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Matrix-assisted laser desorption/ionization (MALDI)-mass spectrometry imaging (MSI) is a powerful technique to visualize the distributions of biomolecules without any labeling. In MALDI-MSI experiments, the choice of matrix deposition method is important for acquiring favorable MSI data with high sensitivity and high reproducibility. Generally, manual or automated spray-coating and automated sublimation methods are used, but these methods have some drawbacks with respect to detection sensitivity, spatial resolution, and data reproducibility. Herein, we present an optimized matrix deposition method of sublimation coupled with recrystallization using 9-aminoacridine (9-AA) as a matrix capable of ionizing endogenous metabolites. The matrix recrystallization process after sublimation was optimized for the solvent concentration and reaction temperature for matrix-metabolite co-crystallization. This optimized method showed excellent reproducibility and spatial resolution compared to the automatic spray-coating method. Furthermore, the recrystallization step after sublimation remarkably improved the detectability of metabolites, including amino acids, nucleotide derivatives, and lipids, compared with the conventional sublimation method. To date, there have been no other reports of 9-AA-based sublimation combined with recrystallization. The present method provides an easy, sensitive, and reproducible matrix deposition method for MALDI-MSI of endogenous metabolites. Graphical Abstract.

The activity of a self-sufficient cytochrome P450 enzyme, CYP505D6, from the lignin-degrading basidiomycete Phanerochaete chrysosporium was characterized. Recombinant CYP505D6 was produced in Escherichia coli and purified. In the presence of NADPH, CYP505D6 used a series of saturated fatty alcohols with C9–18 carbon chain lengths as the substrates. Hydroxylation occurred at the ω-1 to ω-6 positions of such substrates with C9–15 carbon chain lengths, except for 1-dodecanol, which was hydroxylated at the ω-1 to ω-7 positions. Fatty acids were also substrates of CYP505D6. Based on the sequence alignment, the corresponding amino acid of Tyr51, which is located at the entrance to the active-site pocket in CYP102A1, was Val51 in CYP505D6. To understand the diverse hydroxylation mechanism, wild-type CYP505D6 and its V51Y variant and wild-type CYP102A1 and its Y51V variant were generated, and the products of their reaction with dodecanoic acid were analyzed. Compared with wild-type CYP505D6, its V51Y variant generated few products hydroxylated at the ω-4 to ω-6 positions. The products generated by wild-type CYP102A1 were hydroxylated at the ω-1 to ω-4 positions, whereas its Y51V variant generated ω-1 to ω-7 hydroxydodecanoic acids. These observations indicated that Val51 plays an important role in determining the regiospecificity of fatty acid hydroxylation, at least that at the ω-4 to ω-6 positions. Aromatic compounds, such as naphthalene and 1-naphthol, were also hydroxylated by CYP505D6. These findings highlight a unique broad substrate spectrum of CYP505D6, rendering it an attractive candidate enzyme for the biotechnological industry. IMPORTANCEPhanerochaete chrysosporium is a white-rot fungus whose metabolism of lignin, aromatic pollutants, and lipids has been most extensively studied. This fungus harbors 154 cytochrome P450-encoding genes in the genome. As evidenced in this study, P. chrysosporium CYP505D6, a fused protein of P450 and its reductase, hydroxylates fatty alcohols (C9–15) and fatty acids (C9–15) at the ω-1 to ω-7 or ω-1 to ω-6 positions, respectively. Naphthalene and 1-naphthol were also hydroxylated, indicating that the substrate specificity of CYP505D6 is broader than those of the known fused proteins CYP102A1 and CYP505A1. The substrate versatility of CYP505D6 makes this enzyme an attractive candidate for biotechnological applications.

Tobacco plant was known to be a non-fructan-storing plant. However, we demonstrated that fructo-oligosaccharides (FOSs) were formed in cured tobacco leaf on adding sucrose to the leaf in our previous report (Nagai et al., J. Agric. Food Chem., 60, 6606-6612, 2012). Also, it was expected from the results obtained in previous study that FOSs were generated by enzymatic reaction in cured tobacco leaf. The purpose of this study is to confirm and understand the mechanisms of above-mentioned FOSs formation. Thus, we tried to purify the enzymes related to the production of FOSs. The enzymes were extracted from pulverized cured tobacco leaf (burley type leaf), and were purified by charcoal treatment, ultrafiltration, and several chromatography techniques. As a result, one of the enzymes was purified up to 414-fold. It was revealed that this enzyme was acid invertase exhibiting maximum transfructosylation activity at pH 6.0, 60 °C. In addition, general properties of this enzyme were also investigated. The enzyme purified in this study enhanced the ratio of FOSs formation under the condition of high concentrated sucrose. From these results, it was suggested that this enzyme participated in the formation of FOSs in tobacco leaf after curing.

