Preferential degradation of phenolic lignin units by two white rot fungi

Phenolic degradation by catechol dioxygenases is associated with pathogenic fungi with a necrotrophic lifestyle in the Ceratocystidaceae

Fungal species of the Ceratocystidaceae grow on their host plants using a variety of different lifestyles, from saprophytic to highly pathogenic. Although many genomes of fungi in the Ceratocystidaceae are publicly available, it is not known how the genes that encode catechol dioxygenases (CDOs), enzymes involved in the degradation of phenolic plant defense compounds, differ among members of the Ceratocystidaceae. The aim of this study was therefore to identify and characterize the genes encoding CDOs in the genomes of Ceratocystidaceae representatives. We found that genes encoding CDOs are more abundant in pathogenic necrotrophic species of the Ceratocystidaceae and less abundant in saprophytic species. The loss of the CDO genes and the associated 3-oxoadipate catabolic pathway appears to have occurred in a lineage-specific manner. Taken together, this study revealed a positive association between CDO gene copy number and fungal lifestyle in Ceratocystidaceae representatives.

White rot fungal impact on the evolution of simple phenols during decay of silver fir wood by UHPLC-HQOMS

INTRODUCTION

Silver fir (Abies alba Mill.) is one of the most valuable conifer wood species in Europe. Among the main opportunistic pathogens that cause root and butt rot on silver fir are Armillaria ostoyae and Heterobasidion abietinum. Due to the different enzymatic pools of these wood-decay fungi, different strategies in metabolizing the phenols were available.

OBJECTIVE

This work explores the changes in phenolic compounds during silver fir wood degradation.

METHODOLOGY

Phenols were analyzed before and after fungus inoculation in silver fir macerated wood after 2, 4 and 6 months. All samples were analyzed using high-performance liquid chromatography coupled to a hybrid quadrupole-orbitrap mass spectrometer.

RESULTS

Thirteen compounds, including simple phenols, alkylphenyl alcohols, hydroxybenzoketones, hydroxycinnamaldehydes, hydroxybenzaldehydes, hydroxyphenylacetic acids, hydroxycinnamic acids, hydroxybenzoic acids and hydroxycoumarins, were detected. Pyrocatechol, coniferyl alcohol, acetovanillone, vanillin, benzoic acid, 4-hydroxybenzoic acid and vanillic acid contents decreased during the degradation process. Methyl vanillate, ferulic acid and p-coumaric were initially produced and then degraded. Scopoletin was accumulated. Pyrocatechol, acetovanillone and methyl vanillate were found for the first time in both degrading and non-degrading wood of silver fir.

CONCLUSIONS

Despite differences in the enzymatic pool, both fungi caused a significant decrease in the amounts of phenolic compounds with the accumulation of the only scopoletin. Principal component analysis revealed an initial differentiation between the degradation activity of the two fungal species during degradation, but similar phenolic contents at the end of wood degradation.

Obtaining Cellulose-Available Raw Materials by Pretreatment of Common Agro-Forestry Residues With Pleurotus spp

The goals of the present study were to characterize the profile of ligninolytic enzymes in five Pleurotus species and determine their ability to delignify eight common agro-forestry residues. Generally, corn stalks were the optimal inducer of Mn-dependent peroxidase activity, but the activity peak was noted after wheat straw fermentation by P. eryngii (3066.92 U/L). P. florida was the best producer of versatile peroxidase, especially on wheat straw (3028.41 U/L), while apple sawdust induced the highest level of laccase activity in P. ostreatus (49601.82 U/L). Efficiency of the studied enzymes was expressed in terms of substrate dry matter loss, which was more substrate-than species-dependent. Reduction of substrate dry mass ranged between 24.83% in wheat straw and 8.83% in plum sawdust as a result of fermentation with P. florida and P. pulmonarius, respectively. The extent of delignification of the studied substrates was different, ranging from 51.97% after wheat straw fermentation by P. pulmonarius to 4.18% in grapevine sawdust fermented by P. ostreatus. P. pulmonarius was also characterized by the highest cellulose enrichment (6.54) and P. ostreatus by very low one (1.55). The tested biomass is a highly abundant but underutilized source of numerous value-added products, and a cocktail of ligninolytic enzymes of Pleurotus spp. could be useful for its environmentally and economically friendly transformation.

Identifying the Interunit Linkages Connecting Free Phenolic Terminal Units in Lignin

Understanding the linkages connecting phenolic terminal and nonphenolic units in complex branched polymer, lignin, is crucial to facilitate efficient and selective valorization of lignin. In this study, the interunit linkages connecting phenolic units are identified by premethylation of the phenolic hydroxy groups and thioacidolysis-desulfuration. Interestingly, the phenolic units are found to be connected by only β-5, β-1, and β-O-4 linkages. The phenolic unit abundance is approximately 20 %. The result reveals that lignin polymerization terminates with the three linkages by a coupling between a monomer and the polymer terminus, which is reasonably explained by the radical coupling mechanism. Unexpectedly, 5-5, 4-O-5, and β-β linkages connecting the phenolic units are not detected, indicating that these units are further elongated to form nonphenolic units. This study reveals the linkage types connecting phenolic and nonphenolic units and their elongation mechanisms.

