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Conformational study of a guaiacyl beta-O-4 lignin model compound by NMR. Examination of intramolecular hydrogen bonding interactions and conformational flexibility in solution.

Intramolecular H-bonding interactions were investigated in solution for the threo and erythro diastereomeric forms of a guaiacyl beta-O-4 lignin model compound by using the NMR data obtained from hydroxyl protons. Temperature coefficients of the chemical shifts (ddelta/dT) and coupling constants (3J(HCOH)) were measured in aprotic and protic solutions: DMSO-d6, acetone-d6 and acetone-d6-water. The NMR parameters do not support the existence of strong and persistent intramolecular H-bonds that could participate in the stabilization of the guaiacyl beta-O-4 structure in solution, but instead indicate that intermolecular H-bonds to solvent predominate. 1D NOE experiments nevertheless revealed the presence of a direct chemical exchange between the hydroxyl protons, suggesting the possible existence of weak and transient intramolecular H-bonding interactions. The conformational flexibility of the threo structure was also investigated in acetone solution from the measurement of long-range 1H, 1H and 1H, 13C coupling constants and from NOESY experiments. The NMR data are not consistent with any single conformation, indicating that different conformers co-exist in solution. The experimental results support the conformational flexibility predicted by molecular dynamics simulations performed in a previous study. Finally, both experimental and theoretical approaches indicate that weak intramolecular H-bonds can exist transiently in solution, breaking and reforming as the beta-O-4 molecule undergoes conformational interconversion, but cannot be invoked as possible means of conferring rigidity to the beta-O-4 structure.

Algorithms↗

Effect of superoxide and superoxide dismutase on lignin peroxidase-catalyzed veratryl alcohol oxidation.

We have shown that superoxide (O2.-) is produced during the oxidation of veratryl alcohol by lignin peroxidase (LiP) by the reaction of the veratryl alcohol cation radical with hydrogen peroxide (D. B. Barr, M. M. Shah, and S. D. Aust, 1993, J. Biol. Chem. 268, 241-244). Compound III, an inactive form of peroxidases can be formed by reaction of the ferric enzyme with O2.-. We therefore studied the effects of O2.- and superoxide dismutase (SOD) on the veratryl alcohol oxidase activity of LiP. SOD enhanced the rate of veratryl alcohol oxidation by LiP and veratryl alcohol oxidation was inhibited by the addition of KO2. Upon the addition of KO2, activity was also preceded by a lag period. Under steady-state turnover conditions (i.e., for veratryl alcohol oxidation), the addition of KO2 resulted in the formation of LiP compound III. Compound II of LiP was observed following a time period that correlated with the lag prior to veratryl aldehyde formation. The extent of the lag preceding veratryl aldehyde formation increased with increasing concentrations of KO2 and decreased with increasing concentrations of veratryl alcohol. It was postulated that during the lag period the veratryl alcohol cation radical reacted with compound III to regenerate the native enzyme. In this process the veratryl alcohol cation radical was reduced to veratryl alcohol, and thus, no veratryl aldehyde was detected during the lag period.

Agaricales↗

The role of oxalate in lignin peroxidase-catalyzed reduction: protection from compound III accumulation.

Reduction may be an important step in the degradation of some highly oxidized environmental pollutants by Phanerochaete chrysosporium. Lignin peroxidases (LiP) from P. chrysosporium are able to catalyze reductive reactions using veratryl alcohol (VA) as a mediator and either oxalate or EDTA as electron donors. Reduction of oxygen to superoxide, monitored by oxygen consumption, was used as a measure of the reductive activity of LiP. In the presence of EDTA, the rate of O2 reduction catalyzed by LiP decreased with time and increasing concentrations of H2O2. When oxalate replaced EDTA, LiP-catalyzed O2 reduction did not decrease with time, and increasing concentrations of H2O2 increased the duration and extent of O2 reduction. LiP was converted to the compound III state in the presence of EDTA, H2O2, and veratryl alcohol. When oxalate replaced EDTA, compound II was observed. The importance of the veratryl alcohol cation radical (VA.+) in the conversion of LiP compound III to active enzyme has been previously examined (D.P. Barr and S.D. Aust, 1994, Arch. Biochem. Biophys. 311, 378-382). We propose that rapid reduction of VA.+ by EDTA results in accumulation of LiP compound III and the loss of activity resulting in a decrease in LiP-catalyzed reduction reactions. Oxalate is less effective in reducing the VA.+, therefore, some VA.+ remains to convert compound III to active enzyme and maintain LiP-catalyzed reduction reactions. Thus oxalate, a normal secondary metabolite of P. chrysosporium, is a suitable candidate for mediating reduction reactions by LiP in vivo.