Trametes cervina lignin peroxidase (LiP) lacks a catalytic tryptophan strictly conserved in other LiP and versatile peroxidases. It contains tyrosine(181) at the potential catalytic site. This protein and the well-characterized Phanerochaete chrysosporium LiP with the catalytic tryptophan(171) have been chemically modified: the tryptophan-specific modification with N-bromosuccinimide sufficiently disrupted oxidation of veratryl alcohol by P. chrysosporium LiP, whereas the activity of T. cervina LiP was not affected, suggesting no catalytic tryptophan in T. cervina LiP. On the other hand, the tyrosine-specific modification with tetranitromethane did not affect the activities of P. chrysosporium LiP lacking tyrosine but inactivated T. cervina LiP due to the nitration of tyrosine(181). These results strongly suggest that tyrosine(181) is at the catalytic site in T. cervina LiP.

The lignin peroxidase (LiP) from Trametes cervina was cloned, characterized, and identified as a novel fungal peroxidase. The sequence of T. cervina LiP encodes the essential amino acids for shaping the heme cavity and calcium-binding sites, which are conserved in plant and fungal peroxidases. However, a sequence homology analysis showed that T. cervina LiP has two unique features: it lacks the conserved tryptophan residue corresponding to the substrate-oxidation site (Trp171) of Phanerochaete chrysosporium LiP and it has a tyrosine residue (Tyr181) that has never been reported in other lignin peroxidases. A tertiary model of T. cervina LiP showed that Tyr181 sterically adjacent to the 6-propionate group of heme is surrounded by acidic amino acids and is exposed to the exterior. These attributes indicate that Tyr181 could be a T. cervina LiP substrate-oxidation site. A phylogenetic analysis showed that T. cervina LiP does not cluster with any other fungal peroxidases, suggesting that it is a unique molecule that is evolutionarily distant from other peroxidases. Thus, we concluded that T. cervina LiP could be a novel secreted peroxidase, among those produced by fungi, with a new oxidation mechanism probably involving Tyr181.

The white-rot fungus Phanerochaete chrysosporium possesses biodegradative capabilities of polychlorinated dibenzo-p-dioxins (PCDDs). One hundred twenty yeast clones expressing individual P450s of P. chrysosporum (PcCYPs), generated in our previous efforts, were screened for transformation of dioxin, and 40 positive clones were obtained. Of these clones, six clones showed metabolism of 2-chloro-dibenzo-p-dioxin, and a microsomal PcCYP designated as PcCYP11a3 showed much higher activity than any other PcCYPs. The turnover numbers of hydroxylation activities of PcCYP11a3 toward 1-MCDD (58 min(-1)) and 2-MCDD (13 min(-1)) are more than 200 times higher than those of previously reported PcCYP65a2. In addition, PcCYP11a3 catalyzes hydroxylation of 2,3-dichlorodibenzo-p-dioxin. To our best knowledge, PcCYP11a3 has the highest activity toward PCDDs among the known CYPs derived from microorganisms. Although PcCYP11a3 showed no detectable activity toward 2,7-dichloro-dibenzop-dioxin and 2,3,7-trichloro-dibenzo-p-dioxin, PcCYP11a3 is promising as a template whose activity would be enhanced by site-directed mutagenesis.

We cloned full-length cDNAs of 130 cytochrome P450s (P450s) derived from Phanerochaete chrysosporium and successfully expressed 70 isoforms in Saccharomyces cerevisiae. To elucidate substrate specificity of P. chrysosporium P450s, we examined various substrates including steroid hormones, several drugs, flavonoids and polycyclic aromatic hydrocarbons using the recombinant S. cerevisiae cells. Of these P450s, two CYPs designated as PcCYP50c and PcCYP142c with 14% identity in their amino acid sequences catalyse 3'-hydroxylation of flavone and O-deethylation of 7-ethoxycoumarin. Kinetic data of both enzymes on both reactions fitted not to the Michaelis-Menten equation but to Hill's equation with a coefficient of 2, suggesting that two substrates bind to the active site. Molecular modelling of PcCYP50c and a docking study of flavone to its active site supported this hypothesis. The enzymatic properties of PcCYP50c and PcCYP142c resemble mammalian drug-metabolizing P450s, suggesting that their physiological roles are metabolism of xenobiotics. It is noted that these unique P. chrysosporium P450s have a potential for the production of useful flavonoids.

Biofunctional cellulosic interfaces were successfully designed via the self-assembly of cellulose and its derivatives whose reducing ends were selectively modified with thiosemicarbazide. The biological functions of cellulosic self-assembled monolayers (SAMs) formed on a gold surface were investigated using rat liver cells. The cells proliferated well on the cellulose SAM (cellulose I) and methylcellulose SAM, while almost no cells adhered to the regenerated cellulose film (cellulose II) and hydroxyethylcellulose SAM. In the initial cell adhesion, rat liver cells were moderately attached on the cellulose SAM even in serum-free culture, possibly suggesting specific interactions between cells and cellulose SAM with unique surface morphology. The architectural design of cellulosic nanolayers via peculiar vectorial chain immobilization is expected to provide new information for the functional development of structural polysaccharide-based biointerfaces.