An overview of fungal pretreatment processes for anaerobic digestion: Applications, bottlenecks and future needs

Lignin modifying or extracellular enzymes secreted by the white rot fungi have the ability of degrading wide range of lignocellulosic substrates and organic pollutants. Lignocellulosic biomass, despite being a renewable source of energy, is difficult to hydrolyse (hydrolysis being rate-limiting stage in anaerobic digestion process). Various pre-treatment techniques like physical, chemical, thermo-chemical and biological to enhance the accessibility of microbes to carbohydrates have been studied. Recently, usage of white- rot fungi in a biological pre-treatment technique have received renewed interest due to its low cost and eco-friendly nature. This review deals with: a) lignocellulosic biomass recalcitrance, b) various pre-treatment techniques and its economic feasibility, c) delignification and hydrolysis mechanism using white-rot fungi, d) factors controlling white-rot fungi pre- treatment process, and e) improvement in methane production through solid-state anaerobic digestion of white-rot fungi pre-treated lignocellulosic biomass. Finally a future perspective is also included.

Greener Routes to Biomass Waste Valorization: Lignin Transformation Through Electrocatalysis for Renewable Chemicals and Fuels Production

Lignin valorization is essential for biorefineries to produce fuels and chemicals for a sustainable future. Today's biorefineries pursue profitable value propositions for cellulose and hemicellulose; however, lignin is typically used mainly for its thermal energy value. To enhance the profit potential for biorefineries, lignin valorization would be a necessary practice. Lignin valorization is greatly advantaged when biomass carbon is retained in the fuel and chemical products and when energy quality is enhanced by electrochemical upgrading. Though lignin upgrading and valorization are very desirable in principle, many barriers involved in lignin pretreatment, extraction, and depolymerization must be overcome to unlock its full potential. This Review addresses the electrochemical transformation of various lignins with the aim of gaining a better understanding of many of the barriers that currently exist in such technologies. These studies give insight into electrochemical lignin depolymerization and upgrading to value-added commodities with the end goal of achieving a global low-carbon circular economy.

Accelerated directed evolution of dye-decolorizing peroxidase using a bacterial extracellular protein secretion system (BENNY)

Background

Dye-decolorizing peroxidases (DyPs) are haem-containing peroxidases that show great promises in industrial biocatalysis and lignocellulosic degradation. Through the use of Escherichia coli osmotically-inducible protein Y (OsmY) as a bacterial extracellular protein secretion system (BENNY), we successfully developed a streamlined directed evolution workflow to accelerate the protein engineering of DyP4 from Pleurotus ostreatus strain PC15.

Result

After 3 rounds of random mutagenesis with error-prone polymerase chain reaction (epPCR) and 1 round of saturation mutagenesis, we obtained 4D4 variant (I56V, K109R, N227S and N312S) that displays multiple desirable phenotypes, including higher protein yield and secretion, higher specific activity (2.7-fold improvement in k_cat/K_m) and higher H₂O₂ tolerance (sevenfold improvement based on IC₅₀).

Conclusion

To our best knowledge, this is the first report of applying OsmY to simplify the directed evolution workflow and to direct the extracellular secretion of a haem protein such as DyP4.

Electronic supplementary material

The online version of this article (10.1186/s40643-019-0255-7) contains supplementary material, which is available to authorized users.

Mechanistic insight in the selective delignification of wheat straw by three white-rot fungal species through quantitative 13C-IS py-GC-MS and whole cell wall HSQC NMR

BACKGROUND

The white-rot fungi Ceriporiopsis subvermispora (Cs), Pleurotus eryngii (Pe), and Lentinula edodes (Le) have been shown to be high-potential species for selective delignification of plant biomass. This delignification improves polysaccharide degradability, which currently limits the efficient lignocellulose conversion into biochemicals, biofuels, and animal feed. Since selectivity and time efficiency of fungal delignification still need optimization, detailed understanding of the underlying mechanisms at molecular level is required. The recently developed methodologies for lignin quantification and characterization now allow for the in-depth mapping of fungal modification and degradation of lignin and, thereby, enable resolving underlying mechanisms.

