Efficient,environmentally-friendly and specific valorization of lignin: promising role of non-radical lignolytic enzymes

Lignin is the second most abundant bio-resource in nature. It is increasingly important to convert lignin into high value-added chemicals to accelerate the development of the lignocellulose biorefinery. Over the past several decades, physical and chemical methods have been widely explored to degrade lignin and convert it into valuable chemicals. Unfortunately, these developments have lagged because of several difficulties, of which high energy consumption and non-specific cleavage of chemical bonds in lignin remain the greatest challenges. A large number of enzymes have been discovered for lignin degradation and these are classified as radical lignolytic enzymes and non-radical lignolytic enzymes. Radical lignolytic enzymes, including laccases, lignin peroxidases, manganese peroxidases and versatile peroxidases, are radical-based bio-catalysts, which degrade lignins through non-specific cleavage of chemical bonds but can also catalyze the radical-based re-polymerization of lignin fragments. In contrast, non-radical lignolytic enzymes selectively cleave chemical bonds in lignin and lignin model compounds and, thus, show promise for use in the preparation of high value-added chemicals. In this mini-review, recent developments on non-radical lignolytic enzymes are discussed. These include recently discovered non-radical lignolytic enzymes, their metabolic pathways for lignin conversion, their recent application in the lignin biorefinery, and the combination of bio-catalysts with physical/chemical methods for industrial development of the lignin refinery.     

Effect of oxygenation conditions on submerged cultures of Phanerochaete chrysosporium

Summary The effect of the oxygen supply pattern on the onset and development of the lignolytic enzyme system of Phanerochaete chrysosporium was studied in submerged culture employing the serum bottle approach. Periodic or continuous flushing through the head phase, and continuous bubbling through the liquid phase with either oxygen (O₂) or air were applied. The nature of the O₂ supply had a crucial regulatory effect not only on the formation of lignin-degrading peroxidases but also on their decay and on the production of extracellular protease activity and polysaccharides. Continuous oxygenation or aeration increased the glucose consumption rate, extracellular protease activity and polysaccharides. Gassing with air, whether continuous or periodic, sustained Mn-peroxidase activity while ligninase was undetectable. Continuous O₂ supply speeded up ligninase decay, displaying a sharper maximum, while a broader maximum and slower decay of ligninase activity were observed when supplying periodic O₂. Cultures initially grown with free exposure to air displayed a higher but sharper ligninase activity maximum when shifted to continuous rather than periodic O₂ supply. In general, the higher levels of either polysaccharides or protease activity corresponded to the lower levels and faster decay of ligninase and Mn-peroxidase activities. Offprint requests to: H. E. Grethlein     

Chrysonila sitophila (TFB-27441): A hyperlignolytic strain

Summary C. sitophila strain TFB-27441 showed 2–3 times higher lignolytic activity thanPhanerochaete chrysosporium (BKM-F-1767 strain). Lignin had a marked effect on the ligninase activity indicating that some induction or activation mechanism is involved in lignin degradation byC. sitophila.     

Stability testing of ligninase and Mn-peroxidase from Phanerochaete chrysosporium

The white-rot fungus Phanerochaete chrysosporium produces extracellular peroxidases (ligninase and Mn-peroxidase) believed to be involved in lignin degradation. These extracellular enzymes have also been implicated in the degradation of recalcitrant pollutants by the organism. Commercial application of ligninase has been proposed both for biomechanical pulping of wood and for wastewater treatment. In vitro stability of lignin degrading enzymes will be an important factor in determining both the economic and technical feasibility of application for industrial uses, and also will be critical in optimizing commercial production of the enzymes. The effects of a number of variables on in vitro stability of ligninase and Mn-peroxidase are presented in this paper. Thermal stability of ligninase was found to improve by increasing pH and by increasing enzyme concentration. For a fixed pH and enzyme concentration, ligninase stability was greatly enhanced in the presence of its substrate veratryl alcohol (3,4-dimethoxybenzyl alcohol). Ligninase also was found to be inactivated by hydrogen peroxide in a second-order process that is proposed to involve the formation of the unreactive peroxidase intermediate Compound III. Mn-peroxidase was less susceptible to inactivation by peroxide, which corresponds to observations by others that Compound III of Mn-peroxidase forms less readily than Compound III of ligninase.     

