Fungal enzymes for environmental purposes, a molecular biology challenge

In their capacity to transform xenobiotics and polluting compounds, fungal peroxidases and their use in the environmental field have a recognized and important potential. However, both fundamental and practical issues, such as enzyme stability and availability, have delayed the development of industrial applications. Three main protein engineering challenges have been identified: (1) Enhancement of operational stability, specifically hydrogen peroxide stability in the case of fungal peroxidases. (2) Increase of the enzyme redox potential in order to widen the substrate range. (3) Development of heterologous expression and industrial production. The bottlenecks, advances and strategies that have been proven successful are discussed.     

Palm Tree Peroxidases

Over the years novel plant peroxidases have been isolated from palm trees leaves. Some molecular and catalytic properties of palm peroxidases have been studied. The substrate specificity of palm peroxidases is distinct from the specificity of other plant peroxidases. Palm peroxidases show extremely high stability under acidic and alkaline conditions and high thermal stability. Moreover, these enzymes are more stable with respect to hydrogen peroxide treatment than other peroxidases. Due to their extremely high stability, palm peroxidases have been used successfully in the development of new bioanalytical tests, the construction of improved biosensors, and in polymer synthesis.     

Improved operational stability of peroxidases by coimmobilization with glucose oxidase

The operational stability of peroxidases was considerably enhanced by generating hydrogen peroxide in situ from glucose and oxygen. For example, the total turnover number of microperoxidase-11 in the oxidation of thioanisole was increased sevenfold compared with that obtained with continuous addition of H(2)O(2). Coimmobilization of peroxidases with glucose oxidase into polyurethane foams afforded heterogeneous biocatalysts in which the hydrogen peroxide is formed inside the polymeric matrix from glucose and oxygen. The total turnover number of chloroperoxidase in the oxidation of thioanisole and cis-2-heptene was increased to new maxima of 250. 10(3) and 10. 10(3), respectively, upon coimmobilization with glucose oxidase. Soybean peroxidase, which normally shows only classical peroxidase activity, was transformed into an oxygen-transfer catalyst when coimmobilized with glucose oxidase. The combination catalyst mediated the enantioselective oxidation of thioanisole [50% ee (S)] with 210 catalyst turnovers.     

An examination of the peroxidases from Lupinus albus L. hypocotyls

Peroxidases (EC 1.11.1.7) from hypocotyls of Lupinus albus L. cv. Rio Maior have been characterised using one- and two-dimensional, native electrophoretic techniques. Data are presented showing the complexity in charge and molecular size or shape of these peroxidases. We report the finding of a new acidic peroxidase and several new basic peroxidases in these hypocotyls, and of their stability to treatments considered to break ligand-induced variants and conformational variants derived from differences in polypeptide folding. Densitometric data demonstrate that these new peroxidases contribute up to 60 of the total peroxidase activity in hypocotyls. Studies of intercellular fluid, cell-wall and soluble fractions, with assays of purity were conducted in an attempt to define the subcellular locations of these additional peroxidases. The acidic form (pI 4.1) is greatly enriched in soluble fractions, three of the basic peroxidases (pIs 9.5, 9.7 and >9.7) are strongly associated to the cell wall, ad a minor, basic component (pI 9.7) is enriched in the intercellular fluid. Individual peroxidase activities with the substrates coniferyl alcohol, ferulic acid or indole acetic acid were compared by densitometric analysis of zymograms with those for guaiacol, and notable differences between these peroxidases in their capacity to oxidise indole acetic acid in vitro were identified. The possible functions of these peroxidases in vivo and their implications to current understanding of peroxidases in L. albus are discussed.Abbreviations APAGE anionic polyacrylamide gel electrophoresis - CA coniferyl alcohol - CPAGE cationic polyacrylamide gel electrophoresis - IEF isoelectric focusin - NEIEF non-equilibrated isoelectric focusing - 2D two dimensional - pI isoelectric point - RCPAGE reversed current polyacrylamide gel electrophoresis     

Does diphenylene iodonium chloride have any effect on the O2- -generating step of plant peroxidases?