RESULTS

Wheat straw treated by two strains of Cs (Cs1 and Cs12), Pe (Pe3 and Pe6) and Le (Le8 and Le10) was characterized using semi-quantitative py-GC-MS during fungal growth (1, 3, and 7 weeks). The remaining lignin after 7 weeks was quantified and characterized using 13C lignin internal standard based py-GC-MS and whole cell wall HSQC NMR. Strains of the same species showed similar patterns of lignin removal and degradation. Cs and Le outperformed Pe in terms of extent and selectivity of delignification (Cs ≥ Le >> Pe). The highest lignin removal [66% (w/w); Cs1] was obtained after 7 weeks, without extensive carbohydrate degradation (factor 3 increased carbohydrate-to-lignin ratio). Furthermore, though after treatment with Cs and Le comparable amounts of lignin remained, the structure of the residual lignin vastly differed. For example, Cα-oxidized substructures accumulated in Cs treated lignin up to 24% of the total aromatic lignin, a factor two higher than in Le-treated lignin. Contrarily, ferulic acid substructures were preferentially targeted by Le (and Pe). Interestingly, Pe-spent lignin was specifically depleted of tricin (40% reduction). The overall subunit composition (H:G:S) was not affected by fungal treatment.

CONCLUSIONS

Cs and Le are both able to effectively and selectively delignify wheat straw, though the underlying mechanisms are fundamentally different. We are the first to identify that Cs degrades the major β-O-4 ether linkage in grass lignin mainly via Cβ-O-aryl cleavage, while Cα-Cβ cleavage of inter-unit linkages predominated for Le. Our research provides a new insight on how fungi degrade lignin, which contributes to further optimizing the biological upgrading of lignocellulose.

Development of a genetically programed vanillin-sensing bacterium for high-throughput screening of lignin-degrading enzyme libraries

BACKGROUND

Lignin is a potential biorefinery feedstock for the production of value-added chemicals including vanillin. A huge amount of lignin is produced as a by-product of the paper industry, while cellulosic components of plant biomass are utilized for the production of paper pulp. In spite of vast potential, lignin remains the least exploited component of plant biomass due to its extremely complex and heterogenous structure. Several enzymes have been reported to have lignin-degrading properties and could be potentially used in lignin biorefining if their catalytic properties could be improved by enzyme engineering. The much needed improvement of lignin-degrading enzymes by high-throughput selection techniques such as directed evolution is currently limited, as robust methods for detecting the conversion of lignin to desired small molecules are not available.

RESULTS

We identified a vanillin-inducible promoter by RNAseq analysis of Escherichia coli cells treated with a sublethal dose of vanillin and developed a genetically programmed vanillin-sensing cell by placing the 'very green fluorescent protein' gene under the control of this promoter. Fluorescence of the biosensing cell is enhanced significantly when grown in the presence of vanillin and is readily visualized by fluorescence microscopy. The use of fluorescence-activated cell sorting analysis further enhances the sensitivity, enabling dose-dependent detection of as low as 200 µM vanillin. The biosensor is highly specific to vanillin and no major response is elicited by the presence of lignin, lignin model compound, DMSO, vanillin analogues or non-specific toxic chemicals.

CONCLUSIONS

We developed an engineered E. coli cell that can detect vanillin at a concentration as low as 200 µM. The vanillin-sensing cell did not show cross-reactivity towards lignin or major lignin degradation products including vanillin analogues. This engineered E. coli cell could potentially be used as a host cell for screening lignin-degrading enzymes that can convert lignin to vanillin.

Role of surface tryptophan for peroxidase oxidation of nonphenolic lignin

BACKGROUND

Despite claims as key enzymes in enzymatic delignification, very scarce information on the reaction rates between the ligninolytic versatile peroxidase (VP) and lignin peroxidase (LiP) and the lignin polymer is available, due to methodological difficulties related to lignin heterogeneity and low solubility.

RESULTS

Two water-soluble sulfonated lignins (from Picea abies and Eucalyptus grandis) were chemically characterized and used to estimate single electron-transfer rates to the H₂O₂-activated Pleurotus eryngii VP (native enzyme and mutated variant) transient states (compounds I and II bearing two- and one-electron deficiencies, respectively). When the rate-limiting reduction of compound II was quantified by stopped-flow rapid spectrophotometry, from fourfold (softwood lignin) to over 100-fold (hardwood lignin) lower electron-transfer efficiencies (k_3app values) were observed for the W164S variant at surface Trp164, compared with the native VP. These lignosulfonates have ~20-30 % phenolic units, which could be responsible for the observed residual activity. Therefore, methylated (and acetylated) samples were used in new stopped-flow experiments, where negligible electron transfer to the W164S compound II was found. This revealed that the residual reduction of W164S compound II by native lignin was due to its phenolic moiety. Since both native lignins have a relatively similar phenolic moiety, the higher W164S activity on the softwood lignin could be due to easier access of its mono-methoxylated units for direct oxidation at the heme channel in the absence of the catalytic tryptophan. Moreover, the lower electron transfer rates from the derivatized lignosulfonates to native VP suggest that peroxidase attack starts at the phenolic lignin moiety. In agreement with the transient-state kinetic data, very low structural modification of lignin, as revealed by size-exclusion chromatography and two-dimensional nuclear magnetic resonance, was obtained during steady-state treatment (up to 24 h) of native lignosulfonates with the W164S variant compared with native VP and, more importantly, this activity disappeared when nonphenolic lignosulfonates were used.

