Lignin peroxidase compounds II and III. Spectral and kinetic characterization of reactions with peroxides

Agaricales Mushroom Lignin Peroxidase: From Structure-Function to Degradative Capabilities

Lignin biodegradation has been extensively studied in white-rot fungi, which largely belong to order Polyporales. Among the enzymes that wood-rotting polypores secrete, lignin peroxidases (LiPs) have been labeled as the most efficient. Here, we characterize a similar enzyme (ApeLiP) from a fungus of the order Agaricales (with ~13,000 described species), the soil-inhabiting mushroom Agrocybe pediades. X-ray crystallography revealed that ApeLiP is structurally related to Polyporales LiPs, with a conserved heme-pocket and a solvent-exposed tryptophan. Its biochemical characterization shows that ApeLiP can oxidize both phenolic and non-phenolic lignin model-compounds, as well as different dyes. Moreover, using stopped-flow rapid spectrophotometry and 2D-NMR, we demonstrate that ApeLiP can also act on real lignin. Characterization of a variant lacking the above tryptophan residue shows that this is the oxidation site for lignin and other high redox-potential substrates, and also plays a role in phenolic substrate oxidation. The reduction potentials of the catalytic-cycle intermediates were estimated by stopped-flow in equilibrium reactions, showing similar activation by H₂O₂, but a lower potential for the rate-limiting step (compound-II reduction) compared to other LiPs. Unexpectedly, ApeLiP was stable from acidic to basic pH, a relevant feature for application considering its different optima for oxidation of phenolic and nonphenolic compounds.

Transformation of 17beta-estradiol mediated by lignin peroxidase: the role of veratryl alcohol

Lignin peroxidases (LiPs) are a group of extracellular enzymes excreted by certain fungi, e.g., Phanerochaete chrysosporium. These fungi also produce veratryl alcohol (VA) as a secondary metabolite to regulate the performance of LiP. 17ss-Estradiol (E2) is a natural female hormone that is strongly endocrine disruptive when released to the natural environment. The widespread occurrence of E2 and related hormonal chemicals in soil and water environments has been identified, representing an emerging contamination of concern. We report in this study that E2 can be effectively transformed and removed through reactions mediated by LiP and such reactions are significantly enhanced in the presence of VA. We systematically investigated LiP activity and enzymatic reaction kinetics in systems having VA absent or present. The results suggest that VA enhanced the transformation and removal of E2 by the combination of two effects: (i) mitigating LiP inactivation and (ii) modifying the enzyme catalytic kinetics. These findings provide insights into an important pathway that may govern the environmental transformation of E2 and other emerging endocrine-disrupting contaminants of similar nature in the environment, and provide a basis for potential development and optimization of enzyme-based processes for remediation and removal of these contaminants.

Bioelectrocatalytic properties of lignin peroxidase from Phanerochaete chrysosporium in reactions with phenols, catechols and lignin-model compounds

Bioelectrocatalytic reduction of H(2)O(2) catalysed by lignin peroxidase from Phanerochaete chrysosporium (LiP) was studied with LiP-modified graphite electrodes to elucidate the ability of LiP to electro-enzymatically oxidise phenols, catechols, as well as veratryl alcohol (VA) and some other high-redox-potential lignin model compounds (LMC). Flow-through amperometric experiments performed at +0.1 V vs. Ag|AgCl demonstrated that LiP displayed significant bioelectrocatalytic activity for the reduction of H(2)O(2) both directly (i.e., in direct electron transfer (ET) reaction between LiP and the electrode) and using most of studied compounds acting as redox mediators in the LiP bioelectrocatalytic cycle, with a pH optimum of 3.0. The bioelectrocatalytic reduction of H(2)O(2) mediated by VA and effects of VA on the efficiency of bioelectrocatalytic oxidation of other co-substrates acting as mediators were investigated. The bioelectrocatalytic oxidation of phenol- and catechol derivatives and 2,2'-azino-bis(3-ethyl-benzothiazoline-6-sulphonate) by LiP was independent of the presence of VA, whereas the efficiency of the LiP bioelectrocatalysis with the majority of other LMC acting as mediators increased upon addition of VA. Special cases were phenol and 4-methoxymandelic acid (4-MMA). Both phenol and 4-MMA suppressed the bioelectrocatalytic activity of LiP below the direct ET level, which was, however, restored and increased in the presence of VA mediating the ET between LiP and these two compounds. The obtained results suggest different mechanisms for the bioelectrocatalysis of LiP depending on the chemical nature of the mediators and are of a special interest both for fundamental science and for application of LiP in biotechnological processes as solid-phase bio(electro)catalyst for decomposition/detection of recalcitrant aromatic compounds.

