Detection of lignin peroxidase and xylanase by immunocytochemical labeling in wood decayed by basidiomycetes

Fluorescent Imaging of Extracellular Fungal Enzymes Bound onto Plant Cell Walls

Lignocelluloytic enzymes are industrially applied as biocatalysts for the deconstruction of recalcitrant plant biomass. To study their biocatalytic and physiological function, the assessment of their binding behavior and spatial distribution on lignocellulosic material is a crucial prerequisite. In this study, selected hydrolases and oxidoreductases from the white rot fungus Phanerochaete chrysosporium were localized on model substrates as well as poplar wood by confocal laser scanning microscopy. Two different detection approaches were investigated: direct tagging of the enzymes and tagging specific antibodies generated against the enzymes. Site-directed mutagenesis was employed to introduce a single surface-exposed cysteine residue for the maleimide site-specific conjugation. Specific polyclonal antibodies were produced against the enzymes and were labeled using N-hydroxysuccinimide (NHS) ester as a cross-linker. Both methods allowed the visualization of cell wall-bound enzymes but showed slightly different fluorescent yields. Using native poplar thin sections, we identified the innermost secondary cell wall layer as the preferential attack point for cellulose-degrading enzymes. Alkali pretreatment resulted in a partial delignification and promoted substrate accessibility and enzyme binding. The methods presented in this study are suitable for the visualization of enzymes during catalytic biomass degradation and can be further exploited for interaction studies of lignocellulolytic enzymes in biorefineries.

Wood degradation by Fomitiporia mediterranea M. Fischer: Physiologic, metabolomic and proteomic approaches

Fomitiporia mediterranea (Fmed) is one of the main fungal species found in grapevine wood rot, also called "amadou," one of the most typical symptoms of grapevine trunk disease Esca. This fungus is functionally classified as a white-rot, able to degrade all wood structure polymers, i.e., hemicelluloses, cellulose, and the most recalcitrant component, lignin. Specific enzymes are secreted by the fungus to degrade those components, namely carbohydrate active enzymes for hemicelluloses and cellulose, which can be highly specific for given polysaccharide, and peroxidases, which enable white-rot to degrade lignin, with specificities relating to lignin composition as well. Furthermore, besides polymers, a highly diverse set of metabolites often associated with antifungal activities is found in wood, this set differing among the various wood species. Wood decayers possess the ability to detoxify these specific extractives and this ability could reflect the adaptation of these fungi to their specific environment. The aim of this study is to better understand the molecular mechanisms used by Fmed to degrade wood structure, and in particular its potential adaptation to grapevine wood. To do so, Fmed was cultivated on sawdust from different origins: grapevine, beech, and spruce. Carbon mineralization rate, mass loss, wood structure polymers contents, targeted metabolites (extractives) and secreted proteins were measured. We used the well-known white-rot model Trametes versicolor for comparison. Whereas no significant degradation was observed with spruce, a higher mass loss was measured on Fmed grapevine culture compared to beech culture. Moreover, on both substrates, a simultaneous degradation pattern was demonstrated, and proteomic analysis identified a relative overproduction of oxidoreductases involved in lignin and extractive degradation on grapevine cultures, and only few differences in carbohydrate active enzymes. These results could explain at least partially the adaptation of Fmed to grapevine wood structural composition compared to other wood species, and suggest that other biotic and abiotic factors should be considered to fully understand the potential adaptation of Fmed to its ecological niche. Proteomics data are available via ProteomeXchange with identifier PXD036889.

Immunological approaches to plant cell wall and biomass characterization: immunolocalization of glycan epitopes

Plant cell walls are dynamic structures that show changes in composition and configuration depending on the developmental stage, biotic, and abiotic factors. Therefore, it is necessary to have tools for visualizing the components of the cell wall in situ at any stage. Here, we describe how specific monoclonal antibodies can be used to examine the distribution of plant cell wall glycan epitopes at the whole plant, tissue, cell, and subcellular levels. Understanding the basic cell wall structure is essential for devising efficient strategies to convert cell walls to fermentable sugars for ethanol production.

