that enable fungi to grow on particular substrates is important for both fungal ecology and applied uses of different feedstocks in industrial processes. We grew the wood-decaying polypore Fomitopsis pinicola on three different wood species, aspen, pine, and spruce, under various culture conditions. We examined both gene expression (transcription levels) and RNA editing (posttranscriptional modification of RNA, which can potentially yield different proteins from the same gene). We found that F. pinicola is able to modify both gene expression and RNA editing profiles across different substrate species and culture conditions. Many of the genes involved encode enzymes with known or predicted functions in wood decay. This work provides clues to how wood-decaying fungi may adjust their arsenal of decay enzymes to accommodate different host substrates.

Hydrogen-rich water mediates redox regulation of the antioxidant system, mycelial regeneration and fruiting body development in Hypsizygus marmoreus

Hypsizygus marmoreus is an important industrialized mushroom, yet the lack of basic research on this fungus has hindered further development of its economic value. In this study, mycelia injured by scratching were treated with hydrogen-rich water (HRW) to investigate the involvement of the redox system in fruiting body development. Compared to the control group, damaged mycelia treated with HRW regenerated earlier and showed significantly enhanced fruiting body production. Antioxidant capacity increased significantly in damaged mycelia after HRW treatment, as indicated by higher antioxidant enzyme activities and antioxidant contents; the levels of reactive oxygen species (ROS) and malondialdehyde (MDA) were also reduced at the mycelial regeneration stage after treatment with HRW. Furthermore, genes involved in ROS, Ca²⁺, MAPK and oxylipin signaling pathways were up-regulated by HRW treatment. In addition, laccase and manganese peroxidase activities and mycelial biomass were higher after HRW treatment, suggesting that HRW might enhance the substrate-degradation rate to provide more carbon sources for fruiting body production.

Physico-chemical oxidative cleavage strategy facilitates the degradation of recalcitrant crystalline cellulose by cellulases hydrolysis

BACKGROUND

Efficient enzymatic conversion of recalcitrant crystalline cellulose is critical for enabling cost-effective industrial conversion of cellulosic biomass to biofuels and chemicals. Fully understanding enzyme digestion mechanism is paving a new way to design efficient process for biomass conversion. Accordingly, a continuing drive is inspiring to discover new routes to promote crystalline cellulose disruption.

RESULTS

Herein, a physico-chemical oxidative cleavage strategy of irradiation oxidation/post-reduction (IOPR) was employed to treat crystalline cellulose I to cleave glycosidic bonds association with some new oxidized and reduced chain ends, thus boosting downstream degradation by cellulases from Trichoderma reesei. The hydrolysis performance of treated crystalline cellulose was conducted with either T. reesei Cel7A (TrCel7A) alone, or a cellulase enzyme mixture (90% Celluclast 1.5 L, 10% β-glucosidase). 81.6 and/or 97% of conversion efficiency have been reached for 24-h and 48-h cellulase hydrolysis, respectively. The high efficient conversion of crystalline cellulose after IOPR is mainly attributed to generating some new chain ends, which are identified by MAIDI-TOF-MS and HPLC. Furthermore, the nanoscale architectures of crystalline cellulose before and after IOPR are systematically investigated by XRD, EPR, ATR- FTIR, GPC, and XPS techniques. Together with TEM images, the results reveal a fascinating digestion mechanism of "peel-off" and "cavity-formation" paradigms toward degrading crystalline cellulose by cellulase mixtures after IOPR treatment.

CONCLUSIONS

This encouraging results show that the proposed IOPR approach will become a potential competitive alternative to current biomass pretreatment. It opens a new avenue toward the implementation of pretreatment and the design of enzyme cocktails in lignocellulosic biorefinery.

A genomics-informed study of oxalate and cellulase regulation by brown rot wood-degrading fungi