Studies on compound I formation of the lignin peroxidase from Phanerochaete chrysosporium

Ligninase, isolated from the wood-destroying fungus Phanerochaete chrysosporium, catalyzes the oxidation of lignin and lignin-related compounds. Ligninase reacts with H2O2 to form the classical peroxidase intermediates Compounds I and II. We have determined the activation energy of ligninase Compound I formation to be 5.9 kcal/mol. The effect of pH and ionic strength on the rate of ligninase Compound I formation was studied. In contrast to all other peroxidases, no pH effect was observed. This is despite homology of active-site amino acids residues (Tien, M., and Tu, C.-P. D. (1987) Nature 326, 520-523) which are proposed to affect the pH profile of Compound I formation. Ligninase Compound I formation can also be supported by organic peroxides. The second-order rate constants with the organic peroxides are lower, suggesting that H2O2 is the preferred substrate.     

DyP-type peroxidases: a promising and versatile class of enzymes

DyP peroxidases comprise a novel superfamily of heme-containing peroxidases, which is unrelated to the superfamilies of plant and animal peroxidases. These enzymes have so far been identified in the genomes of fungi, bacteria, as well as archaea, although their physiological function is still unclear. DyPs are bifunctional enzymes displaying not only oxidative activity but also hydrolytic activity. Moreover, these enzymes are able to oxidize a variety of organic compounds of which some are poorly converted by established peroxidases, including dyes, β-carotene, and aromatic sulfides. Interestingly, accumulating evidence shows that microbial DyP peroxidases play a key role in the degradation of lignin. Owing to their unique properties, these enzymes are potentially interesting for a variety of biocatalytic applications. In this review, we deal with the biochemical and structural features of DyP-type peroxidases as well as their promising biotechnological potential.     

Selection and Improvement of Lignin-Degrading Microorganisms: Potential Strategy Based on Lignin Model-Amino Acid Adducts

The purpose of this investigation was to test a potential strategy for the ligninase-dependent selection of lignin-degrading microorganisms. The strategy involves covalently bonding amino acids to lignin model compounds in such a way that ligninase-catalyzed cleavage of the models releases the amino acids for growth nitrogen. Here we describe the synthesis of glycine-N-2-(3,4-dimethoxyphenyl)ethane-2-ol (I) and demonstrate that growth (as measured by mycelial nitrogen content) of the known lignin-degrading basidiomycete Phanerochaete chrysosporium Burds. with compound I as the nitrogen source depends on its production of ligninase. Ligninase is shown to catalyze the oxidative C—C cleavage of compound I, releasing glycine, formaldehyde, and veratraldehyde at a 1:1:1 stoichiometry. P. chrysosporium utilizes compound I as a nitrogen source, but only after the cultures enter secondary metabolism (day 3 of growth), at which time the ligninase and the other components of the ligninolytic system (lignin → CO₂) are expressed. Compound I and related adducts have potential not only in the isolation of lignin-degrading microbes but, perhaps of equal importance, in strain improvement.     

Degradation of environmental pollutants byPhanerochaete chrysosporium

The white rot fungi appear to be unique in their ability to degrade lignin by the secretion of hydrogen peroxide and a family of peroxidases now referred to as lignin peroxidases or simply ligninases. The fact that these enzymes are naturally secreted and seem to be capable of initiating the oxidation of lignin by a free-radical mechanism led to the proposal and demonstration that the white rot fungi are able to degrade a wide variety of normally very recalcitrant environmental pollutants. The mineralization of chemicals byPhanerochaete chrysosporium does seem to be dependent upon the lignin degrading system. Thus it should be possible to at least initiate degradation extracellularly, eliminating the need for absorption of the chemical. The nonspecific nature of the system gives the potential for oxidation of a wide variety of chemicals and even mixtures of chemicals. As the lignin peroxidases are synthesized and secreted in response to nutrient starvation there is no requirement for conditioning of the organism. Mineralization can occur in either a water or soil matrix using very economical agricultural or wood wastes as nutrients. The lignin peroxidases can be purified from the extracellular fluid quite easily by fast protein liquid chromatography. They are somewhat typical peroxidases but also have some unique properties. The oxidation of some xenobiotics has been demonstrated and cooxidation is also a possible mechanism.     