Versatile derivatives of carbohydrate-binding modules for imaging of complex carbohydrates approaching the molecular level of resolution

The innate binding specificity of different carbohydrate-binding modules (CBMs) offers a versatile approach for mapping the chemistry and structure of surfaces that contain complex carbohydrates. We have employed the distinct recognition properties of a double His-tagged recombinant CBM tagged with semiconductor quantum dots for direct imaging of crystalline cellulose at the molecular level of resolution, using transmission and scanning transmission electron microscopy. In addition, three different types of CBMs from families 3, 6, and 20 that exhibit different carbohydrate specificities were each fused with either green fluorescent protein (GFP) or red fluorescent protein (RFP) and employed for double-labeling fluorescence microscopy studies of primary cell walls and various mixtures of complex carbohydrate target molecules. CBM probes can be used for characterizing both native complex carbohydrates and engineered biomaterials.

Iron-regulated proteins in Phanerochaete chrysosporium and Lentinula edodes: differential analysis by sodium dodecyl sulfate polyacrylamide gel electrophoresis and two-dimensional polyacrylamide gel electrophoresis profiles

Sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and two-dimensional gel electrophoresis (2-DE) were used to identify iron-responsive proteins in the white-rot species (Phanerochaete chrysosporium and Lentinula edodes), by comparing the differential patterns of cellular and membrane proteins obtained from iron-sufficient and iron-deficient mycelia. Six cellular proteins induced by iron restriction have been observed in SDS-PAGE for P. chrysosporium and twelve for L. edodes. In 2-DE, the numbers of iron-restricted induced proteins were 12 and 9, respectively, in a resolution range of 15-60 kDa and pI 4.5-8.1. SDS-PAGE for the plasma membrane protein did not show differences, whereas the outer-membrane protein profile showed 6 and 5 proteins induced by iron depletion in P. chrysosporium and L. edodes, respectively. The results presented here are important data to unravel mechanisms of biosynthesis and/or transport of the iron-complexing agents in ligninolytic fungi and to further correlate them to the ligninolytic processes.

Modes of cell-wall degradation of Sphagnum fuscum by Acremonium cf. curvulum and Oidiodendron maius

Electron microscopy of cryo-fractured hyaline leaf cells of Sphagnum fuscum Klinggr. revealed that their cell walls consist of three layers: a thick central layer flanked on either side by a thinner, amorphous layer. Acremonium cf. curvulum W. Gams and Oidiodendron maius Barron, both isolated from partly decomposed S. fuscum plants, were capable of degrading leaf cell walls of Sphagnum. Where hyphae of A. curvulum accumulated, the amorphous, outer wall layer of S. fuscum was first fragmented and then removed. The exposed central wall layer consisted of bundles of microfibrils embedded in an amorphous matrix material. After the matrix material and the inner surface wall layer were mostly removed, degradation of microfibrils occurred and localized voids were produced. Unlike A. cf. curvulum, O. maius degraded all wall components more or less simultaneously. In both fungi, active and autolysing hyphae frequently occurred in proximity on the Sphagnum leaves.Key words: hyphomycetes, peat, phenolics, cellulose, SEM.

Copper-dependent depolymerization of lignin in the presence of fungal metabolite, pyridine

Thus far, it has not been recognized that copper complexes are able to depolymerize lignin under physiological conditions of white rot decay. However, we have found that both phenolic and non-phenolic synthetic lignins were intensively depolymerized by Cu(II) and lipid hydroperoxide model compounds in the presence of a metabolite of ligninolytic fungi, pyridine at room temperature in aqueous media. Treatment of 14C-labeled oxygen-prebleached kraft pulp (OKP) by the copper-dependent reaction evidenced effectiveness of this reaction for the delignification of kraft pulps. In contrast to the organic peroxide system, Cu(II)/pyr/H2O2 system was much less effective for the lignin depolymerization. However, treatment of unbleached kraft pulp (UKP) by Cu(II)/H2O2 and Cu(II)/pyr/H2O2 systems demonstrated that the damage of cellulose was suppressed by the coordination of pyridine although high brightness gain was obtained independently of the presence of the coordinator. Spin trapping experiments demonstrated that not hydroxyl radical but superoxide anion is involved in the Cu(II)/pyr/H2O2 system. This finding not only introduces a new concept of non-enzymatic lignin biodegradation by wood-degrading fungi but also presents a new strategy for decomposing lignin and lignin-related compounds by copper complexes and peroxide-producing system.