Wood-degrading fungi that selectively remove carbohydrates (brown rot) combine Fenton-based oxidation and enzymatic hydrolysis to degrade wood. These two steps are incompatible in close proximity. To explain this, brown rot fungi may stagger oxidative reactions ahead of hydrolysis, but the scale and environmental controls for such a mechanism have not been resolved in solid wood. Here, we focused on one reaction control parameter, oxalate. In coordination with Fe³⁺-reducing compounds (e.g., 2,5-dimethoxyhydroquinone), oxalate can either promote Fenton chemistry by mobilizing Fe³⁺ as mono-oxalates (facilitative) or inhibit Fenton chemistry (protective) by restricting reducibility and the formation of Fenton's reagent as Fe³⁺/Fe²-(oxalate)_2,3. Here, we sectioned wood wafers colonized directionally by Postia placenta and Gloeophyllum trabeum to map end-to-end the expression of oxalate synthesis genes and to overlay enzyme activities, metabolites, and wood modifications. Near advancing hyphal fronts, oxaloacetase expression was up upregulated for both fungi, while regulation patterns of paralogous of isocitrate lyases and glyoxylate dehydrogenases varied, suggesting different physiological roles. Oxalate decarboxylase (ODC) expression in G. trabeum was induced in more decayed wood behind the hyphal front, but was constitutively expressed in all P. placenta sections. Relative ODC activities increased and oxalate levels stabilized in more decayed wood behind the hyphal front. Endoglucanase (EG) activity, on the other hand, peaked for both fungi in later decay stages. These oxalate optimization patterns are in line with previous whole-block 'spiking' experiments tracking oxalate, but we provide here information on its genetic controls across a spatial gradient. As a complement, we also demonstrate in vitro the plausibility of a protective role for oxalate, to emphasize that these fungi might be optimizing oxalate at a given level to maximize Fenton reactions but to minimize oxidative damage.

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

Certain wood decay basidiomycetes, collectively referred to as brown rot fungi, rapidly depolymerize cellulose while leaving behind the bulk of cell wall lignin as a modified residue. The mechanism(s) employed is unclear, but considerable evidence implicates the involvement of diffusible oxidants generated via Fenton-like chemistry. Toward a better understanding of this process, we have examined the transcriptome and secretome of Wolfiporia cocos when cultivated on media containing glucose, purified crystalline cellulose, aspen (Populus grandidentata), or lodgepole pine (Pinus contorta) as the sole carbon source. Compared to the results obtained with glucose, 30, 183, and 207 genes exhibited 4-fold increases in transcript levels in cellulose, aspen, and lodgepole pine, respectively. Mass spectrometry identified peptides corresponding to 64 glycoside hydrolase (GH) proteins, and of these, 17 corresponded to transcripts upregulated on one or both woody substrates. Most of these genes were broadly categorized as hemicellulases or chitinases. Consistent with an important role for hydroxyl radical in cellulose depolymerization, high transcript levels and upregulation were observed for genes involved in iron homeostasis, iron reduction, and extracellular peroxide generation. These patterns of regulation differ markedly from those of the closely related brown rot fungus Postia placenta and expand the number of enzymes potentially involved in the oxidative depolymerization of cellulose.

IMPORTANCE

The decomposition of wood is an essential component of nutrient cycling in forest ecosystems. Few microbes have the capacity to efficiently degrade woody substrates, and the mechanism(s) is poorly understood. Toward a better understanding of these processes, we show that when grown on wood as a sole carbon source the brown rot fungus W. cocos expresses a unique repertoire of genes involved in oxidative and hydrolytic conversions of cell walls.

Lignin decomposition is sustained under fluctuating redox conditions in humid tropical forest soils

Lignin mineralization represents a critical flux in the terrestrial carbon (C) cycle, yet little is known about mechanisms and environmental factors controlling lignin breakdown in mineral soils. Hypoxia is thought to suppress lignin decomposition, yet potential effects of oxygen (O₂ ) variability in surface soils have not been explored. Here, we tested the impact of redox fluctuations on lignin breakdown in humid tropical forest soils during ten-week laboratory incubations. We used synthetic lignins labeled with ¹³ C in either of two positions (aromatic methoxyl or propyl side chain C_β ) to provide highly sensitive and specific measures of lignin mineralization seldom employed in soils. Four-day redox fluctuations increased the percent contribution of methoxyl C to soil respiration relative to static aerobic conditions, and cumulative methoxyl-C mineralization was statistically equivalent under static aerobic and fluctuating redox conditions despite lower soil respiration in the latter treatment. Contributions of the less labile lignin C_β to soil respiration were equivalent in the static aerobic and fluctuating redox treatments during periods of O₂ exposure, and tended to decline during periods of O₂ limitation, resulting in lower cumulative C_β mineralization in the fluctuating treatment relative to the static aerobic treatment. However, cumulative mineralization of both the C_β - and methoxyl-labeled lignins nearly doubled in the fluctuating treatment relative to the static aerobic treatment when total lignin mineralization was normalized to total O₂ exposure. Oxygen fluctuations are thought to be suboptimal for canonical lignin-degrading microorganisms. However, O₂ fluctuations drove substantial Fe reduction and oxidation, and reactive oxygen species generated during abiotic Fe oxidation might explain the elevated contribution of lignin to C mineralization. Iron redox cycling provides a potential mechanism for lignin depletion in soil organic matter. Couplings between soil moisture, redox fluctuations, and lignin breakdown provide a potential link between climate variability and the biochemical composition of soil organic matter.

Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi

Basidiomycota (basidiomycetes) make up 32% of the described fungi and include most wood-decaying species, as well as pathogens and mutualistic symbionts. Wood-decaying basidiomycetes have typically been classified as either white rot or brown rot, based on the ability (in white rot only) to degrade lignin along with cellulose and hemicellulose. Prior genomic comparisons suggested that the two decay modes can be distinguished based on the presence or absence of ligninolytic class II peroxidases (PODs), as well as the abundance of enzymes acting directly on crystalline cellulose (reduced in brown rot). To assess the generality of the white-rot/brown-rot classification paradigm, we compared the genomes of 33 basidiomycetes, including four newly sequenced wood decayers, and performed phylogenetically informed principal-components analysis (PCA) of a broad range of gene families encoding plant biomass-degrading enzymes. The newly sequenced Botryobasidium botryosum and Jaapia argillacea genomes lack PODs but possess diverse enzymes acting on crystalline cellulose, and they group close to the model white-rot species Phanerochaete chrysosporium in the PCA. Furthermore, laboratory assays showed that both B. botryosum and J. argillacea can degrade all polymeric components of woody plant cell walls, a characteristic of white rot. We also found expansions in reducing polyketide synthase genes specific to the brown-rot fungi. Our results suggest a continuum rather than a dichotomy between the white-rot and brown-rot modes of wood decay. A more nuanced categorization of rot types is needed, based on an improved understanding of the genomics and biochemistry of wood decay.

Genomewide analysis of polysaccharides degrading enzymes in 11 white- and brown-rot Polyporales provides insight into mechanisms of wood decay

To degrade the polysaccharides, wood-decay fungi secrete a variety of glycoside hydrolases (GHs) and carbohydrate esterases (CEs) classified into various sequence-based families of carbohydrate-active enzymes (CAZys) and their appended carbohydrate-binding modules (CBM). Oxidative enzymes, such as cellobiose dehydrogenase (CDH) and lytic polysaccharide monooxygenase (LPMO, formerly GH61), also have been implicated in cellulose degradation. To examine polysaccharide-degrading potential between white- and brown-rot fungi, we performed genomewide analysis of CAZys and these oxidative enzymes in 11 Polyporales, including recently sequenced monokaryotic strains of Bjerkandera adusta, Ganoderma sp. and Phlebia brevispora. Furthermore, we conducted comparative secretome analysis of seven Polyporales grown on wood culture. As a result, it was found that genes encoding cellulases belonging to families GH6, GH7, GH9 and carbohydrate-binding module family CBM1 are lacking in genomes of brown-rot polyporales. In addition, the presence of CDH and the expansion of LPMO were observed only in white-rot genomes. Indeed, GH6, GH7, CDH and LPMO peptides were identified only in white-rot polypores. Genes encoding aldose 1-epimerase (ALE), previously detected with CDH and cellulases in the culture filtrates, also were identified in white-rot genomes, suggesting a physiological connection between ALE, CDH, cellulase and possibly LPMO. For hemicellulose degradation, genes and peptides corresponding to GH74 xyloglucanase, GH10 endo-xylanase, GH79 β-glucuronidase, CE1 acetyl xylan esterase and CE15 glucuronoyl methylesterase were significantly increased in white-rot genomes compared to brown-rot genomes. Overall, relative to brown-rot Polyporales, white-rot Polyporales maintain greater enzymatic diversity supporting lignocellulose attack.

Genes associated with lignin degradation in the polyphagous white-rot pathogen Heterobasidion irregulare show substrate-specific regulation

The pathogenic white-rot basidiomycete Heterobasidion irregulare is able to remove lignin and hemicellulose prior to cellulose during the colonization of root and stem xylem of conifer and broadleaf trees. We identified and followed the regulation of expression of genes belonging to families encoding ligninolytic enzymes. In comparison with typical white-rot fungi, the H. irregulare genome has exclusively the short-manganese peroxidase type encoding genes (6 short-MnPs) and thereby a slight contraction in the pool of class II heme-containing peroxidases, but an expansion of the MCO laccases with 17 gene models. Furthermore, the genome shows a versatile set of other oxidoreductase genes putatively involved in lignin oxidation and conversion, including 5 glyoxal oxidases, 19 quinone-oxidoreductases and 12 aryl-alcohol oxidases. Their genetic multiplicity and gene-specific regulation patterns on cultures based on defined lignin, cellulose or Norway spruce lignocellulose substrates suggest divergent specificities and physiological roles for these enzymes. While the short-MnP encoding genes showed similar transcript levels upon fungal growth on heartwood and reaction zone (RZ), a xylem defense tissue rich in phenolic compounds unique to trees, a subset of laccases showed higher gene expression in the RZ cultures. In contrast, other oxidoreductases depending on initial MnP activity showed generally lower transcript levels on RZ than on heartwood. These data suggest that the rate of fungal oxidative conversion of xylem lignin differs between spruce RZ and heartwood. It is conceivable that in RZ part of the oxidoreductase activities of laccases are related to the detoxification of phenolic compounds involved in host-defense. Expression of the several short-MnP enzymes indicated an important role for these enzymes in effective delignification of wood by H. irregulare.