Oxidation of polycyclic aromatic hydrocarbons and dibenzo[p]-dioxins by Phanerochaete chrysosporium ligninase

The lignin peroxidase (ligninase) of Phanerochaete chrysosporium catalyzes the oxidation of a variety of lignin-related compounds. Here we report that this enzyme also catalyzes the oxidation of certain aromatic pollutants and compounds related to them, including polycyclic aromatic hydrocarbons with ionization potentials less than or equal to approximately 7.55 eV. This result demonstrates that the H2O2-oxidized states of lignin peroxidase are more oxidizing than the analogous states of classical peroxidases. Experiments with pyrene as the substrate showed that pyrene-1,6-dione and pyrene-1,8-dione are the major oxidation products (84% of total as determined by high performance liquid chromatography), and gas chromatography/mass spectrometry analysis of ligninase-catalyzed pyrene oxidations done in the presence of H2(18)O showed that the quinone oxygens come from water. We found that whole cultures of P. chrysosporium also transiently oxidize pyrene to these quinones. Experiments with dibenzo[p]dioxin and 2-chlorodibenzo[p]dioxin showed that they are also substrates for ligninase. The immediate product of dibenzo[p]dioxin oxidation is the dibenzo[p]dioxin cation radical, which was observed in enzymatic reactions by its electron spin resonance and visible absorption spectra. The cation radical mechanism of ligninase thus applies not only to lignin, but also to other environmentally significant aromatics.     

Role of fungal peroxidases in biological ligninolysis

The degradation of lignin by filamentous fungi is a major route for the recycling of photosynthetically fixed carbon, and the oxidative mechanisms employed have potential biotechnological applications. The lignin peroxidases (LiPs), manganese peroxidases (MnPs), and closely related enzymes of white rot basidiomycetes are likely contributors to fungal ligninolysis. Many of them cleave lignin model compounds to give products consistent with those found in residual white-rotted lignin, and at least some depolymerize synthetic lignins. However, none has yet been shown to delignify intact lignocellulose in vitro. The likely reason is that the peroxidases need to act in concert with small oxidants that can penetrate lignified tissues. Recent progress in the dissolution and NMR spectroscopy of plant cell walls may allow new inferences about the nature of the oxidants involved. Furthermore, increasing knowledge about the genomes of ligninolytic fungi may help us decide whether any of the peroxidases has an essential role.     

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.     

Role of Veratryl Alcohol in Regulating Ligninase Activity in Phanerochaete chrysosporium

Ligninase activity in Phanerochaete chrysosporium is stimulated by incubating cultures with various substrates for the enzyme, including veratryl (3,4-dimethoxybenzyl) alcohol, which is a secondary metabolite of this fungus. This study was designed to provide insight into the mechanism involved in this stimulation. Ligninase activity increased 2 to 4 h after the addition of exogenous veratryl alcohol to ligninolytic cultures. This increase was prevented by inhibitors of protein synthesis. Analysis of the extracellular proteins by high-performance anion-exchange liquid chromatography revealed increases in the amounts of some, but not all, ligninase species. The normal rapid decrease in ligninase activity in aging cultures was not prevented or retarded by veratryl alcohol, indicating that veratryl alcohol does not increase ligninase activity by protecting extant enzyme. We conclude that veratryl alcohol probably functions via an induction type of mechanism, affecting only certain ligninase species. Results with an isolated lignin indicate that lignin (or its biodegradation products) functions in the same way that veratryl alcohol does.     

Structure of the active site of lignin peroxidase isozyme H2: native enzyme, compound III, and reduced form.

The wood-degrading fungus Phanerochaete chrysosporium secretes a number of extracellular enzymes called lignin peroxidases which are involved in the degradation of both lignin and a number of persistent environmental pollutants. Lignin peroxidase isozyme H2, a glycosylated protein of approximately 40 kDa, contains a single heme. X-ray absorption spectroscopy (XAS) has been used to probe the local environment of the iron in the active site of resting enzyme, reduced enzyme, and compound III. For the native and reduced forms, respectively, the average Fe-pyrrole nitrogen distances are 2.055 and 2.02 A (+/- 0.015 A); the Fe-proximal nitrogen distance is 1.93 and 1.91 A (+/- 0.02 A) while the Fe-distal ligand distance is 2.17 and 2.10 A (+/- 0.03 A). Although the results are not as well-defined, the active-site structure of compound III is largely 2.02 +/- 0.015 A for the average Fe-pyrrole nitrogen distance, 1.90 +/- 0.02 for the Fe-proximal nitrogen, and 1.74 +/- 0.03 A for the Fe-distal ligand distance. The heme iron-pyrrole nitrogen distance is more expanded in ligninase H2 than in other peroxidases. The possible significance of this is discussed in relation to other heme proteins.     