Reactions of the class II peroxidases, lignin peroxidase and Arthromyces ramosus peroxidase, with hydrogen peroxide. Catalase-like activity, compound III formation, and enzyme inactivation

The reactions of the fungal enzymes Arthromyces ramosus peroxidase (ARP) and Phanerochaete chrysosporium lignin peroxidase (LiP) with hydrogen peroxide (H(2)O(2)) have been studied. Both enzymes exhibited catalase activity with hyperbolic H(2)O(2) concentration dependence (K(m) approximately 8-10 mm, k(cat) approximately 1-3 s(-1)). The catalase and peroxidase activities of LiP were inhibited within 10 min and those of ARP in 1 h. The inactivation constants were calculated using two independent methods; LiP, k(i) approximately 19 x 10(-3) s(-1); ARP, k(i) approximately 1.6 x 10(-3) s(-1). Compound III (oxyperoxidase) was detected as the majority species after the addition of H(2)O(2) to LiP or ARP, and its formation was accompanied by loss of enzyme activity. A reaction scheme is presented which rationalizes the turnover and inactivation of LiP and ARP with H(2)O(2). A similar model is applicable to horseradish peroxidase. The scheme links catalase and compound III forming catalytic pathways and inactivation at the level of the [compound I.H(2)O(2)] complex. Inactivation does not occur from compound III. All peroxidases studied to date are sensitive to inactivation by H(2)O(2), and it is suggested that the model will be generally applicable to peroxidases of the plant, fungal, and prokaryotic superfamily.

Extracellular heme peroxidases in actinomycetes: a case of mistaken identity

Actinomycetes secrete into their surroundings a suite of enzymes involved in the biodegradation of plant lignocellulose; these have been reported to include both hydrolytic and oxidative enzymes, including peroxidases. Reports of secreted peroxidases have been based upon observations of peroxidase-like activity associated with fractions that exhibit optical spectra reminiscent of heme peroxidases, such as the lignin peroxidases of wood-rotting fungi. Here we show that the appearance of the secreted pseudoperoxidase of the thermophilic actinomycete Thermomonospora fusca BD25 is also associated with the appearance of a heme-like spectrum. The species responsible for this spectrum is a metalloporphyrin; however, we show that this metalloporphyrin is not heme but zinc coproporphyrin. The same porphyrin was found in the growth medium of the actinomycete Streptomyces viridosporus T7A. We therefore propose that earlier reports of heme peroxidases secreted by actinomycetes were due to the incorrect assignment of optical spectra to heme groups rather than to non-iron-containing porphyrins and that lignin-degrading heme peroxidases are not secreted by actinomycetes. The porphyrin, an excretory product, is degraded during peroxidase assays. The low levels of secreted peroxidase activity are associated with a nonheme protein fraction previously shown to contain copper. We suggest that the role of the secreted copper-containing protein may be to bind and detoxify metals that can cause inhibition of heme biosynthesis and thus stimulate porphyrin excretion.

Inactivation of lignin peroxidase during oxidation of the highly reactive substrate ferulic acid

Ferulic acid (4-hydroxy-3-methoxycinnamic acid) (FA) was found to be a highly reactive substrate for lignin peroxidase (LIP), exhibiting a k(cat) of 41.7 s(-1). Despite the high reactivity, two modes of inactivation prevailed during the oxidation of FA. The first, H(2)O(2)-dependent inactivation, was evidenced by incomplete substrate oxidation and accumulation of LIP compound III (LIPIII), even at relatively low H(2)O(2) concentrations. This was attributed to the high turnover rate along with the inability of FA to revert LIPIII to the native state, as evidenced by pre-steady-state kinetics. H(2)O(2)-dependent inactivation could be avoided by inclusion of veratryl alcohol (VA), which efficiently reverts LIPIII to the native state. However, VA also mediated FA oxidation, and significantly decreased the reaction rate, which is unlike for previously reported VA-mediated reactions. The second mechanism of LIP inactivation was attributed to binding of phenoxy radicals or oxidation products to the enzyme and its extent directly correlated with the amount of FA consumed. This inactivation could be considerably suppressed by inclusion of gelatin. Therefore, during the oxidation of highly reactive phenolics, different kinds of protectors are required for efficient oxidation and maintaining LIP activity over time. This is of importance when considering emerging biotechnological applications for LIP.