Cellulose Isolation Methodology for NMR Analysis of Cellulose Ultrastructure

In order to obtain accurate information about the ultrastructure of cellulose from native biomass by ¹³C cross polarization magic angle spinning (CP/MAS) NMR spectroscopy the cellulose component must be isolated due to overlapping resonances from both lignin and hemicellulose. Typically, cellulose isolation has been achieved via holocellulose pulping to remove lignin followed by an acid hydrolysis procedure to remove the hemicellulose components. Using ¹³C CP/MAS NMR and non-linear line-fitting of the cellulose C₄ region, it was observed that the standard acid hydrolysis procedure caused an apparent increase in crystallinity of ~10% or less on the cellulose isolated from Populus holocellulose. We have examined the effect of the cellulose isolation method, particularly the acid treatment time for hemicellulose removal, on cellulose ultrastructural characteristics by studying these effects on cotton, microcrystalline cellulose (MCC) and holocellulose pulped Populus. ¹³C CP/MAS NMR of MCC indicated that holocellulose pulping and acid hydrolysis has little effect on the crystalline ultrastructural components of cellulose. Although any chemical method to isolate cellulose from native biomass will invariably alter substrate characteristics, especially those related to regions accessible to solvents, we found those changes to be minimal and consistent in samples of typical crystallinity and lignin/hemicellulose content. Based on the rate of the hemicellulose removal, as determined by HPLC-carbohydrate analysis and magnitude of cellulose ultrastructural alteration, the most suitable cellulose isolation methodology utilizes a treatment of 2.5 M HCl at 100 °C for a standard residence time between 1.5 and 4 h. However, for the most accurate crystallinity results this residence time should be determined empirically for a particular sample.

Differences in soil mobility and degradability between water-dispersible CdSe and CdSe/ZnS quantum dots

The relative leaching potential and degradation of water-dispersible CdSe and CdSe/ZnS quantum dots (QDs) were evaluated using small-scale soil columns. The potential of QDs to release toxic Cd(2+) and/or Se(2-)/SeO(3)(2-) ions upon degradation is of environmental concern and warrants investigation. Both classes of QDs exhibited limited soil mobility in CaCl(2), with more than 70% of the total Cd and Se species from QDs retained in the top soil after passing 10 column volumes of solution through the soil column. However, mobilization of Cd- and Se-species was observed when EDTA was used as the leaching solution. Approximately 98% of the total Cd(2+) loaded leached out from the Cd(2+)-spiked soil, while only 30% and 60% leached out from the CdSe and CdSe/ZnS QD-spiked soils, respectively. Soil column profiles and analysis of leachates suggest that intact QDs leached through the soil. Longer incubation (15 days) in soil prior to leaching indicated some degradation and/or surface modification of both QDs. These results suggest that chelating agents in the environment can enhance the soil mobility of intact and degraded QDs. It is apparent that QDs in soil, including the polymer-coated CdSe/ZnS QDs that are generally assumed to possess a higher degree of environmental stability, can undergo chemical transformations, which subsequently dictate their overall mobility.

Significant alteration of gene expression in wood decay fungi Postia placenta and Phanerochaete chrysosporium by plant species

Identification of specific genes and enzymes involved in conversion of lignocellulosics from an expanding number of potential feedstocks is of growing interest to bioenergy process development. The basidiomycetous wood decay fungi Phanerochaete chrysosporium and Postia placenta are promising in this regard because they are able to utilize a wide range of simple and complex carbon compounds. However, systematic comparative studies with different woody substrates have not been reported. To address this issue, we examined gene expression of these fungi colonizing aspen (Populus grandidentata) and pine (Pinus strobus). Transcript levels of genes encoding extracellular glycoside hydrolases, thought to be important for hydrolytic cleavage of hemicelluloses and cellulose, showed little difference for P. placenta colonizing pine versus aspen as the sole carbon source. However, 164 genes exhibited significant differences in transcript accumulation for these substrates. Among these, 15 cytochrome P450s were upregulated in pine relative to aspen. Of 72 P. placenta extracellular proteins identified unambiguously by mass spectrometry, 52 were detected while colonizing both substrates and 10 were identified in pine but not aspen cultures. Most of the 178 P. chrysosporium glycoside hydrolase genes showed similar transcript levels on both substrates, but 13 accumulated >2-fold higher levels on aspen than on pine. Of 118 confidently identified proteins, 31 were identified in both substrates and 57 were identified in pine but not aspen cultures. Thus, P. placenta and P. chrysosporium gene expression patterns are influenced substantially by wood species. Such adaptations to the carbon source may also reflect fundamental differences in the mechanisms by which these fungi attack plant cell walls.