Edetic Acid↗

Inactivation of lignin peroxidase by hydrogen peroxide during the oxidation of phenols.

The oxidation of phenols by lignin peroxidase (LiP) was characterized by a rapid decrease in enzyme activity. The initial oxidation rate of phenol decreased at moderately high (i.e., 400 microM) concentrations of H2O2. Similar results were obtained with several phenols. However, LiP was not inactivated during the oxidation of veratryl alcohol (VA). The apparent second-order rate constants for the reaction of compound II with phenol and VA at pH 3.5 were very similar, about 2.1 x 10(4) and 4.7 x 10(4) M-1 s-1, respectively. However, unlike VA, phenols could not convert compound III back to ferric enzyme. The visible absorption spectra of compound II and III were observed during oxidation of VA and phenols, respectively. These results suggest that the inactivation of LiP during the oxidation of phenols was mainly due to the accumulation of compound III, which was attributed to the inability of phenols or phenoxyl radicals to revert compound III to ferric enzyme. All of these results also suggested that the inactivation mechanism of LiP during oxidation of phenols was different from that during oxidation of anisyl alcohol, since anisyl alcohol was neither a substrate of compound II nor could it revert compound III [K. Valli et al. (1990) Biochemistry 29, 8535-8539 and R.S. Koduri and M. Tien (1994) Biochemistry 33, 4225-4230].

Benzyl Alcohols↗

Veratryl alcohol-mediated indirect oxidation of pentachlorophenol by lignin peroxidase.

The oxidation of pentachlorophenol (PCP) by lignin peroxidase (LiP) is characterized by a rapid loss of activity during which time the enzyme is quickly converted to compound III, an inactive form of the enzyme. We investigated the indirect oxidation of PCP by LiP using veratryl alcohol (VA) as a mediator. The oxidation of VA to veratryl aldehyde by LiP was inhibited by PCP. Inhibition was characterized by lag period followed by the same rate of VA oxidation. The lag period before VA oxidation was increased by increasing concentrations of PCP. During the lag period, PCP was oxidized and the extent of PCP oxidation increased with increasing concentrations of VA. The enzyme stayed as compound II during PCP oxidation in the presence of VA, suggesting that VA has a protective role in the LiP catalysis. The kinetics of PCP oxidation in the presence of VA were similar to those of VA oxidation. All these results suggest that PCP is oxidized indirectly via the veratryl alcohol cation radical. 2,3,5,6-Tetrachloro-p-benzoquinone was a stoichiometric product during PCP oxidation in both the presence and the absence of VA. An equivalent amount of inorganic chloride was formed by oxidative 4-dechlorination during PCP oxidation in the presence of VA. The increase in the rate and extent of PCP oxidation by VA results from mediation of PCP oxidation and reversion of inactive compound III to native enzyme, both by the veratryl alcohol cation radical.

Basidiomycota↗

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.

Anisoles↗

2-Chloro-1,4-dimethoxybenzene cation radical: formation and role in the lignin peroxidase oxidation of anisyl alcohol.

2-Chloro-1,4-dimethoxybenzene (2Cl-1,4-DMB) oxidation by lignin peroxidase (LiP) proceeds via the formation of the 2Cl-1,4-DMB cation radical as indicated by ESR and UV/vis spectroscopy. The products of the LiP-catalyzed oxidation of 2Cl-1,4-DMB were identified as 2-chloro-1,4-benzoquinone and the dimers dichlorotetramethoxybiphenyl and chloro(chlorodimethoxyphenyl)benzoquinone. The addition of anisyl alcohol (AA) rapidly quenched the 2Cl-1,4-DMB cation radical optical absorption bands, suggesting that the cation radical directly mediates the oxidation of AA. When LiP reactions are conducted in the presence of 50 microM 2Cl-1,4-DMB, the enzyme is inactivated; however, this inactivation can be prevented by the addition of AA. This also suggests that the 2Cl-1,4-DMB cation radical formed in the reaction, in turn, oxidizes AA.

Anisoles↗

Extracellular mannose-6-phosphatase of Phanerochaete chrysosporium: a lignin peroxidase-modifying enzyme.