Is cellobiose dehydrogenase from Phanerochaete chrysosporium a lignin degrading enzyme?

Cellobiose dehydrogenase (CDH) is an extracellular redox enzyme of ping-pong type, i.e. it has separate oxidative and reductive half reactions. Several wood degrading fungi produce CDH, but the biological function of the enzyme is not known with certainty. It can, however, indirectly generate hydroxyl radicals by reducing Fe(3+) to Fe(2+) and O2 to H2O2. Hydroxyl radicals are then generated by a Fenton type reaction and they can react with various wood compounds, including lignin. In this work we study the effect of CDH on a non-phenolic lignin model compound (3,4-dimethoxyphenyl glycol). The results indicate that CDH can affect lignins in three important ways. (1) It breaks beta-ethers; (2) it demethoxylates aromatic structures in lignins; (3) it introduces hydroxyl groups in non-phenolic lignins. The gamma-irradiated model compound gave a similar pattern of products as the CDH treated model compound, when the samples were analyzed by HPLC, suggesting that hydroxyl radicals are the active component of the CDH system.

Oxidation of aromatic sulfides by lignin peroxidase from Phanerochaete chrysosporium

The reaction of H2O2 with 4-substituted aryl alkyl sulfides (4-XC6H4SR), catalysed by lignin peroxidase (LiP) from Phanerochaete chrysosporium, leads to the formation of sulfoxides, accompanied by diaryl disulfides. The yields of sulfoxide are greater than 95% when X = OMe, but decrease significantly as the electron donating power of the substituent decreases. No reaction is observed for X = CN. The bulkiness of the R group has very little influence on the efficiency of the reaction, except for R = tBu. The reaction exhibits enantioselectivity (up to 62% enantiomeric excess with X = Br, with preferential formation of the sulfoxide with S configuration). Enantioselectivity decreases with increasing electron density of the sulfide. Experiments in H218O show partial or no incorporation of the labelled oxygen into the sulfoxide, with the extent of incorporation decreasing as the ring substituents become more electron-withdrawing. On the basis of these results, it is suggested that LiP compound I (formed by reaction between the native enzyme and H2O2), reacts with the sulfide to form a sulfide radical cation and LiP compound II. The radical cation is then converted to sulfoxide either by reaction with the medium or by a reaction with compound II, the competition between these two pathways depending on the stability of the radical cation.

Oxidative polymerization of ribonuclease A by lignin peroxidase from Phanerochaete chrysosporium. Role of veratryl alcohol in polymer oxidation

The mechanism of lignin peroxidase (LiP) was examined using bovine pancreatic ribonuclease A (RNase) as a polymeric lignin model substrate. SDS/PAGE analysis demonstrates that an RNase dimer is the major product of the LiP-catalyzed oxidation of this protein. Fluorescence spectroscopy and amino acid analyses indicate that RNase dimer formation is due to the LiP-catalyzed oxidation of Tyr residues to Tyr radicals, followed by intermolecular radical coupling. The LiP-catalyzed polymerization of RNase in strictly dependent on the presence of veratryl alcohol (VA). In the presence of 100 microM H2O2, relatively low concentrations of RNase and VA, together but not individually, can protect LiP from H2O2 inactivation. The presence of RNase strongly inhibits VA oxidation to veratraldehyde by LiP; whereas the presence of VA does not inhibit RNase oxidation by LiP. Stopped-flow and rapid-scan spectroscopy demonstrate that the reduction of LiP compound I (LiPI) to the native enzyme by RNase occurs via two single-electron steps. At pH 3.0, the reduction of LiPI by RNase obeys second-order kinetics with a rate constant of 4.7 x 10(4) M-1.s-1, compared to the second-order VA oxidation rate constant of 3.7 x 10(5) M-1.s-1. The reduction of LiP compound II (LiPII) by RNase also follows second-order kinetics with a rate constant of 1.1 x 10(4) M-1.s-1, compared to the first-order rate constant for LiPII reduction by VA. When the reductions of LiPI and LiPIi are conducted in the presence of both VA and RNase, the rate constants are essentially identical to those obtained with VA alone. These results suggest that VA is oxidized by LiP to its cation radical which, while still in its binding site, oxidizes RNase.