Individual methylcellulose (MC) chains and their thermoresponsive assembly were successfully visualized on a highly oriented pyrolytic graphite (HOPG) surface by atomic force microscopy (AFM). Momentary contact of a dilute MC solution at 4 degrees C onto the HOPG substrate permitted clear imaging of individual MC chains having a molecular thickness of ca. 0.5 nm and a hexagonal orientation. By increasing the solution temperature from 4 to 80 degrees C, it was possible to bring about significant changes in the MC nanomorphology from stretched molecular chains to disordered massive aggregates. It was presumed that the hydrophobic interaction between the MC chains and the HOPG pi-conjugated system led to the successful visualization of thermally responsive changes in the MC conformations. These results imply that HOPG substrates could be used for clear nanoimaging of cellulosic polymers and other structural polysaccharides.

Conformational changes in individual carboxymethylcellulose (CMC) chains deposited on a highly oriented pyrolytic graphite (HOPG) surface were investigated by atomic force microscopy (AFM). A small amount of CMC solution with various salt concentrations was deposited onto the HOPG surface. The CMC molecular chains adsorbed onto the HOPG surface were clearly visualized using tapping-mode AFM under ambient conditions, as compared with those on a hydrophilic mica surface. Each CMC chain was distinguishable at the molecular level based on the vertical profiles of the AFM images, and probably aligned along the HOPG crystal lattice. Higher NaCl concentrations brought about dramatic conformational changes from aligned single chains to globular aggregates via the molecular network structure only on the HOPG surface through electrostatic screening of the CM groups. Although CMC is a water-soluble hydrophilic polyelectrolyte, some interaction, possibly due to a CH-pi bonding between the glucopyranosic axial plane of CMC and the aromatic rings of HOPG, is considered to be effective and dominant for the unique molecular attachment. These phenomena would imply the potential use of HOPG as a substrate for not only molecular imaging, but also for nano-scale morphological control of cellulosic polymers and other structural polysaccharides.

Flat cellulose films were prepared and morphologically modified by spin coating a cellulose/N-methylmorpholine-N-oxide/H2O solution onto silicon oxide substrates pre-coated with a cationic polyelectrolyte. Spin-coated cellulose films were allowed to stably form on the silicon oxide substrates by pretreatment with either polydiallyldimethylammonium chloride (PDADMAC) or polyvinylamine (PVAm). The film surfaces obtained were analyzed by X-ray photoelectron spectroscopy (XPS) and atomic force microscopy (AFM). AFM topographical images of the cellulose film surfaces showed a different morphology depending on the underlying polymer, where PVAm pretreatment brought about an anisotropic surface topology. These results suggest that the specific attraction acting at the cellulose/polymer interface influences both the film formation and surface morphology of the cellulose layer. Differences in the solvent used to precipitate cellulose caused variations in the surface roughness by affecting the cellulose separation behavior. The morphological features of spin-coated cellulose film surfaces could be altered to some extent by these film preparation techniques.

The quality of coffee green beans is generally evaluated by the sensory cupping test, rather than by chemical compound-based criteria. In this study, we examined the relationship between metabolites and cupping scores for 36 varieties of beans, using a nontargeted LC-MS-based metabolic profiling technique. The cupping score was precisely predicted with the metabolic information measured using LC-MS. Two markers that strongly correlated with high cupping scores were determined to be isomers of 3-methylbutanoyl disaccharides (3MDs; 0.01-0.035 g/kg of beans) by spectroscopic analyses after purification, and one of them was a novel structure. Further, both the 3MDs were determined to be precursors of 3-methylbutanoic acid that enhance the quality of coffee. The applicability of 3MDs as universal quality indicators was validated with another sample set. It was concluded that 3MDs are the causative metabolites determining beverage quality and can be utilized for green bean selection and as key compounds for improving the beverage quality.

To isolate lignin peroxidase (LiP), extracellular activity of this type of enzyme was assayed against several white-rot basidiomycetes. Trametes cervi72;a was found to show relatively higher lignin peroxidase (LiP) activity in extracellular culture medium. LiP from T. cervina (TCLiP) was purified using several

We cloned full-length cDNA (PcCYP1f) encoding one of the cytochrome P450s in the lignin-degrading basidiomycete Phanerochaete chrysosporium, which showed high homology to P450s in the CYP53 family. PcCYP1f was expressed as an active microsomal protein using the methylotrophic yeast Pichia pastoris expression system. Using the microsomal fraction containing PcCYP1f, a typical P450 CO-difference spectrum was obtained with absorption maximum at 448 nm. Recombinant PcCYP1f catalyzed the hydroxylation of benzoic acid into 4-hydroxybenzoic acid in the presence of NADPH and P. chrysosporium cytochrome P450 oxidoreductase. In contrast to other CYP53 P450s, this enzyme was shown to catalyze the hydroxylation of 3-hydroxybenzoate into 3,4-dihydroxybenzoate. Furthermore, 2- and 3-methylbenzoate were also shown to be substrates of PcCYP1f. This is the first report showing the expression of a functionally active Phanerochaete P450. Finally, real-time quantitative PCR analysis revealed that PcCYP1f is induced at a transcriptional level by exogenous addition of benzoic acid.