The lignin peroxidase (LIP) isozyme profile of the white-rot fungus Phanerochaete chrysosporium changes markedly with culture age. This change occurs extracellularly and results from enzymatic dephosphorylation of LIP isozymes. In this study, a novel mannose 6-phosphatase (M6Pase) from extracellular culture fluid filtrate of P. chrysosporium, shown to be responsible for the extracellular postranslational modification of LIP, was purified and characterized. In vitro incubation of the purified M6Pase with purified LIP isozyme H2 resulted in its conversion to isozyme H1, with an equimolar release of orthophosphate. Using different sugar phosphates as substrate, the enzyme exhibited narrow specificity, showing activity mostly for mannose 6-phosphate (K(m) = 0.483 mM). The enzyme displayed a molecular mass of 82 kDa, as determined by gel filtration, and 40.4 and 39.1 kDa, on SDS-PAGE, suggesting that the native form is a dimer. The N-terminal sequence of the enzyme has no homology with that of other reported phosphatases. M6Pase is a metalloprotein with manganese and cobalt as the preferred metal ions. It is N-glycosylated proteins with an isoelectric point of 4. 7-4.8 and a pH optimum of 5. Based on its characteristics, M6Pase from P. chrysosporium seems to be a unique phosphatase responsible for posttranslation modification of LIP isozymes.

Amino Acid Sequence↗

Substrate specificity of lignin peroxidase and a S168W variant of manganese peroxidase.

Lignin peroxidase (LiP) and manganese peroxidase (MnP) are structurally similar heme-containing enzymes secreted by white-rot fungi. Unlike MnP, which is only specific for Mn(2+), LiP has broad substrate specificity, but it is not known if this versatility is due to multiple substrate-binding sites. We report here that a S168W variant of MnP from Phanerochaete chrysosporium not only retained full Mn(2+) oxidase activity, but also, unlike native or recombinant MnP, oxidized a multitude of LiP substrates, including small molecule and polymeric substrates. The kinetics of oxidation of most nonpolymeric substrates by the MnP variant and LiP were similar. The stoichiometries for veratryl alcohol oxidation by these two enzymes were identical. Some readily oxidizable substrates, such as guaiacol and ferrocyanide, were oxidized by MnP S168W and LiP both specifically and nonspecifically while recombinant MnP oxidized these substrates only nonspecifically. The functional similarities between this MnP variant and LiP provide evidence for the broad substrate specificity of a single oxidation site near the surface tryptophan.

Amino Acid Sequence↗

MnII is not a productive substrate for wild-type or recombinant lignin peroxidase isozyme H2.

The glyceraldehyde-3-phosphate dehydrogenase (gpd) gene promoter was used to drive the homologous expression of the lignin peroxidase (LiP) isozyme H2 gene in primary metabolic cultures of Phanerochaete chrysosporium. The molecular mass, pI, and optical absorption spectra of purified recombinant LiPH2 (rLiPH2) were essentially identical to those of wild-type LiPH2 (wtLiPH2). wtLiPH2 was prepared by growing cells in the absence of MnII, conditions under which P. chrysosporium manganese peroxidase (MnP) is not expressed, ensuring that wtLiPH2 was not contaminated with MnP. The kinetics of veratryl alcohol (VA) oxidation were essentially identical for rLiPH2 and wtLiPH2. The rLiPH2, wtLiPH2, and wild-type LiP isozyme H8 (wt-LiPH8) enzymes were used to reexamine previous claims that LiPH2 can oxidize Mn" at a rate sufficient to promote catalytic turnover of the enzyme. Our results demonstrate that rLiPH2, wtLiPH2, and LiPH8 do not turn over under steady-state conditions, when MnII is the sole reducing substrate. Furthermore, transient-state kinetic analyses show that the reduction rate of the catalytic intermediate, LiP compound I, by VA was at least 2 x 10(3)-fold higher than the rate of reduction in the presence of MnII. No reduction of LiP compound II was observed in the presence of MnII. In contrast to previous claims, these data strongly suggest that MnII is not a productive substrate for LiPH2 or LiPH8.

Catalytic Domain↗

Crystal structures of pristine and oxidatively processed lignin peroxidase expressed in Escherichia coli and of the W171F variant that eliminates the redox active tryptophan 171. Implications for the reaction mechanism.