Nitration of veratryl alcohol by lignin peroxidase and tetranitromethane

Lignin peroxidase (LiP), from Phanerochaete chrysosporium, in the presence of H2O2 and tetranitromethane (TNM), oxidizes veratryl (3,4-dimethoxybenzyl) alcohol (VA) (I) to veratraldehyde (IV), 4,5-dimethoxy-2-nitrobenzyl alcohol (V), and 3,4-dimethoxy-nitrobenzene (VI). The formation of these products is explained by a mechanism involving the one-electron oxidation of VA by LiP to produce the corresponding cation radical, which loses a proton to generate the benzylic radical. The latter reduces TNM to generate the trinitromethane anion (VIII) and the nitrogen dioxide radical (.NO2). .NO2 couples with the VA cation radical, and the subsequent loss of a proton leads to V. Alternatively, the attack of .NO2 at C-1 of the VA cation radical, followed by aromatization and loss of formaldehyde (VII), yields VI. Isotopic labeling experiments confirm that V is generated by the reaction of .NO2 with the VA cation radical, rather than with the benzylic radical. The nitration of two other LiP substrates, 1,4-dimethoxybenzene (II) and tyrosine (III), also was examined. Product analysis of reactions conducted in the presence of H2O2 with these substrates indicated less nitrated product was formed from 1,4-dimethoxybenzene and no nitrated product was formed from tyrosine. However, significant amounts of nitrated products were formed from 1,4-dimethoxybenzene and tyrosine when glucose and glucose oxidase were used as an H2O2 source. These results suggest that a reductant, either the veratryl alcohol benzylic radical or superoxide, is required in the reaction to reduce TNM to generate .NO2. These results provide further evidence for the formation of the VA cation radical and the first chemical evidence for the formation of the VA benzylic radical in LiP-catalyzed reactions.

Stabilization of lignin peroxidases in white rot fungi by tryptophan

Supplementation of various cultures of white rot fungi with tryptophan was found to have a large stimulatory effect on lignin peroxidase activity levels. This enhancement was greater than that observed in the presence of the lignin peroxidase recycling agent veratryl alcohol. Using reverse transcription-PCR, we found that tryptophan does not act to induce lignin peroxidase expression at the level of gene transcription. Instead, the activity enhancement observed is likely to result from the protective effect of tryptophan against H2O2 inactivation. In experiments using a partially purified lignin peroxidase preparation, tryptophan and its derivative indole were determined to function in the same way as veratryl alcohol in converting compound II, an oxidized form of lignin peroxidase, to ferric enzyme, thereby completing the catalytic cycle. Furthermore, tryptophan was found to be a better substrate for lignin peroxidase than veratryl alcohol. Inclusion of either tryptophan or indole enhanced the oxidation of the azo dyes methyl orange and Eriochrome blue black. Stimulation of azo dye oxidations by veratryl alcohol has previously been shown to be due to its enzyme recycling function. Our data allow us to propose that tryptophan stabilizes lignin peroxidase by acting as a reductant for the enzyme.

Oxidation of dimethoxylated aromatic compounds by lignin peroxidase from Phanerochaete chrysosporium

The stabilities of the cation radicals of veratryl alcohol, 3,4-dimethoxytoluene and 1,4-dimethoxybenzene were compared by monitoring the formation of dimeric products during the oxidation of these substrates by lignin peroxidase (LiP). LiP oxidized veratryl alcohol to generate veratraldehyde as the major product. Several other monomeric products were obtained in low yield. Dimeric products resulting from the coupling of two cation radicals, or a cation radical with a neutral molecule, were obtained only in trace amounts or not at all. This suggests that the cation radical of veratryl alcohol rapidly loses a benzylic proton to form a benzylic radical which undergoes further reactions to form veratraldehyde. In contrast, the LiP oxidation of 3,4-dimethoxytoluene generated the dimeric product 3-(2,3-dimethoxy-6-methylphenyl)-4-methyl-1,2-benzoquinone as the major product. Several other monomeric and dimeric products were produced in lower yields. The generation of these dimeric products indicates that the cation radical of 3,4-dimethoxytoluene is considerably more stable than that of veratryl alcohol. This suggests that the electronegative benzylic oxygen of veratryl alcohol increases the acidity of the benzylic protons, destabilizing the veratryl alcohol cation radical. LiP oxidized 1,4-dimethoxybenzene to generate 1,4-benzoquinone and 2-(2,5-dimethoxyphenyl)-1,4-benzoquinone as the major products. The formation of these products indicates that the cation radical of 1,4-dimethoxybenzene also is relatively stable, as previously demonstrated by ESR. All of these results indicate that the veratryl alcohol cation radical generated by LiP oxidation is unstable, suggesting that it would not act as a diffusable radical mediator in LiP-catalyzed reactions.