Fate of prions in soil: a review

Prions are the etiological agents of transmissible spongiform encephalopathies (TSSEs), a class of fatal neurodegenerative diseases affecting humans and other mammals. The pathogenic prion protein is a misfolded form of the host-encoded prion protein and represents the predominant, if not sole, component of the infectious agent. Environmental routes of TSE transmission areimplicated in epizootics of sheep scrapie and chronic wasting disease (CWD) of deer, elk, and moose. Soil represents a plausible environmental reservoir of scrapie and CWD agents, which can persist in the environment for years. Attachment to soil particles likely influences the persistence and infectivity of prions in the environment. Effective methods to inactivate TSE agents in soil are currently lacking, and the effects of natural degradation mechanisms on TSE infectivity are largely unknown. An improved understanding of the processes affecting the mobility, persistence, and bioaviailability of prions in soil is needed for the management of TSE-contaminated environments.

Characterisation of the initial degradation stage of Scots pine (Pinus sylvestris L.) sapwood after attack by brown-rot fungus Coniophora puteana

In our study, early period degradation (10 days) of Scots pine (Pinus sylvestris L.) sapwood by the brown-rot fungus Coniophora puteana (Schum.: Fr.) Karst. (BAM Ebw.15) was followed at the wood chemical composition and ultrastructure-level, and highlighted the generation of reactive oxygen species (ROS). An advanced decay period of 50 days was chosen for comparison of the degradation dynamics. Scanning UV microspectrophotometry (UMSP) analyses of lignin distribution in wood cells revealed that the linkages of lignin and polysaccharides were already disrupted in the early period of fungal attack. An increase in the lignin absorption A(280) value from 0.24 (control) to 0.44 in decayed wood was attributed to its oxidative modification which has been proposed to be generated by Fenton reaction derived ROS. The wood weight loss in the initial degradation period was 2%, whilst cellulose and lignin content decreased by 6.7% and 1%, respectively. Lignin methoxyl (-OCH3) content decreased from 15.1% (control) to 14.2% in decayed wood. Diffuse reflectance Fourier-transform infrared (DRIFT) spectroscopy corroborated the moderate loss in the hemicellulose and lignin degradation accompanying degradation. Electron paramagnetic resonance spectra and spin trapping confirmed the generation of ROS, such as hydroxyl radicals (HO∙), in the early wood degradation period. Our results showed that irreversible changes in wood structure started immediately after wood colonisation by fungal hyphae and the results generated here will assist in the understanding of the biochemical mechanisms of wood biodegradation by brown-rot fungi with the ultimate aim of developing novel wood protection methods.

Multidimensional NMR analysis reveals truncated lignin structures in wood decayed by the brown rot basidiomycete Postia placenta

Lignocellulose biodegradation, an essential step in terrestrial carbon cycling, generally involves removal of the recalcitrant lignin barrier that otherwise prevents infiltration by microbial polysaccharide hydrolases. However, fungi that cause brown rot of wood, a major route for biomass recycling in coniferous forests, utilize wood polysaccharides efficiently while removing little of the lignin. The mechanism by which these basidiomycetes breach the lignin remains unclear. We used recently developed methods for solubilization and multidimensional (1) H-(13) C solution-state NMR spectroscopy of ball-milled lignocellulose to analyse aspen wood degraded by Postia placenta. The results showed that decay decreased the content of the principal arylglycerol-β-aryl ether interunit linkage in the lignin by more than half, while increasing the frequency of several truncated lignin structures roughly fourfold over the level found in sound aspen. These new end-groups, consisting of benzaldehydes, benzoic acids and phenylglycerols, accounted for 6-7% of all original lignin subunits. Our results provide evidence that brown rot by P. placenta results in significant ligninolysis, which might enable infiltration of the wood by polysaccharide hydrolases even though the partially degraded lignin remains in situ. Recent work has revealed that the P. placenta genome encodes no ligninolytic peroxidases, but has also shown that this fungus produces an extracellular Fenton system. It is accordingly likely that P. placenta employs electrophilic reactive oxygen species such as hydroxyl radicals to disrupt lignin in wood.