The heme enzyme lignin peroxidase (LiP) from the white rot fungus Phanerochaete chrysosporium contains a solvent exposed redox active tryptophan residue (Trp171) that carries a unique hydroxy group stereo-specifically attached to its C(beta) atom. A Trp171Phe mutant has no activity at all towards the substrate veratryl alcohol. The mechanism of veratryl alcohol oxidation involving beta-hydroxy-Trp171 is largely unknown. Here, we present the first crystal structures of LiP isozyme H8 at high resolution in its pristine non-hydroxylated form, of the C(beta)-hydroxylated form, and of the Trp171Phe mutant using recombinantly expressed and refolded protein produced from Escherichia coli. As a consequence, all structures are unglycosylated. Structural changes in response to the mutation are marginal and allow us to attribute the complete lack of activity exclusively to the absence of the redox active indole side-chain. The origin of the stereospecificity of the Trp171 hydroxylation can be explained on structural grounds. A reaction mechanism involving Trp171 is proposed and the possible function of the modification is discussed. Another important result regarding the ongoing debate on the co-ordination state of the heme iron in the resting state is that the iron is six co-ordinate in all cases the data being collected at room temperature. The mean distance from the iron to the distal water ligand is 2.18(+/-0.08) A. The radical scavenger orcinol was found to decrease radiation damage to the crystals, during data collection at room temperature.

Amino Acid Substitution↗

Immobilization as a tool for the stabilization of lignin peroxidase produced by Phanerochaete chrysosporium INA-12.

Lignin peroxidase immobilization was achieved by covalent coupling on CNBr-Sepharose 4B. Protein immobilization yield was around 80%. For veratryl alcohol oxidation, in the presence of hydrogen peroxide, both soluble and bound enzymes exhibited the same pH profile with an optimum near 2.5. Catalytic parameters (kc and Km) were seriously affected by immobilization. On the other hand, immobilization provided a noticeable stabilization of the enzyme against acidic pH and high temperatures. A 15-20 increase in the half-inactivation times at pH 2.2 and 2.7, respectively, could be observed. Bound enzyme was also much more thermostable than soluble.

Basidiomycota↗

Metabolic response against sulfur-containing heterocyclic compounds by the lignin-degrading basidiomycete Coriolus versicolor.

The fungal conversions of sulfur-containing heterocyclic compounds were investigated using the lignin-degrading basidiomycete Coriolus versicolor. The fungus metabolized a series of sulfur compounds--25 structurally related thiophene derivatives--via several different pathways. Under primary metabolic conditions, C. versicolor utilized thiophenes, such as 2-hydroxymethyl-, 2-formyl-, and 2-carboxyl-thiophenes, as a nutrient sulfur source for growth; thus, the fungus degraded these compounds more effectively in a non-sulfur-containing medium than in conventional medium. The product analysis revealed that several redox reactions, decarboxylation reactions, and C-S cleavage reactions were involved in the fungal conversion of non-aromatic thiophenes. On the other hand, benzothiophene (BT) and dibenzothiophene (DBT) skeletons were converted to water-soluble products. All the products and metabolic intermediates were more hydrophilic than the starting substrates. These metabolic actions seemed to be a chemical stress response against exogenously added xenobiotics. These metabolic reactions were optimized under ligninolytic conditions, also suggesting the occurrence of a fungal xenobiotic response. Furthermore, the fungus converted a series of BTs and DBTs via several different pathways, which seemed to be controlled by the chemical structure of the substrates. DBT, 4-methylDBT, 4, 6-dimethylDBT, 2-methylBT, and 7-methylBT were immediately oxidized to their S-oxides. BTs and DBTs with the hydroxymethyl substituent were converted to their xylosides without S-oxidation. Those with carboxyl and formyl substituents were reduced to form a hydroxymethyl group, then xylosidated. These observations strongly suggested the involvement of a fungal substrate-recognition and metabolic response mechanism in the metabolism of sulfur-containing heterocyclic compounds by C. versicolor.

Benzaldehydes↗

Catalytic activity of lignin peroxidase and partition of veratryl alcohol in AOT/isooctane/toluene/water reverse micelles.

The activity of lignin peroxidase (LiP) and the partition of its optimum substrate veratryl alcohol (VA) in sodium bis(2-ethylhexyl)sulfosuccinate (AOT)/isooctane/toluene/water reverse micelles were studied in this paper to understand the microheterogeneous effect of the medium on the catalytic properties of LiP hosted in the reverse micelle. Results showed that LiP from Phanerochaete chrysosporium could express its activity in the reverse micelles, but its activity depended, to a great extent, on the composition of the reverse micelles. Optimum activity occurred at a molar ratio of water to AOT (omega0) of 11, a pH value of 3.6, and a volume ratio of isooctane to toluene of 7-9. Under optimum conditions, the half-life of LiP was circa 12 h. The dependence of LiP activity on the volume fraction of water in the medium (theta), at a constant omega0 value of 11, indicated that VA was mainly solubilized in the pseudophase of the reverse micelle. Based on the pseudobiphasic model and the corresponding kinetic method, a linear line can be obtained in a plot of apparent Michaelis constant of VA vs theta, and the partition coefficient of VA between the pseudophase and the organic solvent phase was determined to be 35.8, which was higher than that (22.3) between bulk water and the corresponding mixed organic solvent. H2O2 inhibited LiP at concentrations higher than 80 microM; this concentration value seems to be different from that in aqueous solution (about 3 mM). The differences mentioned above should be ascribed to the microheterogeneity and the interface of the AOT reverse micelle.