Composite sheets composed of biodegradable polymers (BP) and paper were prepared, and their physical and biodegradable properties were investigated. The paper sheets were soaked in BP emulsions and cured at 100°C for 20 min. The wet strength of composite sheets with the same basis weight increased significantly with increasing BP content, although dry strength increased only moderately. A 0.5% addition of a common wet paper-strengthening agent, poly(amidoamine-epichlorohydrin) (PAE) resin, enhanced the wet strength, which reached 9.3 MPa, of composite sheets consisting of a BP : paper ratio of 20 : 80. Further enhancement was achieved by the addition of polyvinylamines (PVAm). The wet tensile strength of composite sheets consisting of BP and paper (20 : 80) increased by 27% with the addition of 0.2% PVAm and 0.5% PAE, whereas it was enhanced by only 3–4% with the addition of 0.7% PAE. The biodegradability of the composite sheets was somewhat retarded by the addition of PAE and PVAm. However, a 90% weight loss was observed 60 days after placing composite sheet samples in soil. A similar weight loss was observed after 45 days for composites without additives and after 30 days for base paper alone. © 2005 Wiley Periodicals, Inc. J Appl Polym Sci 96: 861–866, 2005

The complete degradation of Yperite (bis(2-chloroethyl) sulfide), a chemical warfare agent, was achieved by two basidiomycetous cultures. Two distinct metabolic pathways were detected in each fungus during degradation of Yperite. The major path involved a non-enzymatic hydrolysis to generate thiodiglycol. In the minor path, the sulfide bond was cleaved prior to the hydrolytic dechlorination reaction, yielding chloroethanol and chloromercaptoethane, both of which were then metabolized completely.

Matrix-assisted laser desorption/ionization-mass spectrometry imaging (MALDI-MSI) is a powerful technique for visualizing the distribution of a wide range of biomolecules within tissue sections. However, methodology for visualizing a bioactive ellagitannin has not yet been established. This paper presents a novel in situ label-free MALDI-MSI technique for visualizing the distribution of strictinin, a bioactive ellagitannin found in green tea, within mammalian kidney after oral dosing. Among nine representative matrix candidates, 1,5-diaminonaphthalene (1,5-DAN), harmane, and ferulic acid showed higher sensitivity to strictinin spotted onto a MALDI sample plate. Of these, 1,5-DAN enables visualization of a two-dimensional image of strictinin directly spotted on mouse kidney sections with the highest sensitivity. Furthermore, 1,5-DAN-based MALDI-MSI could detect the unique distribution of orally dosed strictinin within kidney sections. This in situ label-free imaging technique will contribute to the localization analysis of strictinin and its biological mechanisms.

Mechanism of lignin biodegradation caused by basidiomycetes and the history of lignin biodegradation studies were briefly reviewed. The important roles of fungal extracellular ligninolytic enzymes such as lignin and manganese peroxidases (LiP and MnP) were also summarized. These enzymes were unique in their catalytic mechanisms and substrate specificities. Either LiP or MnP system is capable of oxidizing a variety of aromatic substrates via a one-electron oxidation. Extracellular fungal system for aromatic degradation is non-specific, which recently attracts many people working in a bioremediation field. On the other hand, an intracellular degradation system for aromatic compounds is rather specific in the fungal cell. Structurally similar compounds were prepared and metabolized, indicating that an intracellular degradation strategy consisted of the cellular systems for substrate recognition and metabolic response. It was assumed that lignin-degrading fungi might be needed to develop multiple metabolic pathways for a variety of aromatic compounds caused by the action of non-specific ligninolytic enzymes on lignin. Our recent results on chemical stress responsible factors analyzed using mRNA differential display techniques were also mentioned.

The interaction of hydroxylamine (HA) withArthromyces ramosus peroxidase (ARP) was investigated by kinetic, spectroscopic, and x-ray crystallographic techniques. HA inhibited the reaction of native ARP with H2O2in a competitive manner. Electron absorption and resonance Raman spectroscopic studies indicated that pentacoordinate high spin species of native ARP are converted to hexacoordinate low spin species upon the addition of HA, strongly suggesting the occurrence of a direct interaction of HA with ARP heme iron. Kinetic analysis exhibited that the apparent dissociation constant is 6.2 mm at pH 7.0 and that only one HA molecule likely binds to the vicinity of the heme. pH dependence of HA binding suggested that the nitrogen atom of HA could be involved in the interaction with the heme iron. X-ray crystallographic analysis of ARP in complex with HA at 2.0 A resolution revealed that the electron density ascribed to HA is located in the distal pocket between the heme iron and the distal His56. HA seems to directly interact with the heme iron but is too far away to interact with Arg52. In HA, it is likely that the nitrogen atom is coordinated to the heme iron and that hydroxyl group is hydrogen bonded to the distal His56.