CONCLUSIONS

We demonstrate for the first time that the surface tryptophan conserved in most LiPs and VPs (Trp164 of P. eryngii VPL) is strictly required for oxidation of the nonphenolic moiety, which represents the major and more recalcitrant part of the lignin polymer.

Enzymatic hydrolysis of biomass from wood

Current research and development in cellulosic ethanol production has been focused mainly on agricultural residues and dedicated energy crops such as corn stover and switchgrass; however, woody biomass remains a very important feedstock for ethanol production. The precise composition of hemicellulose in the wood is strongly dependent on the plant species, therefore different types of enzymes are needed based on hemicellulose complexity and type of pretreatment. In general, hardwood species have much lower recalcitrance to enzymes than softwood. For hardwood, xylanases, beta‐xylosidases and xyloglucanases are the main hemicellulases involved in degradation of the hemicellulose backbone, while for softwood the effect of mannanases and beta‐mannosidases is more relevant. Furthermore, there are different key accessory enzymes involved in removing the hemicellulosic fraction and increasing accessibility of cellulases to the cellulose fibres improving the hydrolysis process. A diversity of enzymatic cocktails has been tested using from low to high densities of biomass (2–20% total solids) and a broad range of results has been obtained. The performance of recently developed commercial cocktails on hardwoods and softwoods will enable a further step for the commercialization of fuel ethanol from wood.

From gene to biorefinery: microbial β-etherases as promising biocatalysts for lignin valorization

The set-up of biorefineries for the valorization of lignocellulosic biomass will be core in the future to reach sustainability targets. In this area, biomass-degrading enzymes are attracting significant research interest for their potential in the production of chemicals and biofuels from renewable feedstock. Glutathione-dependent β-etherases are emerging enzymes for the biocatalytic depolymerization of lignin, a heterogeneous aromatic polymer abundant in nature. They selectively catalyze the reductive cleavage of β-O-4 aryl-ether bonds which account for 45–60% of linkages present in lignin. Hence, application of β-etherases in lignin depolymerization would enable a specific lignin breakdown, selectively yielding (valuable) low-molecular-mass aromatics. Albeit β-etherases have been biochemically known for decades, only very recently novel β-etherases have been identified and thoroughly characterized for lignin valorization, expanding the enzyme toolbox for efficient β-O-4 aryl-ether bond cleavage. Given their emerging importance and potential, this mini-review discusses recent developments in the field of β-etherase biocatalysis covering all aspects from enzyme identification to biocatalytic applications with real lignin samples.

Interactions between fungal growth, substrate utilization, and enzyme production during solid substrate cultivation of Phanerochaete chrysosporium on cotton stalks

Fungal pretreatment, using lignin-degrading microorganisms to improve lignocellulosic feedstocks with minimal energy input, is a potential alternative to physiochemical pretreatment methods. Identifying the kinetics for fungal pretreatment during solid substrate cultivation is needed to help establish the processing conditions for effective scale up of this technology. In this study, a set of mathematical models were proposed for describing the interactions between holocellulose consumption, lignin degradation, cellulase, ligninolytic enzyme, and the growth of Phanerochaete chrysosporium during a 14 day fungal pretreatment process. Model parameters were estimated and validated by the System Biology Toolbox in MatLab. Developed models provided sufficiently accurate predictions for fungal growth (R (2) = 0.97), holocellulose consumption (R (2) = 0.97), lignin degradation (R (2) = 0.93) and ligninolytic enzyme production (R (2) = 0.92), and fair prediction for cellulase production (R (2) = 0.61). The models provide valuable information for understanding the interactive mechanisms in biological systems as well as for fungal pretreatment process scale up and improvement.

Temporal alterations in the secretome of the selective ligninolytic fungus Ceriporiopsis subvermispora during growth on aspen wood reveal this organism's strategy for degrading lignocellulose

The white-rot basidiomycetes efficiently degrade all wood cell wall polymers. Generally, these fungi simultaneously degrade cellulose and lignin, but certain organisms, such as Ceriporiopsis subvermispora, selectively remove lignin in advance of cellulose degradation. However, relatively little is known about the mechanism of selective ligninolysis. To address this issue, C. subvermispora was grown in liquid medium containing ball-milled aspen, and nano-liquid chromatography-tandem mass spectrometry was used to identify and estimate extracellular protein abundance over time. Several manganese peroxidases and an aryl alcohol oxidase, both associated with lignin degradation, were identified after 3 days of incubation. A glycoside hydrolase (GH) family 51 arabinofuranosidase was also identified after 3 days but then successively decreased in later samples. Several enzymes related to cellulose and xylan degradation, such as GH10 endoxylanase, GH5_5 endoglucanase, and GH7 cellobiohydrolase, were detected after 5 days. Peptides corresponding to potential cellulose-degrading enzymes GH12, GH45, lytic polysaccharide monooxygenase, and cellobiose dehydrogenase were most abundant after 7 days. This sequential production of enzymes provides a mechanism consistent with selective ligninolysis by C. subvermispora.