Comparative transcriptome and secretome analysis of wood decay fungi Postia placenta and Phanerochaete chrysosporium

Cellulose degradation by brown rot fungi, such as Postia placenta, is poorly understood relative to the phylogenetically related white rot basidiomycete, Phanerochaete chrysosporium. To elucidate the number, structure, and regulation of genes involved in lignocellulosic cell wall attack, secretome and transcriptome analyses were performed on both wood decay fungi cultured for 5 days in media containing ball-milled aspen or glucose as the sole carbon source. Using liquid chromatography-tandem mass spectrometry (LC-MS/MS), a total of 67 and 79 proteins were identified in the extracellular fluids of P. placenta and P. chrysosporium cultures, respectively. Viewed together with transcript profiles, P. chrysosporium employs an array of extracellular glycosyl hydrolases to simultaneously attack cellulose and hemicelluloses. In contrast, under these same conditions, P. placenta secretes an array of hemicellulases but few potential cellulases. The two species display distinct expression patterns for oxidoreductase-encoding genes. In P. placenta, these patterns are consistent with an extracellular Fenton system and include the upregulation of genes involved in iron acquisition, in the synthesis of low-molecular-weight quinones, and possibly in redox cycling reactions.

Laccase and its role in production of extracellular reactive oxygen species during wood decay by the brown rot basidiomycete Postia placenta

Brown rot basidiomycetes initiate wood decay by producing extracellular reactive oxygen species that depolymerize the structural polysaccharides of lignocellulose. Secreted fungal hydroquinones are considered one contributor because they have been shown to reduce Fe(3+), thus generating perhydroxyl radicals and Fe(2+), which subsequently react further to produce biodegradative hydroxyl radicals. However, many brown rot fungi also secrete high levels of oxalate, which chelates Fe(3+) tightly, making it unreactive with hydroquinones. For hydroquinone-driven hydroxyl radical production to contribute in this environment, an alternative mechanism to oxidize hydroquinones is required. We show here that aspen wood undergoing decay by the oxalate producer Postia placenta contained both 2,5-dimethoxyhydroquinone and laccase activity. Mass spectrometric analysis of proteins extracted from the wood identified a putative laccase (Joint Genome Institute P. placenta protein identification number 111314), and heterologous expression of the corresponding gene confirmed this assignment. Ultrafiltration experiments with liquid pressed from the biodegrading wood showed that a high-molecular-weight component was required for it to oxidize 2,5-dimethoxyhydroquinone rapidly and that this component was replaceable by P. placenta laccase. The purified laccase oxidized 2,5-dimethoxyhydroquinone with a second-order rate constant near 10(4) M(-1) s(-1), and measurements of the H(2)O(2) produced indicated that approximately one perhydroxyl radical was generated per hydroquinone supplied. Using these values and a previously developed computer model, we estimate that the quantity of reactive oxygen species produced by P. placenta laccase in wood is large enough that it likely contributes to incipient decay.

Induction of extracellular hydroxyl radical production by white-rot fungi through quinone redox cycling

A simple strategy for the induction of extracellular hydroxyl radical (OH) production by white-rot fungi is presented. It involves the incubation of mycelium with quinones and Fe(3+)-EDTA. Succinctly, it is based on the establishment of a quinone redox cycle catalyzed by cell-bound dehydrogenase activities and the ligninolytic enzymes (laccase and peroxidases). The semiquinone intermediate produced by the ligninolytic enzymes drives OH production by a Fenton reaction (H(2)O(2) + Fe(2+) --> OH + OH(-) + Fe(3+)). H(2)O(2) production, Fe(3+) reduction, and OH generation were initially demonstrated with two Pleurotus eryngii mycelia (one producing laccase and versatile peroxidase and the other producing just laccase) and four quinones, 1,4-benzoquinone (BQ), 2-methoxy-1,4-benzoquinone (MBQ), 2,6-dimethoxy-1,4-benzoquinone (DBQ), and 2-methyl-1,4-naphthoquinone (menadione [MD]). In all cases, OH radicals were linearly produced, with the highest rate obtained with MD, followed by DBQ, MBQ, and BQ. These rates correlated with both H(2)O(2) levels and Fe(3+) reduction rates observed with the four quinones. Between the two P. eryngii mycelia used, the best results were obtained with the one producing only laccase, showing higher OH production rates with added purified enzyme. The strategy was then validated in Bjerkandera adusta, Phanerochaete chrysosporium, Phlebia radiata, Pycnoporus cinnabarinus, and Trametes versicolor, also showing good correlation between OH production rates and the kinds and levels of the ligninolytic enzymes expressed by these fungi. We propose this strategy as a useful tool to study the effects of OH radicals on lignin and organopollutant degradation, as well as to improve the bioremediation potential of white-rot fungi.