The O2*- -generating step of plant peroxidases during their catalytic cycle is represented by the decay of compound III (CoIII) into ferriperoxidase, which most likely involves the dissociation of a ferric-O2*- complex to yield the ferric form of the enzyme and O2*-. Diphenylene iodonium chloride (DPI), at 50-100 microM, does not significantly enhance the stability of CoIII of peroxidase, as judged by the values of k(decay), and therefore, DPI appears to have no effect on the O2*- -generating step of plant peroxidases. From these results, it is concluded that caution should be exercised when considering peroxidase as a possible enzyme target of O2*- -mediated plant physiological processes sensitive to DPI inhibition.     

Relative stability of recombinant versus native peroxidases from Phanerochaete chrysosporium.

Two types of glycosylated peroxidases are secreted by the white-rot fungus Phanerochaete chrysosporium, lignin peroxidase (LiP) and manganese peroxidase (MnP). The thermal stabilities of recombinant LiPH2, LiPH8, and MnPH4, which were expressed without glycosylation in Escherichia coli, were lower than those of corresponding native peroxidases isolated from P. chrysosporium. Recovery of thermally inactivated recombinant enzyme activities was higher than with that of the thermally inactivated native peroxidases. Removal of N-linked glycans from native LiPH8 and MnPH4 did not affect enzyme activities or thermal stabilities of the enzymes. Although LiPH2, LiPH8, and MnPH4 contained O-linked glycans, only the O-linked glycans from MnPH4 could be removed by O-glycosidase, and the glycan-depleted MnPH4 exhibited essentially the same activity as nondeglycosylated MnPH4, but thermal stability decreased. Periodate-treated MnPH4 exhibited even lower thermal stability than O-glycosidase treated MnPH4. The role of O-linked glycans in protein stability was also evidenced with LiPH2 and LiPH8. Based on these data, we propose that neither N- nor O-linked glycans are likely to have a direct role in enzyme activity of native LiPH2, LiPH8, and MnPH4 and that only O-linked glycans may play a crucial role in protein stability of native peroxidases.     

Homology among multiple extracellular peroxidases from Phanerochaete chrysosporium

The extracellular peroxidases of Phanerochaete chrysosporium were separated into 21 proteins by analytical isoelectric focusing. Fifteen of these enzymes oxidized veratryl alcohol (lignin peroxidases) in the presence of H2O2. Six enzymes were Mn(II)-dependent peroxidases. The Mn(II)-dependent enzymes appeared and reached their maximal activity earlier than the lignin peroxidases in the cultures. Peptide mapping, amino acid analysis, and reaction against specific antibodies showed that all the Mn(II)-dependent peroxidases were probably products of one gene. A great degree of homology was also present among the various lignin peroxidases.     

3'UTRs of glutathione peroxidases differentially affect selenium-dependent mRNA stability and selenocysteine incorporation efficiency

Selenoprotein mRNAs are particular in several aspects. They contain a specific secondary structure in their 3'UTR, called Secis (selenocysteine inserting sequence), which is indispensable for selenocysteine incorporation, and they are degraded under selenium-limiting conditions according to their ranking in the hierarchy of selenoproteins. In the familiy of selenium-dependent glutathione peroxidases (GPx) the ranking is GI-GPx > or = PHGPx > cGPx = pGPx. This phenomenon was studied by mutually combining the coding regions of GI-GPx, PHGPx and cGPx with their 3'UTRs. HepG2 cells were stably transfected with the resulting constructs. Expression of glutathione peroxidases was estimated by activity measurement and Western blotting, the selenium-dependent mRNA stability by real-time PCR. Whereas 3'UTRs from stable PHGPx and GI-GPx could be exchanged without loss of stability, they were not able to stabilize cGPx mRNA. cGPx 3'UTR rendered GI-GPx and PHGPx mRNA unstable. Thus, cGPx mRNA contains selenium-responsive instability elements in both the translated and the untranslated region, which cannot be compensated by one of the stable homologs. Stabilizing efficiency of an individual GPx 3'UTR did not correlate with the efficiency of selenocysteine incorporation. PHGPx 3'UTR was equally effective as cGPx 3'UTR in enhancing GPx activity in all constructs, while GI-GPx 3'UTR showed a markedly lower efficacy. We conclude that different mRNA sequences and/or RNA-binding proteins might regulate mRNA stability and translation of selenoprotein mRNA.     