Role of laccase as an enzymatic pretreatment method to improve lignocellulosic saccharification

The saccharification of wheat straw was improved when an incubation step was performed withTrametes versicolorlaccase (TvL) and the mediator 1-hydroxybenzotriazole (1-HBT) prior to an alkaline peroxide extraction (APE).

New colorimetric screening assays for the directed evolution of fungal laccases to improve the conversion of plant biomass

Background

Fungal laccases are multicopper oxidases with huge applicability in different sectors. Here, we describe the development of a set of high-throughput colorimetric assays for screening laccase libraries in directed evolution studies.

Results

Firstly, we designed three colorimetric assays based on the oxidation of sinapic acid, acetosyringone and syringaldehyde with λ_max of 512, 520 and 370 nm, respectively. These syringyl-type phenolic compounds are released during the degradation of lignocellulose and can act as laccase redox mediators. The oxidation of the three compounds by low and high-redox potential laccases evolved in Saccharomyces cerevisiae produced quantifiable and linear responses, with detection limits around 1 mU/mL and CV values below 16%. The phenolic substrates were also suitable for pre-screening mutant libraries on solid phase format. Intense colored-halos were developed around the yeast colonies secreting laccase. Furthermore, the oxidation of violuric acid to its iminoxyl radical (λ_max of 515 nm and CV below 15%) was devised as reporter assay for laccase redox potential during the screening of mutant libraries from high-redox potential laccases. Finally, we developed three dye-decolorizing assays based on the enzymatic oxidation of Methyl Orange (470 nm), Evans Blue (605 nm) and Remazol Brilliant Blue (640 nm) giving up to 40% decolorization yields and CV values below 18%. The assays were reliable for direct measurement of laccase activity or to indirectly explore the oxidation of mediators that do not render colored products (but promote dye decolorization). Every single assay reported in this work was tested by exploring mutant libraries created by error prone PCR of fungal laccases secreted by yeast.

Conclusions

The high-throughput screening methods reported in this work could be useful for engineering laccases for different purposes. The assays based on the oxidation of syringyl-compounds might be valuable tools for tailoring laccases precisely enhanced to aid biomass conversion processes. The violuric assay might be useful to preserve the redox potential of laccase whilst evolving towards new functions. The dye-decolorizing assays are useful for engineering ad hoc laccases for detoxification of textile wastewaters, or as indirect assays to explore laccase activity on other natural mediators.

Evaluation of Biological Pretreatment of Rubberwood with White Rot Fungi for Enzymatic Hydrolysis

e effects of biological pretreatment on the rubberwood (Hevea brasiliensis), was evaluated after cultivation of white rot fungi Ceriporiopsis subvermispora, Trametes versicolor, and a mixed culture of C. subvermispora and T. versicolor. The analysis of chemical compositions indicated that C. subvermispora had greater selectivity for lignin degradation with the highest lignin and hemicellulose loss at 45.06% and 42.08%, respectively, and lowest cellulose loss (9.50%) after 90 days among the tested samples. X-ray analysis showed that pretreated samples had a higher crystallinity than untreated samples. The sample pretreated by C. subvermispora presented the highest crystallinity of all the samples which might be caused by the selective degradation of amorphous components. Fourier transform infrared (FT-IR) spectroscopy demonstrated that the content of lignin and hemicellulose decreased during the biological pretreatment process. A study on hydrolysis of rubberwood treated with C. subvermispora, T. versicolor, and mixed culture for 90 days resulted in an increased sugar yield of about 27.67%, 16.23%, and 14.20%, respectively, as compared with untreated rubberwood (2.88%). The results obtained demonstrate that rubberwood is a potential raw material for industrial applications and white rot fungus C. subevermispora provides an effective method for improving the enzymatic hydrolysis of rubberwood.

Structural characterization of alkaline hydrogen peroxide pretreated grasses exhibiting diverse lignin phenotypes

BACKGROUND

For cellulosic biofuels processes, suitable characterization of the lignin remaining within the cell wall and correlation of quantified properties of lignin to cell wall polysaccharide enzymatic deconstruction is underrepresented in the literature. This is particularly true for grasses which represent a number of promising bioenergy feedstocks where quantification of grass lignins is particularly problematic due to the high fraction of p-hydroxycinnamates. The main focus of this work is to use grasses with a diverse range of lignin properties, and applying multiple lignin characterization platforms, attempt to correlate the differences in these lignin properties to the susceptibility to alkaline hydrogen peroxide (AHP) pretreatment and subsequent enzymatic deconstruction.