Electron and fluorescence microscopy of extracellular glucan and aryl-alcohol oxidase during wheat-straw degradation by Pleurotus eryngii

The ligninolytic fungus Pleurotus eryngii grown in liquid medium secreted extracellular polysaccharide (87% glucose) and the H2O2-producing enzyme aryl-alcohol oxidase (AAO). The production of both was stimulated by wheat-straw. Polyclonal antibodies against purified AAO were obtained, and a complex of glucanase and colloidal gold was prepared. With these tools, the localization of AAO and extracellular glucan in mycelium from liquid medium and straw degraded under solid-state fermentation conditions was investigated by transmission electron microscopy (TEM) and fluorescence microscopy. These studies revealed that P. eryngii produces a hyphal sheath consisting of a thin glucan layer. This sheath appeared to be involved in both mycelial adhesion to the straw cell wall during degradation and AAO immobilization on hyphal surfaces, with the latter evidenced by double labelling. AAO distribution during differential degradation of straw tissues was observed by immunofluorescence microscopy. Finally, TEM immunogold studies confirmed that AAO penetrates the plant cell wall during P. eryngii degradation of wheat straw.

Biodegradation of lignin

Lignin is an aromatic polymer forming up to 30% of woody plant tissues, providing rigidity and resistance to biological attack. Because it is insoluble, chemically complex, and lacking in hydrolysable linkages, lignin is a difficult substrate for enzymatic depolymerization. Certain fungi, mostly basidiomycetes, are the only organisms able to extensively biodegrade it; white-rot fungi can completely mineralize lignin, whereas brown-rot fungi merely modify lignin while removing the carbohydrates in wood. Several oxidative and reductive extracellular enzymes (lignin peroxidase, manganese peroxidase, laccase, and cellobiose:quinone oxidoreductase) have been isolated from ligninolytic fungi; the role of these enzymes in lignin biodegradation is being intensively studied. Enzymatic combustion, a process wherein enzymes generate reactive intermediates, but do not directly control the reactions leading to lignin breakdown, has been proposed as the mechanism of lignin biodegradation. The economic consequences of lignin biodegradation include wood decay and the biogeochemical cycling of woody biomass. Efforts are being made to harness the delignifying abilities of white-rot fungi to aid wood and straw pulping and pulp bleaching. These fungi can also be used to degrade a variety of pollutants in wastewaters and soils, to increase the digestibility of lignocellulosics, and possibly to bioconvert lignins to higher value products. Key words: delignification, white-rot fungi, biobleaching, lignin peroxidase, manganese peroxidase, laccase.

Wood degradation by Phellinus noxius: ultrastructure and cytochemistry

An ultrastructural and cytochemical investigation of the development of Phellinus noxius, a white-rot fungus, in wood chips of Betula papyrifera was done to gain insight into the cellular mechanisms of wood cell wall degradation. Extracellular sheaths and microhyphae were seen to be involved in wood colonization. Close association was observed between these fungal structures and wood cell walls at both early and advanced stages of wood alteration. Fungal sheaths were often seen deep inside host cell walls, sometimes enclosing residual wood fragments. Investigations using gold probes indicated the occurrence of β-1,3-glucans within the fungal sheaths, while β-1,4-glucans were detected only within the fungal septa. The positive reaction with the PATAg test revealed that polysaccharides such as β-1,6-glucans were important components of the sheath. Chitin, pectin, β-glucosides, galactosamine, mannose, sialic acid, fucose, and fimbrial proteins were not found to be present in the sheath. Our data suggest that extracellular sheaths and microphyphae produced by P. noxius during wood cell wall colonization play an important role in wood degradation.Key words: cellulose, Phellinus, sheath, wood degradation.

Fungal degradation of recalcitrant nonphenolic lignin structures without lignin peroxidase

Lignin peroxidases (LiPs) are likely catalysts of ligninolysis in many white-rot fungi, because they have the unusual ability to depolymerize the major, recalcitrant, non-phenolic structures of lignin. Some white-rot fungi have been reported to lack LiP when grown on defined medium, but it is not clear whether they exhibit full ligninolytic competence under these conditions. To address this problem, we compared the abilities of a known LiP producer, Phanerochaete chrysosporium, with those of a reported nonproducer, Ceriporiopsis subvermispora, to degrade a synthetic lignin with normal phenolic content, a lignin with all phenolic units blocked, and a dimer, 1-(4-ethoxy-3-methoxyphenyl)-2-(2-methoxyphenoxy)propane-1,3-diol, that represents the major nonphenolic structure in lignin. P. chrysosporium mineralized all three models rapidly in defined medium, but C. subvermispora showed appreciable activity only toward the more labile phenolic compound under these conditions. However, in wood, its natural environment, C. subvermispora mineralized all of the models as rapidly as P. chrysosporium did. Defined media therefore fail to elicit a key component of the ligninolytic system in C. subvermispora. A double-labeling experiment with the dimeric model showed that a LiP-dependent pathway was responsible for at least half of dimer mineralization in wood by P. chrysosporium but was responsible for no more than 6-7% of mineralization by C. subvermispora in wood. Therefore, C. subvermispora has mechanisms for degradation of nonphenolic lignin that are as efficient as those in P. chrysosporium but that do not depend on LiP.