Engineered nanomaterial transformation under oxidative environmental conditions: development of an in vitro biomimetic assay

Once released into the environment, engineered nanomaterials may be transformed by microbially mediated redox processes altering their toxicity and fate. Little information currently exists on engineered nanomaterial transformation under environmentally relevant conditions. Here, we report the development of an in vitro biomimetic assay for investigation of nanomaterial transformation under simulated oxidative environmental conditions. The assay is based on the extracellular hydroquinone-driven Fenton's reaction used by lignolytic fungi. We demonstrate the utility of the assay using CdSe(core)/ZnS(shell) quantum dots (QDs) functionalized with poly(ethylene glycol). QD transformation was assessed by UV-visible spectroscopy, inductively coupled plasma-optical emission spectroscopy, dynamic light scattering, transmission electron microscopy (TEM), and energy dispersive X-ray spectroscopy (EDX). QDs were readily degraded under simulated oxidative environmental conditions: the ZnS shell eroded and cadmium was released from the QD core. TEM, electron diffraction analysis, and EDX of transformed QDs revealed formation of amorphous Se aggregates. The biomimetic hydroquinone-driven Fenton's reaction degraded QDs to a larger extent than did H202 and classical Fenton's reagent (H2O2 + Fe2+). This assay provides a new method to characterize transformations of nanoscale materials expected to occur under oxidative environmental conditions.

Cloning and characterization of the genes encoding the high-affinity iron-uptake protein complex Fet3/Ftr1 in the basidiomycete Phanerochaete chrysosporium

MCO1, a multicopper oxidase from Phanerochaete chrysosporium exhibiting strong ferroxidase activity, has recently been described. This enzyme shows biochemical and structural similarities with the yeast Fet3p, a type I membrane glycoprotein that efficiently oxidizes Fe(II) to Fe(III) for its subsequent transport to the intracellular compartment by the iron permease Ftr1p. The genome database of P. chrysosporium was searched to verify whether it includes a canonical fet3 in addition to mco1, and single copies of fet3 and ftr1 orthologues were found, separated by a divergent promoter. Pc-fet3 encodes a 628 aa protein that exhibits overall identities of about 40 % with other reported Fet3 proteins. In addition to a secretion signal, it has a C-terminal transmembrane domain, characteristic of these cell-surface-attached ferroxidases. Structural modelling of Pc-Fet3 revealed that the active site has all the residues known to be essential for ferroxidase activity. Pc-ftr1 encodes a 393 aa protein that shows about 38 % identity with several Ftr1 proteins from ascomycetes. Northern hybridization studies showed that the mRNA levels of both genes are reduced upon supplementation of the growth medium with iron, supporting the functional coupling of Fet3 and Ftr1 proteins in vivo.

Fungal hydroquinones contribute to brown rot of wood

The fungi that cause brown rot of wood initiate lignocellulose breakdown with an extracellular Fenton system in which Fe(2+) and H(2)O(2) react to produce hydroxyl radicals (.OH), which then oxidize and cleave the wood holocellulose. One such fungus, Gloeophyllum trabeum, drives Fenton chemistry on defined media by reducing Fe(3+) and O(2) with two extracellular hydroquinones, 2,5-dimethoxyhydroquinone (2,5-DMHQ) and 4,5-dimethoxycatechol (4,5-DMC). However, it has never been shown that the hydroquinones contribute to brown rot of wood. We grew G. trabeum on spruce blocks and found that 2,5-DMHQ and 4,5-DMC were each present in the aqueous phase at concentrations near 20 microM after 1 week. We determined rate constants for the reactions of 2,5-DMHQ and 4,5-DMC with the Fe(3+)-oxalate complexes that predominate in wood undergoing brown rot, finding them to be 43 l mol(-1) s(-1) and 65 l mol(-1) s(-1) respectively. Using these values, we estimated that the average amount of hydroquinone-driven .OH production during the first week of decay was 11.5 micromol g(-1) dry weight of wood. Viscometry of the degraded wood holocellulose coupled with computer modelling showed that a number of the same general magnitude, 41.2 micromol oxidations per gram, was required to account for the depolymerization that occurred in the first week. Moreover, the decrease in holocellulose viscosity was correlated with the measured concentrations of hydroquinones. Therefore, hydroquinone-driven Fenton chemistry is one component of the biodegradative arsenal that G. trabeum expresses on wood.