RESULTS

We were able to determine that the enzymatic hydrolysis of cellulose to to glucose (i.e. digestibility) of four grasses with relatively diverse lignin phenotypes could be correlated to total lignin content and the content of p-hydroxycinnamates, while S/G ratios did not appear to contribute to the enzymatic digestibility or delignification. The lignins of the brown midrib corn stovers tested were significantly more condensed than a typical commercial corn stover and a significant finding was that pretreatment with alkaline hydrogen peroxide increases the fraction of lignins involved in condensed linkages from 88-95% to ~99% for all the corn stovers tested, which is much more than has been reported in the literature for other pretreatments. This indicates significant scission of β-O-4 bonds by pretreatment and/or induction of lignin condensation reactions. The S/G ratios in grasses determined by analytical pyrolysis are significantly lower than values obtained using either thioacidolysis or 2DHSQC NMR due to presumed interference by ferulates.

CONCLUSIONS

It was found that grass cell wall polysaccharide hydrolysis by cellulolytic enzymes for grasses exhibiting a diversity of lignin structures and compositions could be linked to quantifiable changes in the composition of the cell wall and properties of the lignin including apparent content of the p-hydroxycinnamates while the limitations of S/G estimation in grasses is highlighted.

Fungal strain and incubation period affect chemical composition and nutrient availability of wheat straw for rumen fermentation

Eleven white-rot fungi were examined for their potency to degrade lignin and to improve the rumen fermentability of wheat straw. The straw was inoculated with the fungi and incubated under solid state conditions at 24°C for 0-49 days to determine changes in in vitro gas production and chemical composition. Results show that some fungi could degrade lignin by as much as 63%, yet the delignification was highly correlated with the degradation of hemicellulose (r=0.96). Reduction in lignin was poorly (r=0.47), but the ratio between lignin and cellulose loss was strongly (r=0.87) correlated with the increase in gas production. Treatment with Ceriporiopsis subvermispora for 49 days increased total gas production of the straw from 200 to 309 ml/g organic matter (OM). It was concluded that some fungi highly selective for lignin and not for cellulose are able to improve the nutritive value of wheat straw as a ruminant feed.

Lignin-degrading peroxidases from genome of selective ligninolytic fungus Ceriporiopsis subvermispora

The white-rot fungus Ceriporiopsis subvermispora delignifies lignocellulose with high selectivity, but until now it has appeared to lack the specialized peroxidases, termed lignin peroxidases (LiPs) and versatile peroxidases (VPs), that are generally thought important for ligninolysis. We screened the recently sequenced C. subvermispora genome for genes that encode peroxidases with a potential ligninolytic role. A total of 26 peroxidase genes was apparent after a structural-functional classification based on homology modeling and a search for diagnostic catalytic amino acid residues. In addition to revealing the presence of nine heme-thiolate peroxidase superfamily members and the unexpected absence of the dye-decolorizing peroxidase superfamily, the search showed that the C. subvermispora genome encodes 16 class II enzymes in the plant-fungal-bacterial peroxidase superfamily, where LiPs and VPs are classified. The 16 encoded enzymes include 13 putative manganese peroxidases and one generic peroxidase but most notably two peroxidases containing the catalytic tryptophan characteristic of LiPs and VPs. We expressed these two enzymes in Escherichia coli and determined their substrate specificities on typical LiP/VP substrates, including nonphenolic lignin model monomers and dimers, as well as synthetic lignin. The results show that the two newly discovered C. subvermispora peroxidases are functionally competent LiPs and also suggest that they are phylogenetically and catalytically intermediate between classical LiPs and VPs. These results offer new insight into selective lignin degradation by C. subvermispora.

Fungal pretreatment: An alternative in second-generation ethanol from wheat straw

The potential of a fungal pretreatment combined with a mild alkali treatment to replace or complement current physico-chemical methods for ethanol production from wheat straw has been investigated. Changes in substrate composition, secretion of ligninolytic enzymes, enzymatic hydrolysis efficiency and ethanol yield after 7, 14 and 21 days of solid-state fermentation were evaluated. Most fungi degraded lignin with variable selectivity degrees, although only eight of them improved sugar recovery compared to untreated samples. Glucose yield after 21 days of pretreatment with Poria subvermispora and Irpex lacteus reached 69% and 66% of cellulose available in the wheat straw, respectively, with an ethanol yield of 62% in both cases. Conversions from glucose to ethanol reached around 90%, showing that no inhibitors were generated during this pretreatment. No close correlations were found between ligninolytic enzymes production and sugar yields.