MS imaging (MSI) is a remarkable new technology that enables us to determine the distribution of biological molecules present in tissue sections by direct ionization and detection. This technique is now widely used for in situ imaging of endogenous or exogenous molecules such as proteins, lipids, drugs and their metabolites, and it is a potential tool for pathological analysis and the investigation of disease mechanisms. MSI is also thought to be a technique that could be used for biomarker discovery with spatial information. The application of MSI to the study of endogenous metabolites has received considerable attention because metabolites are the result of the interactions of a system's genome with its environment and a total set of these metabolites more closely represents the phenotype of an organism under a given set of conditions. Recent studies have suggested the importance of in situ metabolite imaging in biological discovery and biomedical applications, but several issues regarding the technical application limits of MSI still remained to be resolved. In this review, we describe the capabilities of the latest MSI techniques for the imaging of endogenous metabolites in biological samples, and also discuss the technical problems and new challenges that need to be addressed for effective and widespread application of MSI in both preclinical and clinical settings.

We discovered the phenyllactate (PLA)-producing fungal strain Wickerhamia fluorescens TK1 and purified phenylpyruvate reductase (PPR) from fungal cell-free extracts. The PPR used both NADPH and NADH as cofactors with more preference for the former. The enzyme reaction as well as the fungal culture produced optically active d-PLA. The gene for the PPR (pprA) was cloned and expressed in Escherichia coli cells. Purified preparations of both native and recombinant PPR used hydroxyphenylpyruvate, glyoxylate and hydroxypyruvate as substrates but not pyruvate, oxaloacetate or benzoylformate. The predicted PPR protein had sequence similarity to proteins in the d-isomer-specific 2-hydroxyacid dehydrogenase family. Phylogenetic analyses indicated that the predicted PPR protein together with fungal predicted proteins constitutes a novel group of glyoxylate/hydroxypyruvate reductases. The fungus efficiently converted phenylalanine and phenylpyruvate to d-PLA. These compounds up-regulated the transcription of pprA, suggesting that it plays a role in fungal phenylalanine metabolism.

We identified two aryl-aldehyde dehydrogenase proteins (PcALDH1 and PcALDH2) from the white-rot basidiomycete Phanerochaete chrysosporium. Both PcALDHs were translationally up-regulated in response to exogenous addition of vanillin, one of the key aromatic compounds in the pathway of lignin degradation by basidiomycetes. To clarify the catalytic functions of PcALDHs, we isolated full-length cDNAs encoding these proteins and heterologously expressed the recombinant enzymes using a pET/Escherichia coli system. The open reading frames of both PcALDH1 and PcALDH2 consisted of 1503 nucleotides. The deduced amino acid sequences of both proteins showed high homologies with aryl-aldehyde dehydrogenases from other organisms and contained ten conserved domains of ALDHs. Moreover, a novel glycine-rich motif "GxGxxxG" was located at the NAD(+)-binding site. The recombinant PcALDHs catalyzed dehydrogenation reactions of several aryl-aldehyde compounds, including vanillin, to their corresponding aromatic acids. These results strongly suggested that PcALDHs metabolize aryl-aldehyde compounds generated during fungal degradation of lignin and various aromatic xenobiotics.

Paramagnetic (13)C and (15)N nuclear magnetic resonance (NMR) spectroscopy of heme-bound cyanide ((13)C(15)N) was applied to 11 cytochrome c peroxidase (CcP) and Coprinus cinereus peroxidase (CIP) mutants to investigate contributions to the push and pull effects of conserved amino acids around heme. The (13)C and (15)N NMR data for the distal His and Arg mutants indicated that distal His is the key amino acid residue creating the strong pull effect and that distal Arg assists. The mutation of distal Trp of CcP to Phe, the amino acid at this position in CIP, changed the push and pull effects so they resembled those of CIP, whereas the mutation of distal Phe of CIP to Trp changed this mutant to become CcP-like. The (13)C NMR shifts for the proximal Asp mutants clearly showed that the proximal Asp-His hydrogen bonding strengthens the push effect. However, even in the absence of a hydrogen bond, the push effect of proximal His in peroxidase is significantly stronger than in globins. Comparison of these NMR data with the compound I formation rate constants and crystal structures of these mutants showed that (1) the base catalysis of the distal His is more critical for rapid compound I formation than its acid catalysis, (2) the primary function of the distal Arg is to maintain the distal heme pocket in favor of rapid compound I formation via hydrogen bonding, and (3) the push effect is the major contributor to the differential rates of compound I formation in wild-type peroxidases.