Benzyl Alcohols↗

Transformation of macromolecules from a brown coal by lignin peroxidase

Indirect evidence has suggested that lignin peroxidase (LiP) of the white-rot fungus Phanerochaete chrysosporium catalyses oxidative decolourisation and depolymerisation of macromolecules from brown coal in vivo. In this study we show that LiP catalyses these transformations in vitro. Unmethylated (USC45 coal) and methylated (MWSC6 coal) fractions of solubilised macromolecules (M(r) > 30,000) from a brown coal were treated with a semi-purified preparation of LiP isozymes from P. chrysosporium. Both coal fractions were decolourised, losing between 26% and 39% of their absorbance at both 280 nm and 400 nm, in reactions that had an absolute requirement for H2O2 and veratryl alcohol. Neither coal fraction was transformed when the enzyme was heat-inactivated or in the presence of the LiP inhibitor metavanadate. Gel-permeation chromatography showed that MWSC6 coal but not USC45 was depolymerised and yielded low-molecular-mass (M(r) < 30,000) fragments. Nine monomeric products were identified by GC-MS.

Journal Article↗

Coniferyl alcohol, a lignin precursor, stimulates Rhizobium rhizogenes A4 virulence.

Rhizobium rhizogenes, a soil bacterium, is the causative agent of the neoplastic disease hairy root. Upon incubation of Rhizobium rhizogenes A4 with coniferyl alcohol, a lignin precursor, bacterial virulence on cotton cotyledon slices was stimulated. This was observed both in numbers of root hairs produced and in their length. Stimulation was maximized after exposure of bacteria to 150 microg/mL of coniferyl alcohol for 4 h. This was shown to be at the early log phase of bacterial growth.

Culture Media↗

Inactivation of lignin peroxidase by phenylhydrazine and sodium azide.

Lignin peroxidase (LiP) is rapidly inactivated in a concentration-dependent manner by H2O2 and either phenylhydrazine or sodium azide. Full inactivation of isozyme 2b (H8) requires approximately 50 eq of phenylhydrazine or 80 eq of sodium azide. Anaerobic incubation of isozyme 2b with [14C]phenylhydrazine and H2O2 results in 77% loss of catalytic activity and covalent binding of 0.45 mol radiolabel/mol of enzyme. Comparable but not identical results are obtained with an isozyme mixture. A lag period is observed before the peroxidative activity can be measured when an aliquot of an incubation with sodium azide is diluted into the mixture used to assay residual catalytic activity. This lag is associated with reversible accumulation of a catalytically inert species with a Compound III-like spectrum. No meso-phenyl, iron-phenyl, or N-phenyl adducts are formed with phenylhydrazine but a low yield of what appears to be delta-meso-azidoheme is obtained with sodium azide. LiP is thus less susceptible to meso heme additions and more susceptible to oxidative heme degradation than horseradish peroxidase. The data suggest that the active of LiP resembles the closed structure of horseradish peroxidase more than it does the open structure of the globins, catalase, chloroperoxidase, or cytochrome P450.

Azides↗

Characterization of two lignin peroxidase clones from Phanerochaete chrysosporium.

Two cDNA clones encoding lignin peroxidase isozymes from Phanerochaete chrysosporium have been isolated and characterized. One of the clones, lambda ML-4, encodes isozyme H8 as does the previously reported clone lambda ML-1 [Tien, M. and Tu, C.-P.D. Nature 326 (1987) 520-523; 328, 742]. Our data are consistent with lambda ML-1 and lambda ML-4 being allelic variants. The other clone, lambda ML-5, encodes a homologous isozyme. We have also isolated the genomic clone corresponding to lambda ML-4 cDNA. Conserved residues thought to be essential for peroxidase function were identified in the predicted amino acid sequences of both cDNA clones. Northern blot analyses indicate that these isozymes are expressed during secondary metabolism, appearing on day 4 of growth and increasing on days 5 and 6.

Amino Acid Sequence↗