Ubiquity of lignin-degrading peroxidases among various wood-degrading fungi

Phanerochaete chrysosporium is rapidly becoming a model system for the study of lignin biodegradation. Numerous studies on the physiology, biochemistry, chemistry, and genetics of this system have been performed. However, P. chrysosporium is not the only fungus to have a lignin-degrading enzyme system. Many other ligninolytic species of fungi, as well as other distantly related organisms which are known to produce lignin peroxidases, are described in this paper. In this study, we demonstrated the presence of the peroxidative enzymes in nine species not previously investigated. The fungi studied produced significant manganese peroxidase activity when they were grown on an oak sawdust substrate supplemented with wheat bran, millet, and sucrose. Many of the fungi also exhibited laccase and/or glyoxal oxidase activity. Inhibitors present in the medium prevented measurement of lignin peroxidase activity. However, Western blots (immunoblots) revealed that several of the fungi produced lignin peroxidase proteins. We concluded from this work that lignin-degrading peroxidases are present in nearly all ligninolytic fungi, but may be expressed differentially in different species. Substantial variability exists in the levels and types of ligninolytic enzymes produced by different white not fungi.

A Cytochemical Study of Extracellular Sheaths Associated with Rigidoporus lignosus during Wood Decay

An ultrastructural and cytochemical investigation of the development of Rigidoporus lignosus , a white-rot fungus inoculated into wood blocks, was carried out to gain better insight into the structure and role of the extracellular sheaths produced by this fungus during wood degradation. Fungal sheaths had a dense or loose fibrillar appearance and were differentiated from the fungal cell wall early after wood inoculation. Close association between extracellular fibrils and wood cell walls was observed at both early and advanced stages of wood alteration. Fungal sheaths were often seen deep in host cell walls, sometimes enclosing residual wood fragments. Specific gold probes were used to investigate the chemical nature of R. lignosus sheaths. While labeling of chitin, pectin, β-1,4- and β-1,3-glucans, β-glucosides, galactosamine, mannose, sialic acid, RNA, fucose, and fimbrial proteins over fungal sheaths did not succeed, galactose residues and laccase (a fungal phenoloxidase) were found to be present. The positive reaction of sheaths with the PATAg test indicates that polysaccharides such as β-1,6-glucans are important components. Our data suggest that extracellular sheaths produced by R. lignosus during host cell colonization play an important role in wood degradation. Transportation of lignin-degrading enzymes by extracellular fibrils indicates that alteration of plant polymers may occur within fungal sheaths. It is also proposed that R. lignosus sheaths may be involved in recognition mechanisms in fungal cell-wood surface interactions.

Spatial and temporal accumulation of mRNAs encoding two common lignin peroxidases in Phanerochaete chrysosporium

Accumulation of peroxidases and their mRNAs was localized in colonies of Phanerochaete chrysosporium sandwiched between perforated polycarbonate membranes. Northern (RNA) blot analyses of colonial rings and in situ hybridizations with specific probes for manganese(II)-dependent peroxidase (MnP-1) and lignin peroxidase (LiP H8) mRNAs indicated that the expression of MnP-1 and Lip H8 genes started simultaneously in the central area of 3-day-old colonies. With time the signals for both transcripts spread to more-peripheral areas while decreasing in intensity. Furthermore, the appearance of MnP protein, as detected with specific immune serum, immediately followed accumulation of the MnP-1 mRNA transcript. However, LiP protein could be detected only some time after accumulation of LiP H8 mRNA.