7 páginas, 7 figuras, 2 tablas -- PAGS. nros. 208-214 Heterologous expression of Trametes cervina lignin peroxidase (LiP), the only basidiomycete peroxidase that has a catalytic tyrosine, was investigated. The mature LiP cDNA was cloned into the pET vector and used to transform Escherichia coli. Recombinant LiP protein accumulated in inclusion bodies as an inactive form. Refolding conditions for its in vitro activation—including incorporation of heme and structural Ca2+ ions, and formation of disulfide bridges—were optimized taking as a starting point those reported for other plant and fungal peroxidases. The absorption spectrum of the refolded enzyme was identical to that of wild LiP from T. cervina suggesting that it was properly folded. The enzyme was able to oxidize 1,4-dimethoxybenzene and ferrocytochrome c confirming its high redox potential and ability to oxidize large substrates. However, during oxidation of veratryl alcohol (VA), the physiological LiP substrate, an unexpected initial lag period was observed. Possible modification of the enzyme was investigated by incubating it with H2O2 and VA (for 30 min before dialysis). The pretreated enzyme showed normal kinetics traces for VA oxidation, without the initial lag previously observed. Steady-state kinetics of the pretreated LiP were almost the same as the recombinant enzyme before the pretreatment. Moreover, the catalytic constant (kcat) for VA oxidation was comparable to that of wild LiP from T. cervina, although the Michaelis–Menten constant (Km) was 8-fold higher. The present heterologous expression system provides a valuable tool to investigate structure–function relationships, and autocatalytic activation of the unique T. cervina LiP This work was supported by the Spanish Projects BIO2007-65890-C02-01 and BIO2008-01533, and the BIORENEW project of the European Union (Contract NMP2-CT-2006-026456). Y.M. and F.J.R.-D. acknowledge two EU project contracts, and M.M. acknowledges a FPI fellowship of the Spanish MICINN

Homogeneous manganese peroxidase catalyzed the in vitro partial depolymerization of four different 14C-labeled synthetic lignin preparations. Gel permeation profiles demonstrated significant depolymerization of 14C-sidechain-labeled syringyl lignin, a 14C-sidechain-labeled syringyl-guaiacyl copolymer (angiosperm lignin), and depolymerization of 14C-sidechain- and 14C-ring-labeled guaiacyl lignins (gymnosperm lignin). 3,5-Dimethoxy-1,4-benzoquinone, 3,5-dimethoxy-1,4-hydroquinone, and syringylaldehyde were identified as degradation products of the syringyl and syringyl-guaiacyl lignins. These results suggest that manganese peroxidase plays a significant role in the depolymerization of lignin by Phanerochaete chrysosporium .

Individual cellulose macromolecules were successfully visualized on a highly oriented pyrolytic graphite (HOPG) surface by tapping-mode atomic force microscopy under ambient condition. Monomolecular-level dispersion of cellulose chains was achieved through the momentary contact of dilute cellulose/cupri-ethylenediamine (Cu-ED) solution onto the HOPG substrate. Both concentrations of cellulose and Cu-ED provided critical impacts on the topographical images. Single cellulose chains with molecular height of ca. 0.55 nm could be observed under the optimal conditions, showing rigid molecular rods with a unique morphology of hexagonal regularity. It was strongly suggested that the cellulose chains were aligned along the HOPG crystal lattice through a specific attraction, possibly due to a CH-pi interaction between the axial plane of cellulose and the HOPG pi-conjugated system. These phenomena would imply the potential applications of an HOPG substrate for not only nano-level imaging, but also for molecular alignment of cellulose and other structural polysaccharides.

Using the differential display reverse-transcriptional polymerase chain reaction (DDRT-PCR) technique, several cDNA fragments were isolated as chemical stress responsive genes from the white-rot basidiomycete, Coriolus versicolor, exposed to either 4-methyldibenzothiophene-5-oxide (4MDBTO) or dibenzothiophene-5-oxide (DBTO). A database search on deduced amino acid sequences of cDNAs revealed that they showed a high similarity with various proteins from other organisms. These results strongly suggested that cell responding systems might be involved in the fungal metabolism of exogenous chemicals by C. versicolor. One of the significantly up-regulated cDNA fragments by MDBTO, DD16gc, showed a high similarity to arylalcohol dehydrogenases (AADs) from several microorganisms. The full-length cDNA sequence of the DD16gc determined by 5' rapid amplification of cDNA ends method revealed that the gene consisted 1,295 nucleotide and poly(A) tail, encoding 394 amino acids in an open reading frame. The deduced protein showed a remarkable homology to AAD from Phanerochaete chrysosporium (66% identity) and to that from Saccharomyces cerevisiae (54% identity). The AAD gene was specifically transcripted under chemically-stressed conditions by 4MDBTO, suggesting that the enzyme encoded by the stress responsive gene may play an important role in the fungal conversion of 4MDBTO or its metabolic product(s).