Laccases and their natural mediators: biotechnological tools for sustainable eco-friendly processes

Laccases are oxidoreductases which oxidize a variety of aromatic compounds using oxygen as the electron acceptor and producing water as by-product. The interest for these old enzymes (first described in 19th century) has progressively increased due to their outstanding biotechnological applicability. The presence of redox mediators is required for a number of biotechnological applications, providing the oxidation of complex substrates not oxidized by the enzyme alone. The efficiency of laccase-mediator systems to degrade recalcitrant compounds has been demonstrated, but still the high cost and possible toxicity of artificial mediators hamper their application at the industrial scale. Here, we present a general outlook of how alternative mediators can change this tendency. We focus on phenolic compounds related to lignin polymer that promotes the in vitro transformation of recalcitrant non-phenolic structures by laccase and are seemingly the natural mediators of laccases. The use of eco-friendly mediators easily available from lignocellulose, could contribute to the industrial implementation of laccases and the development of the 21th century biorefineries.

Isolation and characterization of an ether-type polyurethane-degrading micro-organism and analysis of degradation mechanism by Alternaria sp

AIMS

To degrade ether-type polyurethane (ether-PUR), ether-PUR-degrading micro-organism was isolated. Moreover, ether-PUR-degrading mechanisms were analysed using model compounds of ether-PUR.

METHODS AND RESULTS

A fungus designated as strain PURDK2, capable of changing the configuration of ether-PUR, has been isolated. This isolated fungus was identified as Alternaria sp. Using a scanning electron microscope, the grid structure of ether-PUR was shown to be melted and disrupted by the fungus. The degradation of ether-PUR by the fungus was analysed, and the ether-PUR was degraded by the fungus by about 27.5%. To analyse the urethane-bond degradation by the fungus, a degraded product of ethylphenylcarbamate was analysed using GC/MS. Aniline and ethanol were detected by degradation with the supernatant, indicating that the fungus secreted urethane-bond-degrading enzyme(s). PURDK2 also degraded urea bonds when diphenylmethane-4,4'-dibutylurea was used as a substrate.

CONCLUSIONS

The enzyme(s) from PURDK2 degraded urethane and urea bonds to convert the high molecular weight structure of ether-PUR to small molecules; and then the fungus seems to use the small molecules as an energy source.

SIGNIFICANCE AND IMPACT OF THE STUDY

Ether-PUR-degrading fungus, strain PURDK2, was isolated, and the urethane- and urea-bonds-degrading enzymes from strain PURDK2 could contribute to the material recycling of ether-PUR.

Microbial pretreatment of cotton stalks by submerged cultivation of Phanerochaete chrysosporium

This study used the fungus, Phanerochaete chrysosporium, to pretreat cotton stalks with two methods, shallow stationary and agitated cultivation, at three supplemental salt concentrations. Pretreatment efficiencies were compared by evaluating lignin degradation, solid recovery and carbohydrate availability over a 14-day period. Shallow stationary cultivation with no salts gave 20.7% lignin degradation along with 76.3% solid recovery and 29.0% carbohydrate availability. The highest lignin degradation of 33.9% at a corresponding solid recovery and carbohydrate availability of 67.8% and 18.4%, respectively, was obtained through agitated cultivation with Modified NREL salts. Cultivation beyond 10 days did not significantly increase lignin degradation during 14 days of pretreatment. Manganese addition during shallow stationary and agitated cultivation resulted in higher solid recoveries of over 80% but lower lignin degradation. Although agitated cultivation resulted in better delignification, results indicate that pretreatment under submerged shallow stationary conditions provides a better balance between lignin degradation and carbohydrate availability.

Bio-softening of mature coconut husk for facile coir recovery

Bio-softening of the mature coconut husk using Basidiomyceteous fungi was attempted to recover the soft and whiter fibers. The process was faster and more efficient in degrading lignin and toxic phenolics. Phanerochaete chrysosporium, Pleurotus eryngii and Ceriporiopsis subvermispora were found to degrade lignin efficiently without any appreciable loss of cellulose, yielding good quality fiber ideal for dyeing.

Reusing ethyl acetate and aqueous exhausted fractions of dry olive mill residue by saprobe fungi

Some saprobe fungi (Phlebia radiata, Trametes versicolor, Coriolopsis rigida, Pycnoporus cinnabarinus, Fomes sclerodermus or Pleurotus pulmonarius) were able to bioconvert the ethyl acetate fraction (DEAF) and the corresponding aqueous exhausted fraction (EAF) of dry olive mill residue (DOR), reducing their phytotoxicity on Lepidium sativum seeds. Large amount of hydroxytyrosol together with other eight monomeric phenols were found in the native DEAF fraction, which represents a good source of antioxidants. P. radiata, T. versicolor and F. sclerodermus caused an effective phytotoxicity reduction of EAF in the concentration range of 25-3 gl(-1). In particular, in the range between 12.5 and 3 gl(-1), the EAF samples inoculated with P. radiata and F. sclerodermus surprisingly stimulated the germinability of L. sativum, suggesting their use as a potential biofertilizer. This is the first report which showed the bioconversion of the above fractions in shorter time with respect to the previous findings concerning DOR. The possible implications of laccase in the decrease of DEAF and EAF phytotoxicity was also discussed.