Ultrastructural and Immunocytochemical Studies on the H 2 O 2 -Producing Enzyme Pyranose Oxidase in Phanerochaete chrysosporium Grown under Liquid Culture Conditions

The ultrastructural distribution of the sugar-oxidizing enzyme pyranose 2-oxidase (POD) in hyphae of Phanerochaete chrysosporium K-3 grown under liquid culture conditions optimal for the enzyme's production was studied by transmission electron microscopy immunocytochemistry. Using the 3-dimethylaminobenzoic acid-3-methyl-2-benzothiazolinone hydrazone hydrochloride H 2 O 2 peroxidase spectrophotometric assay, POD was detected in mycelial extracts from days 7 to 18, with maximum activity recorded on day 12. Onset of POD activity occurred in the secondary phase of hyphal development at a time of stationary growth, glucose limitation, and pH increase. POD was also detected extracellularly in the culture fluid from days 7 to 18, with maximum activity recorded on day 13. At early stages of development (3 to 4 days), using anti-POD antibodies and immunogold labeling, POD was localized in multivesicular and electron-dense bodies and in cell membrane regions. After 10 to 12 days of growth, at maximum POD activity, POD was concentrated within the periplasmic space where it was associated with membrane-bound vesicles and other membrane structures. At later stages of development (17 to 18 days), when the majority of hyphae were lysed, POD was observed associated with residual intracellular membrane systems and vesicles. Transmission electron microscopy immunocytochemical studies also demonstrated an extracellular distribution of the enzyme at the stationary growth phase, showing its association with fungal extracellular slime. In studies of ligninolytic cultures of the same fungus, POD was found to have a similar intracellular and extracellular distribution in slime as that recorded for cultures grown with cornsteep. POD's peripheral cytoplasmic distribution shows similarities to the cellular distribution of that reported previously for H 2 O 2 -dependent lignin and manganese peroxidases in P. chrysosporium.

Immunocytochemical localization of laccase L1 in wood decayed by Rigidoporus lignosus

The cellular distribution of laccase L1 during degradation of wood chips by Rigidoporus lignosus, a tropical white rot fungus, was investigated by using anti-laccase L1 polyclonal antisera in conjunction with immunolabeling techniques. The enzyme was localized in the fungal cytoplasm and was associated with the plasmalemma and the fungal cell wall. An extracellular sheath, often observed around fungal cells, often contained laccase molecules. Diffusion of laccase within apparently unaltered wood was seldom observed. The enzyme penetrated all degraded cell walls, from the secondary wall toward the primary wall, including the middle lamella. Xylem cells showing advanced stages of decay were sometimes devoid of significant labeling. These data suggest that the initial attack on wood was not performed by laccase L1 of R. lignosus. Previous alteration of the lignocellulose complex may facilitate the movement of laccase within the wood cell walls. This immunogold study revealed that laccase localization during wood degradation seems limited not in space but in time.

Medium temperature epoxy resin for immunocytochemistry: Quetol 651 with water

The addition of 1% water to the epoxy resin Quetol increased the labeling intensity of the sample. The significant decrease of the curing temperature of the epoxy resin may assist in preservation of antigens. Water may also reduce the cross-linkage of the resin allowing more antigen to be available to the antibodies. The modified Quetol resin is an option for use in immunocytochemistry studies.

Comparative Studies of Delignification Caused by Ganoderma Species

Isolates of six species of Ganoderma in the G. lucidum complex were evaluated for their ability to decay wood of Quercus hypoleucoides A. Camus and Abies concolor (Gord. and Glend.) Lindl. ex. Hildebr. by using in vitro agar block decay tests. Morphological, ultrastructural, and chemical studies of decayed wood were used to determine the extent of delignification or simultaneous decay caused by each species of Ganoderma. All species decayed both white fir and oak wood; however, less percent weight loss (%WL) occurred in white fir than oak. In white fir, isolates of two undescribed Ganoderma species (RLG16161, RLG16162, JEA615, and JEA625) caused significantly higher%WL (21 to 26%) than that in G. colossum, G. oregonense, G. meredithiae, and G. zonatum (10 to 16%). Only Ganoderma sp. isolates JEA615 and JEA625 caused delignification, with JEA615 causing a lignin-to-glucose gram loss ratio of 1.6:1. Morphological and ultrastructural studies confirmed delignification by this fungus and showed that some delignification had occurred by all of the species, although areas of delignification were limited to small regions adjacent to simultaneously decayed cells. In oak, G. colossum caused significantly less%WL (22 to 35%) than the other species (38 to 52%). All of the species, except G. meredithiae, caused delignification with lignin-to-glucose gram loss ratios ranging from 1.4 to 4.9:1. Extensive delignification by isolates of G. colossum and G. oregonense was observed; moderate delignification was caused by the other species. Ganoderma meredithiae caused a simultaneous decay, with only small localized regions of cells delignified, while delignification by G. zonatum was irregular, with specific zones within the cell wall delignified. The thermophilic and chlamydosporic G. colossum has the capacity to cause extensive delignification and appears ideally suited for use in lignin degradation studies and biotechnological applications of lignin-degrading fungi.