Under secondary metabolic conditions, the white-rot basidiomycete Coriolus versicolormetabolized 4-methyldibenzothiophene (MDBT), which is a recalcitrant organic sulfur contaminant found in petroleum. The pathway of the transformation of MDBT was elucidated by the identification of fungal metabolites upon the addition of MDBT and its metabolic intermediates. S-oxidation to form MDBT-5-oxide was the initial step of MDBT metabolism. Then, the metabolic pathway was branched to form MDBT-5-dioxide, which was a dead-end product, and hydroxymethylDBT (HMDBT)-5-oxide. Extracellular ligninolytic enzymes such as lignin and manganese peroxidases and laccase did not catalyze the oxidation of either MDBT or MDBT-5-oxide. HMDBT-5-oxide was then oxidized to HMDBT-5-dioxide. Piperonyl butoxide, an inhibitor of cytochrome P450, suppressed fungal oxidation of MDBT to its oxide, MDBT-5-oxide to dioxide and to HMDBT-5-oxide, and HMDBT-5-oxide to dioxide. The efficiency of the inhibition varied for each substrate, suggesting that each oxidation was catalyzed by different enzymes. The hydroxylation of methyl substituents to the hydroxymethyl group was suggested to be catalyzed by a novel monooxygenase. HMDBT-5-dioxide was finally xylosylated most likely by xylosyltrasferase to yield 10-(beta-D-xylopyranosyloxy)-4-methyldibenzothiophene-5-dioxide. The final xyloside product and metabolic intermediates are water-extractable compounds, which would give us a novel strategy for biodesulfurization technology.

The degradation of thiodiglycol (I) and benzyl sulfide (II) was attempted using Coriolus versicolor and Tyromyces palustris to investigate the potential ability of basidiomycetes to degrade Yperite (bis(2-chloroethyl) sulfide), a mass-produced and stored chemical warfare agent. I was very rapidly degraded by both fungi. The metabolic pathway of II was elucidated, showing that the initial step was the hydrolytic cleavage of the thioether bond to yield benzyl alcohol and benzyl mercaptan. Benzyl alcohol was further oxidized and finally mineralized. Benzyl mercaptan is reversibly converted to benzyl disulfide and also converted to benzyl alcohol. Finally, the effective degradation of bis(2-bromoethyl) sulfide strongly suggests that basidiomycete would be a potential tool for Yperite degradation.

The effect of oxalate, malonate, lactate, and succinate chelators on the reduction of Phanerochaete chrysosporium manganese peroxidase compound II by MnII was investigated using stopped-flow techniques. All rate data were collected from single-turnover experiments under pseudo-first-order conditions. With oxalate, the reduction of compound II by MnII exhibited saturation behavior when the observed pseudo-first-order rate constants were plotted against oxalate concentration. The plots passed through the origin, indicating that the reduction by MnII is irreversible at all concentrations of oxalate. Maximal stimulation of the rate of compound II reduction occurred at 2 mM oxalate, the concentration of oxalate found in the extracellular medium of agitated cultures of this fungus. In contrast, maximal stimulation of the reduction of compound II by MnII only was observed at high (> 20 mM) nonphysiological concentrations of malonate and lactate. Furthermore, at low concentrations of malonate and lactate, the reduction of compound II appeared to be reversible. These results suggest that at physiological concentrations oxalate chelates and stabilizes MnIII, enhancing its efficient removal from the enzyme. The rate constants for compound II reduction exhibited bell-shaped curves as a function of pH and had optima at pHs 5.0-5.4. In the presence of succinate, triphasic kinetics were observed for compound II reduction by MnII. In contrast to the reduction of compound II by MnII, various chelators had no observable effect on the formation of compound I. However, they did affect the steady-state oxidation of 2,6-dimethoxyphenol.

The crystal structure of lignin peroxidase (LiP) from the basidiomycete Phanerochaete chrysosporium has been determined to 2.6 A resolution by usine multiple isomorphous replacement methods and simulated annealing refinement. Of the 343 residues, residues 3-335 have been accounted for in the electron density map, including four disulfide bonds. The overall three-dimensional structure is very similar to the only other peroxidase in this group for which a high-resolution crystal structure is available, cytochrome c peroxidase, despite the fact that the sequence identity is only approximately 20%, LiP has four disulfide bonds, while cytochrome c peroxidase has none, and LiP is larger (343 vs. 294 residues). The basic helical fold and connectivity defined by 11 helical segments with the heme sandwiched between the distal and proximal helices found in cytochrome c peroxidase is maintained in LiP. Both enzymes have a histidine as a proximal heme ligand, which is hydrogen bonded to a buried aspartic acid side chain. The distal or peroxide binding pocket also is similar, including the distal arginine and histidine. The most striking difference is that, whereas cytochrome c peroxidase has tryptophans contacting the distal and proximal heme surfaces, LiP has phenylalanines. This in part explains why, in the reaction with peroxides, cytochrome c peroxidase forms an amino acid-centered free radical, whereas LiP forms a porphyrin pi cation radical.