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.     

Ligninase-mediated phenoxy radical formation and polymerization unaffected by cellobiose:quinone oxidoreductase

Phanerochete chrysosporium ligninase (+ H2O2) oxidized the lignin substructure-related compound acetosyringone to a phenoxy radical which was identified by ESR spectroscopy. Cellobiose:quinone oxidoreductase (CBQase) + cellobiose, previously suggested to be a phenoxy radical reducing system, was without effect on the radical. Ligninase polymerized guaiacol and it increased the molecular size of a synthetic lignin. These polymerizations, reflecting phenoxy radical coupling reactions, were also unaffected by the CBQase system. We conclude that ligninase catalyzes phenol polymerization via phenoxy radicals, which CBQase does not affect. The CBQase system also did not produce H2O2, and its physiological role remains obscure. Glucose oxidase + glucose did produce H2O2 as expected, but, like CBQase, it did not reduce the phenoxy radical of acetosyringone. Because intact cultures of P. chrysosporium depolymerize lignins, it is likely that phenol polymerization by ligninase is prevented or reversed in vivo by an as yet undescribed system.     

The suppression of AtPrx52 affects fibers but not xylem lignification in Arabidopsis by altering the proportion of syringyl units

Lignins result from the oxidative polymerization of three hydroxycinnamyl (p‐coumaryl, coniferyl and sinapyl) alcohols in a reaction mediated by peroxidases (EC 1.11.1.7) and laccases (EC 1.10.3.2), yielding H, G and S units, respectively. Although both acidic and basic peroxidases can oxidize p‐coumaryl and coniferyl alcohol, only basic peroxidases are able to oxidize sinapyl alcohol. The AtPrx52 from Arabidopsis is a basic peroxidase that has been reported to be highly homologous to the basic peroxidase of Zinnia elegans, the only peroxidase which has been unequivocally linked to lignin formation. Here, we show how the suppression of AtPrx52 causes a change in lignin composition, mainly at the level of stem interfascicular fibers. Quantification of lignins in two different atprx52 knock‐out mutants revealed a decrease of lignin amount compared with wild type. The S/G ratio, obtained by both nitrobenzene oxidation and thioacidolysis, indicated a decrease in S units in the atprx52 mutants. As deduced from Wiesner and mainly Mäule staining, this reduction in S unit content appears to be restricted to the interfascicular fibers. Moreover, quantitative polymerase chain reaction analysis in atprx52 plants showed a general downregulation of genes involved in lignin biosynthetic pathway, as well as genes related to secondary cell wall. On the other hand, other routes from phenylpropanoid metabolism were induced. Taken together, our results indicate that AtPrx52 is involved in the synthesis of S units in interfascicular fibers at late stages of the lignification process.     

Influence of Molecular Size and Ligninase Pretreatment on Degradation of Lignins by Xanthomonas sp. Strain 99

The purpose of this study was to examine the relationship between the molecular size of lignin in several preparations and extent of degradation (mineralization) by Xanthomonas sp. strain 99. The influence of ligninase pretreatment was also examined. Five synthetic lignins and one ¹⁴C-methylated spruce lignin were used. The extent of mineralization to ¹⁴CO₂ was greatest for the samples containing the most low-molecular-weight material, and the low-molecular-weight portions were preferentially (or perhaps solely) degraded. Pretreatment of the five synthetic lignins with crude ligninase increased their molecular size and decreased their degradability by the xanthomonad. Pretreatment of the methylated spruce lignin with crude ligninase caused both polymerization and depolymerization but resulted in a net decrease in bacterial degradability. Our results suggest that the xanthomonad can degrade lignins only up to a molecular weight of 600 to 1,000.     