Degradation of lignin in wheat straw during growth of the oyster mushroom (Pleurotus ostreatus) using off-line thermochemolysis with tetramethylammonium hydroxide and solid-state (13)C NMR

The oyster mushroom (Pleurotus ostreatus) is widely cultivated on wheat straw (Triticum aestivum); however, there is a need to better understand the relationship between the chemical composition of the compost and mushroom growth. Wheat straw was degraded over a period of 63 days by P. ostreatus during which time it was sampled at weekly intervals. Off-line thermochemolysis with tetramethylammonium hydroxide and solid-state (13)C NMR were then used in the molecular characterization of the undegraded wheat straw and the degraded samples. The degraded wheat straw samples had a lower proportion of syringyl- to guaiacyl-derived moieties and cinnamyl- to guaiacyl-derived moieties than the undegraded control. There were increases in both guaiacyl and syringyl acid to aldehyde ratios with composting time, which showed that side-chain oxidation has been mediated by P. ostreatus. The (13)C NMR spectra confirmed the increase in carboxyl content but indicated that the overall lignin and methoxyl contents remained relatively constant, although some nonsystematic variations were observed. The spectra also showed a decrease in amorphous noncellulosic polysaccharides in relation to the crystalline cellulose upon degradation.

A search for ligninolytic peroxidases in the fungus pleurotus eryngii involving alpha-keto-gamma-thiomethylbutyric acid and lignin model dimers

Because there is some controversy concerning the ligninolytic enzymes produced by Pleurotus species, ethylene release from alpha-keto-gamma-thiomethylbutyric acid (KTBA), as described previously for Phanerochaete chrysosporium lignin peroxidase (LiP), was used to assess the oxidative power of Pleurotus eryngii cultures and extracellular proteins. Lignin model dimers were used to confirm the ligninolytic capabilities of enzymes isolated from liquid and solid-state fermentation (SSF) cultures. Three proteins that oxidized KTBA in the presence of veratryl alcohol and H2O2 were identified (two proteins were found in liquid cultures, and one protein was found in SSF cultures). These proteins are versatile peroxidases that act on Mn2+, as well as on simple phenols and veratryl alcohol. The two peroxidases obtained from the liquid culture were able to degrade a nonphenolic beta-O-4 dimer, yielding veratraldehyde, as well as a phenolic dimer which is not efficiently oxidized by P. chrysosporium peroxidases. The former reaction is characteristic of LiP. The third KTBA-oxidizing peroxidase oxidized only the phenolic dimer (in the presence of Mn2+). Finally, a fourth Mn2+-oxidizing peroxidase was identified in the SSF cultures on the basis of its ability to oxidize KTBA in the presence of Mn2+. This enzyme is related to the Mn-dependent peroxidase of P. chrysosporium because it did not exhibit activity with veratryl alcohol and Mn-independent activity with dimers. These results show that P. eryngii produces three types of peroxidases that have the ability to oxidize lignin but lacks a typical LiP. Similar enzymes (in terms of N-terminal sequence and catalytic properties) are produced by other Pleurotus species. Some structural aspects of P. eryngii peroxidases related to the catalytic properties are discussed.

Metabolism of phenanthrene by the white rot fungus Pleurotus ostreatus

The white rot fungus Pleurotus ostreatus, grown for 11 days in basidiomycetes rich medium containing [14C] phenanthrene, metabolized 94% of the phenanthrene added. Of the total radioactivity, 3% was oxidized to CO2. Approximately 52% of phenanthrene was metabolized to trans-9,10-dihydroxy-9,10-dihydrophenanthrene (phenanthrene trans-9,10-dihydrodiol) (28%), 2,2'-diphenic acid (17%), and unidentified metabolites (7%). Nonextractable metabolites accounted for 35% of the total radioactivity. The metabolites were extracted with ethyl acetate, separated by reversed-phase high-performance liquid chromatography, and characterized by 1H nuclear magnetic resonance, mass spectrometry, and UV spectroscopy analyses. 18O2-labeling experiments indicated that one atom of oxygen was incorporated into the phenanthrene trans-9,10-dihydrodiol. Circular dichroism spectra of the phenanthrene trans-9,10-dihydrodiol indicated that the absolute configuration of the predominant enantiomer was 9R,10R, which is different from that of the principal enantiomer produced by Phanerochaete chrysosporium. Significantly less phenanthrene trans-9,10-dihydrodiol was observed in incubations with the cytochrome P-450 inhibitor SKF 525-A (77% decrease), 1-aminobenzotriazole (83% decrease), or fluoxetine (63% decrease). These experiments with cytochrome P-450 inhibitors and 18O2 labeling and the formation of phenanthrene trans-9R,10R-dihydrodiol as the predominant metabolite suggest that P. ostreatus initially oxidizes phenanthrene stereoselectively by a cytochrome P-450 monoxygenase and that this is followed by epoxide hydrolase-catalyzed hydration reactions.