Stopped-flow rapid scan techniques were used to obtain a spectrum of nearly homogeneous lignin peroxidase compound I (LiPI) under pseudo-first order conditions at the unusually low pH optimum (3.0) for the enzyme. The LiPI spectrum had a Soret band at 407 nm with approximately 60% reduced intensity and a visible maximum at 650 nm. Under steady-state conditions a Soret spectrum for lignin peroxidase compound II (LiPII) was also obtained. The Soret maximum of LiPII at 420 nm was only approximately 15% reduced in intensity compared to native LiP. Transient state kinetic results confirmed the pH independence of LiPI formation over the pH range 3.06-7.39. The rate constant was (6.5 +/- 0.2) x 10(5) M-1 S-1. Addition of excess veratryl alcohol to LiPI resulted in its reduction to LiPII with subsequent reduction of LiPII to the native enzyme. Reactions of LiPI and LiPII with veratryl alcohol exhibited marked pH dependencies. For the LiPI reaction the rate constants ranged from 2.5 x 10(6) M-1 S-1 at pH 3.06 to 4.1 x 10(3) M-1 S-1 at pH 7.39; for the LiPII reaction, 1.6 x 10(5) M-1 S-1 (pH 3.06) to 2.3 x 10(3) M-1 S-1 (pH 5.16). These single turnover experiments demonstrate directly that the pH dependence of these reactions dictates the overall pH dependence of this novel enzyme. These results are consistent with the one-electron oxidation of veratryl alcohol to an aryl cation radical by LiPI and by LiPII.

In the presence of MnII, H2O2, and glutathione (GSH), manganese peroxidase oxidized veratryl alcohol (I) to veratraldehyde (IV). Anisyl alcohol (II) and benzyl alcohol (III) were also oxidized by this system to their corresponding aldehydes (V and VI). In the presence of GSH, chemically prepared MnIII or gamma-irradiation also catalyzed the oxidation of I, II, and III to IV, V, and VI, respectively. GSH and dithiothreitol rapidly reduced MnIII to MnII in the absence of aromatic substrates and the dithiothreitol was oxidized to its disulfide (4,5-dihydroxyl-1,2-dithiane). These results indicate that the thiol is oxidized by enzyme-generated MnIII to a thiyl radical. The latter abstracts a hydrogen from the substrate, forming a benzylic radical which reacts with another thiyl radical to yield an intermediate which decomposes to the benzaldehyde product. In the presence of MnII, GSH, and H2O2, manganese peroxidase also oxidized 1-(4-ethoxy-3-methoxy-phenyl)-2-(4'-hydroxymethyl-2'-methoxyphenoxy)- 1,3-dihydroxypropane (XII) to yield vanillyl alcohol (VII), vanillin (VIII), 1-(4-ethoxy-3-methoxyphenyl)-1,3-dihydroxypropane (XVI), 1-(4-ethoxy-3-methoxyphenyl)-1-oxo-3-hydroxypropane (XIX), and several C alpha oxidized dimeric products. Abstraction of the C alpha (A ring) hydrogen of the dimer (XII) yields a benzylic radical, leading to C beta oxygen ether cleavage. The resultant intermediates yield the ketone (XIX) and vanillyl alcohol (VII) or vanillin (VIII). Alternatively, benzylic radical formation at the C' alpha position (B ring) leads to radical cleavage, yielding a quinone methide and a C beta radical, which yield vanillin and the 1,3-diol (XVI), respectively. In these reactions, MnIII oxidizes a thiol to a thiyl radical which subsequently abstracts a hydrogen from the substrate to form a benzylic radical. The latter undergoes nonenzymatic reactions to yield the final products.

A thorough understanding of the sequence–structure–function relationships of cytochrome P450 (P450) is necessary to better understand the metabolic diversity of living organisms. Significant amounts of pure enzymes are sometimes required for biochemical studies, and their acquisition often relies on the possibility of their heterologous expression. In this study, we performed extensive heterologous expression of fungal P450s in Escherichia coli using 304 P450 isoforms. Using large-scale screening, we confirmed that at least 27 P450s could be expressed with/without simple sequence deletion at the 5′ end of cDNAs, which encode the N-terminal hydrophobic domain of the enzyme. Moreover, we identified N-terminal amino acid sequences that can potentially be used to construct chimeric P450s, which could dramatically improve their expression levels even when the expression of the wild-type sequence was unpromising. These findings will help increase the chance of heterologous expression of a variety of fungal and other eukaryotic membrane-bound P450s in E. coli.

At pH 3.0 in the absence of a reducing substrate and the presence of only 20 equivalents of H2O2, lignin peroxidase (LiP) is readily converted to LiP compound III (LiPIII) (Fe(III)O−2 - complex). LiPIII which is produced via the reaction of LiP compound II (LiPII) with H2O2 is not part of the peroxidase catalytic cycle, and is readily and irreversibly inactivated. Veratryl alcohol (VA), a Phanerochaete chrysosporium secondary metabolite, protects the enzyme from inactivation via two mechanisms. Acting as a substrate, VA reduces LiPII to regenerate the native enzyme. Secondly, the binding of VA to LiPIII rapidly displaces O.−2/HO.−2, thereby converting LiPIII directly to the native enzyme. VA is not consumed during this displacement reaction. These results help to explain the role of VA in stabilizing the enzyme in the presence of excess H2O2.