Outlines of an “exploding” network of metabolites generated from the fluoroquinolone enrofloxacin by the brown rot fungus Gloeophyllum striatum

Degradation of the veterinary fluoroquinolone antibiotic enrofloxacin (EFL) was studied with three strains of Gloeophyllum, basidiomycetous fungi thought to produce extracellular hydroxyl radicals. Metabolites generated in a mineral medium were analyzed by combined high-performance liquid chromatography/high-resolution electrospray ionization mass spectrometry. Their origin was inferred from peak doublets representing 12C and 14C isotopomers detected at a defined proportion. From each exact molecular mass, the molecular formula was derived for which the most probable chemical structure was postulated, using for guidance 18 known EFL metabolites. All supernatants provided similar metabolite patterns, with the most comprehensive consisting of 87 compounds. These metabolites belonged to five families headed by EFL, its oxidatively decarboxylated or defluorinated congeners, an isatin-, and an anthranilic acid-type derivative. Metabolites hydroxylated in the aromatic part suggested the formation of three catechols and two oxidizable ortho-aminophenol-type compounds. After oxidation to the respective ortho-quinones or ortho-quinone imines and oxidative ring cleavage at one of three alternative sites, the formation of various cis,cis-muconic acid-type derivatives is likely, one of which could be detected. Anthranilic acid-type compounds provided two additional sites for ortho-aminophenol formation and aromatic ring cleavage. An "exploding" network of diverse EFL congeners produced by Gloeophyllum suggests the broad utility of our model for studying biodegradation.

Purification, identification and molecular cloning of glycoside hydrolase family 15 glucoamylase from the brown-rot basidiomyceteFomitopsis palustris

The brown-rot basidiomycete Fomitopsis palustris produces a major extracellular enzyme of 72 kDa when the fungus is incubated in cellulose culture with 0.2% cellobiose. This protein was purified by column chromatography, and the amino acid sequences of its proteolytic fragments were analyzed. The N-terminal amino acid sequence of one of the fragments showed high identity with fungal glycoside hydrolase family 15 glucoamylases. As its kinetic efficiency increased in proportion to the degree of polymerization of the substrate, the protein was identified as a glucoamylase. A cDNA encoding the glucoamylase (gla) was cloned by reverse transcriptase PCR.

Processive endoglucanase active in crystalline cellulose hydrolysis by the brown rot basidiomycete Gloeophyllum trabeum

Brown rot basidiomycetes have long been thought to lack the processive cellulases that release soluble sugars from crystalline cellulose. On the other hand, these fungi remove all of the cellulose, both crystalline and amorphous, from wood when they degrade it. To resolve this discrepancy, we grew Gloeophyllum trabeum on microcrystalline cellulose (Avicel) and purified the major glycosylhydrolases it produced. The most abundant extracellular enzymes in these cultures were a 42-kDa endoglucanase (Cel5A), a 39-kDa xylanase (Xyn10A), and a 28-kDa endoglucanase (Cel12A). Cel5A had significant Avicelase activity--4.5 nmol glucose equivalents released/min/mg protein. It is a processive endoglucanase, because it hydrolyzed Avicel to cellobiose as the major product while introducing only a small proportion of reducing sugars into the remaining, insoluble substrate. Therefore, since G. trabeum is already known to produce a beta-glucosidase, it is now clear that this brown rot fungus produces enzymes capable of yielding assimilable glucose from crystalline cellulose.

Differential stress-induced regulation of two quinone reductases in the brown rot basidiomycete Gloeophyllum trabeum

Quinone reductases (QRDs) have two important functions in the basidiomycete Gloeophyllum trabeum, which causes brown rot of wood. First, a QRD is required to generate biodegradative hydroxyl radicals via redox cycling between two G. trabeum extracellular metabolites, 2,5-dimethoxyhydroquinone (2,5-DMHQ) and 2,5-dimethoxy-1,4-benzoquinone (2,5-DMBQ). Second, because 2,5-DMBQ is cytotoxic and 2,5-DMHQ is not, a QRD is needed to maintain the intracellular pool of these metabolites in the reduced form. Given their importance in G. trabeum metabolism, QRDs could prove useful targets for new wood preservatives. We have identified two G. trabeum genes, each existing in two closely related, perhaps allelic variants, that encode QRDs in the flavodoxin family. Past work with QRD1 and heterologous expression of QRD2 in this study confirmed that both genes encode NADH-dependent, flavin-containing QRDs. Real-time reverse transcription PCR analyses of liquid- and wood-grown cultures showed that qrd1 expression was maximal during secondary metabolism, coincided with the production of 2,5-DMBQ, and was moderately up-regulated by chemical stressors such as quinones. By contrast, qrd2 expression was maximal during fungal growth when 2,5-DMBQ levels were low, yet was markedly up-regulated by chemical stress or heat shock. The total QRD activity in lysates of G. trabeum mycelium was significantly enhanced by induction beforehand with a cytotoxic quinone. The promoter of qrd2 contains likely antioxidant, xenobiotic, and heat shock elements, absent in qrd1, that probably explain the greater response of qrd2 transcription to stress. We conclude from these results that QRD1 is the enzyme G. trabeum routinely uses to detoxify quinones during incipient wood decay and that it could also drive the biodegradative quinone redox cycle. However, QRD2 assumes a more important role when the mycelium is stressed.