Lignan models as inhibitors of Phanerochaete chrysosporium lignin peroxidase

The lignan 8,8'-bis-(methylenedioxy)cinnamic acid (BMDCA) is a powerful competitive inhibitor (K1 = 2.0 microM) of the lignin peroxidase (LiP) from Phanerochaete chrysosporium and of the extracellular peroxidase of Phlebia radiata (I0.5 = 10 microM). BMDCA derivatives with the same double bond system also inhibited these enzymes to some extent. If the double bonds were hydrogenated, the inhibitory effect was lost. HRP-VIII and HRP-XI were slightly inhibited by BMDCA (I0.5 > 50 microM) and two plant peroxidases described as efficient lignan synthesizers were unaffected. Liquid cultures of P chrysosporium did not discolour the dve Poly R478 when 250 microM of BMDCA was present.

Oxidation of ferrocytochrome c by lignin peroxidase

We demonstrate direct oxidation of ferrocytochrome c by lignin peroxidase (LiP) from the lignin-degrading basidiomycete, Phanerochaete chrysosporium. Steady-state kinetic data fit a peroxidase ping-pong mechanism rather than an ordered bi-bi ping-pong mechanism, suggesting that the reductions of LiP compounds I and II by ferrocytochrome c are irreversible. The pH dependence of the overall reaction apparently is controlled by two factors, the pH dependence of the electron-transfer rate and the pH dependence of enzyme inactivation in the presence of H2O2. In the presence of 100 microM H2O2, veratryl alcohol (VA) significantly enhanced cytochrome c oxidation at pH 3.0 but had little effect above pH 4.5. In the presence of < 10 microM H2O2, the stimulating effect of VA on the reaction is greatly diminished. As with cytochrome c peroxidase reactions, LiP oxidation of ferrocytochrome c decreased as the ionic strength increased, implying the involvement of electrostatic interactions between the polymeric substrate and enzyme. The reaction product ferricytochrome c inhibited VA oxidation by LiP in a noncompetitive manner, suggesting that cytochrome c binds to LiP at a site different from the small aromatic substrate binding site. Recent crystallographic studies show that the heme is buried in the LiP protein and unavailable for direct interaction with polymeric substrates, suggesting that electron transfer from ferrocytochrome c to LiP occurs over a relatively long range. The role of VA in this electron-transfer reaction is discussed.(ABSTRACT TRUNCATED AT 250 WORDS)

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.

Oxidation of monomethoxylated aromatic compounds by lignin peroxidase: role of veratryl alcohol in lignin biodegradation

Lignin peroxidase (LiP), an extracellular heme enzyme from the lignin-degrading fungus Phanerochaete chrysosporium, catalyzes the H2O2-dependent oxidation of a variety of nonphenolic lignin model compounds. The oxidation of monomethoxylated lignin model compounds, such as anisyl alcohol (AA), and the role of veratryl alcohol (VA) in LiP reactions were studied. AA oxidation reached a maximum at relatively low H2O2 concentrations, beyond which the extent of the reactions decreased. The presence of VA did not affect AA oxidation at low molar ratios of H2O2 to enzyme; however, at ratios above 100, the presence of VA abolished the decrease in AA oxidation. Addition of stoichiometric amounts of AA to LiP compound II (LiPII) resulted in its reduction to the native enzyme at rates that were significantly faster than the spontaneous rate of reduction, indicating that AA and other monomethoxylated aromatics are directly oxidized by LiP, albeit slowly. Under steady-state conditions in the presence of excess H2O2 and VA, a visible spectrum for LiPII was obtained. In contrast, under steady-state conditions in the presence of AA a visible spectrum was obtained for LiPIII*, a noncovalent complex of LiPIII and H2O2. AA competitively inhibited the oxidation of VA by LiP; the Ki for AA inhibition was 32 microM. Addition of VA to LiPIII* resulted in its conversion to the native enzyme. In contrast, AA did not convert LiPIII* to the native enzyme; instead, LiPIII* was bleached in the presence of AA. Thus, AA does not protect LiP from inactivation by H2O2.(ABSTRACT TRUNCATED AT 250 WORDS)