Two pathogenesis-related peroxidases in greengram (Vigna radiata (L.) wilczek) leaves and cultured cells induced by Macrophomina phaseolina (Tassi) Goid. and its elicitor

An elicitor has been isolated from Macrophomina phaseolina, the root rot and leaf blight pathogen of greengram. Suspension-cultured cells of greengram were established which responded to the fungal elicitor. When greengram leaves were inoculated with M. phaseolina two new peroxidases appeared. Similarly, two new peroxidases could be detected in suspension-cultured greengram cells when treated with the fungal elicitor. These peroxidases were purified by column chromatography and their molecular masses were 27 and 38 kDa. The new peroxidases detected in both leaves and cultured cells appear to be similar with the same molecular weights.     

Chemical modification of chloroperoxidase for enhanced stability and activity

Chloroperoxidase from Caldariomyces fumago (CPO, EC 1.11.1.10) is one of the most interesting enzymes from the group of heme peroxidases and has been extensively applied in synthetic processes. Nevertheless, the practical application of CPO is limited due to its very low operational stability, especially in the presence of peroxidative compounds. For this reason, effect of chemical modifications of CPO in the stability of the enzyme was studied. Side-chain selective modifications of amino groups of Lys residues, and carboxyl groups of Asp and Glu residues, as well as crosslinking and periodate oxidation of sugar moiety were carried out. The stability of modified CPOs was evaluated at elevated pH and temperature, and in the presence of tert-butyl hydroperoxide. Effect of modification of CPO on the performance of the reaction of Cbz-ethanolamine oxidation was studied as well. Those modifications that involved carboxyl groups via carbodiimide coupled method and the periodate oxidation of the sugar moiety produced better catalysts than native CPO in terms of stability and activity at elevated pH values and temperatures.     

Oxidoreductases on their way to industrial biotransformations

Fungi produce heme-containing peroxidases and peroxygenases, flavin-containing oxidases and dehydrogenases, and different copper-containing oxidoreductases involved in the biodegradation of lignin and other recalcitrant compounds. Heme peroxidases comprise the classical ligninolytic peroxidases and the new dye-decolorizing peroxidases, while heme peroxygenases belong to a still largely unexplored superfamily of heme-thiolate proteins. Nevertheless, basidiomycete unspecific peroxygenases have the highest biotechnological interest due to their ability to catalyze a variety of regio- and stereo-selective monooxygenation reactions with H₂O₂ as the source of oxygen and final electron acceptor. Flavo-oxidases are involved in both lignin and cellulose decay generating H₂O₂ that activates peroxidases and generates hydroxyl radical. The group of copper oxidoreductases also includes other H₂O₂ generating enzymes - copper-radical oxidases - together with classical laccases that are the oxidoreductases with the largest number of reported applications to date. However, the recently described lytic polysaccharide monooxygenases have attracted the highest attention among copper oxidoreductases, since they are capable of oxidatively breaking down crystalline cellulose, the disintegration of which is still a major bottleneck in lignocellulose biorefineries, along with lignin degradation. Interestingly, some flavin-containing dehydrogenases also play a key role in cellulose breakdown by directly/indirectly “fueling” electrons for polysaccharide monooxygenase activation. Many of the above oxidoreductases have been engineered, combining rational and computational design with directed evolution, to attain the selectivity, catalytic efficiency and stability properties required for their industrial utilization. Indeed, using ad hoc software and current computational capabilities, it is now possible to predict substrate access to the active site in biophysical simulations, and electron transfer efficiency in biochemical simulations, reducing in orders of magnitude the time of experimental work in oxidoreductase screening and engineering. What has been set out above is illustrated by a series of remarkable oxyfunctionalization and oxidation reactions developed in the frame of an intersectorial and multidisciplinary European RTD project. The optimized reactions include enzymatic synthesis of 1-naphthol, 25-hydroxyvitamin D₃, drug metabolites, furandicarboxylic acid, indigo and other dyes, and conductive polyaniline, terminal oxygenation of alkanes, biomass delignification and lignin oxidation, among others. These successful case stories demonstrate the unexploited potential of oxidoreductases in medium and large-scale biotransformations.     