Genomic Analysis Enlightens Agaricales Lifestyle Evolution and Increasing Peroxidase Diversity

As actors of global carbon cycle, Agaricomycetes (Basidiomycota) have developed complex enzymatic machineries that allow them to decompose all plant polymers, including lignin. Among them, saprotrophic Agaricales are characterized by an unparalleled diversity of habitats and lifestyles. Comparative analysis of 52 Agaricomycetes genomes (14 of them sequenced de novo) reveals that Agaricales possess a large diversity of hydrolytic and oxidative enzymes for lignocellulose decay. Based on the gene families with the predicted highest evolutionary rates—namely cellulose-binding CBM1, glycoside hydrolase GH43, lytic polysaccharide monooxygenase AA9, class-II peroxidases, glucose–methanol–choline oxidase/dehydrogenases, laccases, and unspecific peroxygenases—we reconstructed the lifestyles of the ancestors that led to the extant lignocellulose-decomposing Agaricomycetes. The changes in the enzymatic toolkit of ancestral Agaricales are correlated with the evolution of their ability to grow not only on wood but also on leaf litter and decayed wood, with grass-litter decomposers as the most recent eco-physiological group. In this context, the above families were analyzed in detail in connection with lifestyle diversity. Peroxidases appear as a central component of the enzymatic toolkit of saprotrophic Agaricomycetes, consistent with their essential role in lignin degradation and high evolutionary rates. This includes not only expansions/losses in peroxidase genes common to other basidiomycetes but also the widespread presence in Agaricales (and Russulales) of new peroxidases types not found in wood-rotting Polyporales, and other Agaricomycetes orders. Therefore, we analyzed the peroxidase evolution in Agaricomycetes by ancestral-sequence reconstruction revealing several major evolutionary pathways and mapped the appearance of the different enzyme types in a time-calibrated species tree.     

Lignin Peroxidase Activity Is Not Important in Biological Bleaching and Delignification of Unbleached Kraft Pulp by Trametes versicolor

The discovery in 1983 of fungal lignin peroxidases able to catalyze the oxidation of nonphenolic aromatic lignin model compounds and release some CO₂ from lignin has been seen as a major advance in understanding how fungi degrade lignin. Recently, the fungus Trametes versicolor was shown to be capable of substantial decolorization and delignification of unbleached industrial kraft pulps over 2 to 5 days. The role, if any, of lignin peroxidase in this biobleaching was therefore examined. Several different assays indicated that T. versicolor can produce and secrete peroxidase proteins, but only under certain culture conditions. However, work employing a new lignin peroxidase inhibitor (metavanadate ions) and a new lignin peroxidase assay using the dye azure B indicated that secreted lignin peroxidases do not play a role in the T. versicolor pulp-bleaching system. Oxidative activity capable of degrading 2-keto-4-methiolbutyric acid (KMB) appeared unique to ligninolytic fungi and always accompanied pulp biobleaching.     

Recent advances in fungal cellobiose oxidoreductases

When grown on cellulose, the white-rot fungus Phanerochaete chrysosporium (Sporotrichum pulverulentum), produces two cellobiose oxidoreductases, i.e., cellobiose:quinone oxidoreductase (CBQ) and cellobiose oxidase (CBO). Similar cellobiose-oxidizing enzymes, capable of utilizing a wide variety of electron acceptors, have been detected in many other fungi. However, the role of the cellobiose oxidoreductases in white-rot fungi, or in any fungi for that matter, is still not known. The original role ascribed to CBQ was as a link between cellulose and lignin degradation. CBQ has been shown to reduce quinones and phenoxyradicals released during lignin degradation concomitantly oxidizing cellobiose and other cellodextrins released during cellulose degradation. Thus, one function proposed for the cellobiose oxidoreductases is to prevent repolymerization of phenoxyradicals formed when phenoloxidases (peroxidases and laccases) attack lignin and lignin degradation products. However, evidence obtained so far indicates that the presence of CBO/CBQ with lignin peroxidases and laccases actually reduces the rate of oxidation of lignin degradation products. CBQ has a molecular mass of about 60 kD and contains an FAD cofactor. CBO contains both heme and FAD, and has a mass of about 90 kD. It has recently been demonstrated that CBO can be proteolytically cleaved into FAD and heme domains. The FAD domain of CBO seems to have all the properties of CBQ, suggesting that CBQ is a cleavage product of CBO. Whether CBO is a precursor of CBQ is not yet known. CBO and CBQ can be distinguished not only by the differences in their spectral properties, but also by the ability of CBO, but not CBQ, to reduce cytochrome c. Both CBO and CBQ have a cellulose-binding domain (CBD), as do a large number of endoglucanases and cellobiohydrolases. The induction-repression patterns regulating cellobiose oxidoreductase genes are not known in any detail. Most reports point to induction during cellulose degradation, but repression has not been studied. Induction has also been suggested to occur by addition of lignosulfonate to the medium.