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

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

Peroxidases

The family of human peroxidases described includes myeloperoxidase, eosinophil peroxidase, uterine peroxidase, lactoperoxidase, salivary peroxidase, thyroid peroxidase and prostaglandin H1/2 synthases. The chemical identity of the peroxidase compound I and II oxidation states for the different peroxidases are compared. The identities of the distal and proximal amino acids of the catalytic site of each peroxidase are also compared. The gene characteristics and chromosomal location of the human peroxidase family have been tabulated and their molecular evolution discussed. Myeloperoxidase polymorphism and the mutations identified so far that affect myeloperoxidase activity and modulate their susceptibility to disease is described. The mechanisms for hypohalous and hypothiocyanate formation by the various peroxidases have been compared. The cellular function of the peroxidases and their hypohalites have been described as well as their inflammatory effects. The peroxidase catalysed cooxidation of drugs and xenobiotics that results in oxygen activation by redox cycling has been included. Low-density lipoprotein oxidation (initiation of atherosclerosis), chemical carcinogenesis, idiosyncratic drug reactions (e.g. agranulocytosis), liver necrosis or teratogenicity initiated by the cooxidation of endogenous substrates, plasma amino acids, drugs and xenobiotics catalysed by peroxidases or peroxidase containing cells have also been compared. Finally, peroxidase inhibitors currently in use for treating various diseases are described.     

Purification,characterization and accumulation of three virus-induced cucumber peroxidases

Three anionic peroxidases (EC 1.11.1.7), named Prx1, 2, and 3, which are rapidly accumulated in cucumber (Cucumis sativus L., cv. Laura) reacting hypersensitively to tobacco necrosis virus, were purified to homogeneity. The three enzymes had an isoelectric point about 4.3, and the relative molecular masses of Prx1, 2, and 3 estimated by SDS-PAGE were 40 700, 38 000, and 37 100, respectively. These peroxidases had a similar pH stability, but differed in their specific activity, pH optimum, and thermal stability By Ouchterlony double diffusion tests with antisera raised against the three purified enzymes, close serological relationships have been demonstrated between the three peroxidases.     

Kinetic studies on veratryl alcohol transformation by horseradish peroxidase

A number of peroxidases, such as lignin peroxidase and manganese peroxidase have proved to be useful for industrial applications. Some studies on the effects of temperature and pH stability have been carried out. It is known that veratryl alcohol increases their stability in the range 28-50 degrees C and is oxidized, leading to veratryl aldehyde formation. Similar results with horseradish peroxidase (HRP) in the presence of cofactors were found, but the oxidation of veratryl alcohol in the absence of cofactors was extremely labile at acid pH and inactivated in a few minutes. Considering the growing industrial application of HRP, knowledge of its stability and denaturation kinetics is required. In this study, horseradish peroxidase pool (HRP-VI) and its isoenzymes HRP-VIII (acid) and HRP-IX (basic) have been shown to catalyze the oxidation of veratryl alcohol to veratryl aldehyde in the presence of hydrogen peroxide at pH 5.8 in the 35-45 degrees C range and in the absence of any cofactors. Heat and pH denaturation experiments in the presence and absence of veratryl alcohol incubation were conducted with HRP-VI and HRP-IX isoenzymes. HRP-IX was the most active isoenzyme acting on veratryl alcohol but HRP-VI was the most stable for the temperature range tested. At 35 degrees C the HRP pool presented decay constant (Kd) values of 5.5 x 10(-2) h(-1) and 1.4 10(-2) h(-1) in the absence and presence of veratryl alcohol, respectively, with an effective ratio of 3.9. These results present a new feature of peroxidases that opens one more interesting application of HRP to industrial processes.     

Antigenic relationships between petunia peroxidase a and specific peroxidase isoenzymes in other Solanaceae

Summary A highly specific rabbit antiserum raised against peroxidase (PRXa) from petunia (Petunia hybrida) was used to investigate the antigenic relatedness of peroxidases in the Solanaceae. After SDS-PAGE of crude leaf extracts from a large number of species of this family, immunoblotting revealed that cross-reacting protein bands were present in all species tested. In order to determine whether these protein bands represent peroxidases, the peroxidase isoenzymes in thorn apple (Datura stramonium L.), tobacco (Nicotiana tabacum L.), sweet pepper (Capsicum annuum L.), potato (Solanum tuberosum L.), and tomato (Lycopersicon esculentum Mill.) were further analyzed. Immunoblots obtained after native PAGE revealed that the antiserum only recognized fast-moving peroxidase isoenzymes that are localized in the apoplast. Despite their serological relatedness, these peroxidases differed with respect to heat stability and apparent molecular weight. Differences in avidity for the petunia PRXa antiserum were suggested by immunoprecipitation with antibodies bound to protein A-Sepharose. The antiserum did not react with peroxidases from horseradish (Armoracea rusticana Gaertn., Mey and Scherb), turnip (Brassica napus L.), African marigold (Tagetes cresta L.), maize (Zea mays L.), and oats (Avena sativa L.). Apparently, the Solanaceae contain orthologous genes encoding the fast-moving anionic peroxidases homologous to petunia PRXa.     

Performing the paradoxical: how plant peroxidases modify the cell wall

Since their appearance in the first land plants, genes encoding class III peroxidases have been duplicated many times during evolution and now compose a large multigene family. The reason for these many genes is elusive, and we are still searching for the specific function of every member of the family. Nevertheless, our current understanding implicates peroxidases as key players during the whole life cycle of a plant, and particularly in cell wall modifications, in roles that can be antagonistic depending on the developmental stage. This diversity of functions derives in part from two possible catalytic cycles of peroxidases involving the consumption or release of H(2)O(2) and reactive oxygen species (e.g. O(2)(-), H(2)O(2), OH).     

Purification and properties of cytochrome c and two peroxidases from spinach leaves

1. A simultaneous purification procedure of cytochrome c, peroxidases,ferredoxin, ferredoxin-NADP reductase and sulfite reductasefrom spinach leaves is described. Cytochrome c, ferredoxin andferredoxin-NADP reductase were prepared in crystalline states.The two peroxidases were obtained in homogeneous states as evidencedby their electrophoretic patterns on acrylamide gel and sedimentationanalysis. 2. Crystalline cytochrome c showed a molecular weight of 13,800and an E₀' of 270 mv at pH 7.0. In addition to these properties,its spectral pattern also indicated that this cytochrome c wasderived from mitochondria. 3. Two peroxidases were isolated in high spin forms after treatmentwith HgCl₂. They had a-peaks at 556 mµ in their reducedforms. Although both peroxidases showed small differences inchromatographic behavior on a carboxymethyl cellulose column,' they had similar spectral properties, dissociation constantsof peroxidase-cyanide complex and rate constants for peroxidasereactions. (Received December 24, 1970; )     

Cadmium-induced microsomal membrane-bound peroxidases mediated hydrogen peroxide production in barley roots

The effect of cadmium on microsomal membrane-bound peroxidases and their involvement in hydrogen peroxide production was studied in barley roots. One anionic and two cationic peroxidases were detected, which were strongly activated by Cd treatment. Positive correlation was found between root growth inhibition and increased peroxidase, NADH oxidase activity and H₂O₂ generation in root microsomal membrane fraction of Cd-treated barley roots.     

Catalytic Profile of Arabidopsis Peroxidases,AtPrx-2, 25 and 71, Contributing to Stem Lignification

Lignins are aromatic heteropolymers that arise from oxidative coupling of lignin precursors, including lignin monomers (p-coumaryl, coniferyl, and sinapyl alcohols), oligomers, and polymers. Whereas plant peroxidases have been shown to catalyze oxidative coupling of monolignols, the oxidation activity of well-studied plant peroxidases, such as horseradish peroxidase C (HRP-C) and AtPrx53, are quite low for sinapyl alcohol. This characteristic difference has led to controversy regarding the oxidation mechanism of sinapyl alcohol and lignin oligomers and polymers by plant peroxidases. The present study explored the oxidation activities of three plant peroxidases, AtPrx2, AtPrx25, and AtPrx71, which have been already shown to be involved in lignification in the Arabidopsis stem. Recombinant proteins of these peroxidases (rAtPrxs) were produced in Escherichia coli as inclusion bodies and successfully refolded to yield their active forms. rAtPrx2, rAtPrx25, and rAtPrx71 were found to oxidize two syringyl compounds (2,6-dimethoxyphenol and syringaldazine), which were employed here as model monolignol compounds, with higher specific activities than HRP-C and rAtPrx53. Interestingly, rAtPrx2 and rAtPrx71 oxidized syringyl compounds more efficiently than guaiacol. Moreover, assays with ferrocytochrome c as a substrate showed that AtPrx2, AtPrx25, and AtPrx71 possessed the ability to oxidize large molecules. This characteristic may originate in a protein radical. These results suggest that the plant peroxidases responsible for lignin polymerization are able to directly oxidize all lignin precursors.