Evolution of structure and function of Class I peroxidases

The phylogenetics of Class I of the heme peroxidase-catalase superfamily currently representing over 940 known sequences in all available genomes of prokaryotes and eukaryotes has been analysed. The robust reconstructed tree for 193 Class I peroxidases with 6 selected Class II representatives reveals all main trends of molecular evolution. It suggests how the ancestral peroxidase gene might have been transferred from prokaryotic into eukaryotic genomes. Besides well known families of catalase-peroxidases, cytochrome c peroxidases and ascorbate peroxidases, the phylogenetic analysis shows for the first time the presence of two new well separated clades of hybrid-type peroxidases that might represent evolutionary bridges between catalase-peroxidases and cytochrome c peroxidases (type A) as well as between ascorbate peroxidases and Class II peroxidases (type B). Established structure-function relationships are summarized. Presented data give useful hints on the origin and evolution of catalytic promiscuity and specificity and will be a valuable basis for future functional analysis of Class I enzymes as well as for de novo design.     

Peroxidases and the metabolism of capsaicin in Capsicum annuum L.

Capsaicinoids are acid amides of C₉ - C₁₁ branched-chain fatty acids and vanillylamine. These compounds are responsible for the pungency of the Capsicum species and of cultivars regarded as hot peppers. Moreover, it has been suggested that these compounds play an ecological role in seed dispersal. Because they are used in the pharmacological, food and pesticide industries, much attention has been paid on knowing how their accumulation is controlled, both in the fruit and in cell cultures. Such control involves the processes of biosynthesis, conjugation and catabolism. Recent progress has been made on the biosynthetic pathway, and several of the genes coding for biosynthetic enzymes have been cloned and expression studies performed. With regard to catabolism, cumulative evidence supports that capsaicinoids are oxidized in the pepper by peroxidases. Peroxidases are efficient in catalyzing in vitro oxidation of both capsaicin and dihydrocapsaicin. These enzymes are mainly located in placental and the outermost epidermal cell layers of pepper fruits, as occurs with capsaicinoids, and some peroxidases are present in the organelle of capsaicinoid accumulation, that is, the vacuole. Hence, peroxidases are in the right place for this function. The products of capsaicin oxidation by peroxidases have been characterized in vitro, and some of them have been found to appear in vivo in the Capsicum fruit. Details on the kinetics and catalytic cycle for capsaicin oxidation by peroxidases are also discussed.     

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.     

Extracellular Heme Peroxidases in Actinomycetes: a Case of Mistaken Identity

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

Molecular cloning of two novel peroxidases and their response to salt stress and salicylic acid in the living fossil Ginkgo biloba

Background and Aims

Peroxidase isoenzymes play diverse roles in plant physiology, such as lignification and defence against pathogens. The actions and regulation of many peroxidases are not known with much accuracy. A number of studies have reported direct involvement of peroxidase isoenzymes in the oxidation of monolignols, which constitutes the last step in the lignin biosynthesis pathway. However, most of the available data concern only peroxidases and lignins from angiosperms. This study describes the molecular cloning of two novel peroxidases from the ‘living fossil’ Ginkgo biloba and their regulation by salt stress and salicylic acid.

Methods

Suspension cell cultures were used to purify peroxidases and to obtain the cDNAs. Treatments with salicylic acid and sodium chloride were performed and peroxidase activity and gene expression were monitored.

Key Results

A novel peroxidase was purified, which preferentially used p-hydroxycinnamyl alcohols as substrates and was able to form dehydrogenation polymers in vitro from coniferyl and sinapyl alcohols. Two peroxidase full-length cDNAs, GbPrx09 and GbPrx10, were cloned. Both peroxidases showed high similarity to other basic peroxidases with a putative role in cell wall lignification. Both GbPrx09 and GbPrx10 were expressed in leaves and stems of the plant. Sodium chloride enhanced the gene expression of GbPrx09 but repressed GbPrx10, whereas salicylic acid strongly repressed both GbPrx09 and GbPrx10.

Conclusions

Taken together, the data suggest the participation of GbPrx09 and GbPrx10 in the developmental lignification programme of the cell wall. Both peroxidases possess the structural characteristics necessary for sinapyl alcohol oxidation. Moreover, GbPrx09 is also involved in lignification induced by salt stress, while salicylic acid-mediated lignification is not a result of GbPrx09 and GbPrx10 enzymatic activity.     

Characteristics and function of a low-molecular-weight compound with reductive activity from Phanerochaete chrysosporium in lignin biodegradation

A novel reductive compound with molecular weight of about 1000 Da, named Pc reducer, was purified from the liquid culture of a white-rot basidiomycete Phanerochaete chrysosporium. It was likely to have an alkene-ester structure according to Fourier-transform infrared spectroscopy (FT-IR) and nuclear magnetic resonance (NMR) spectra. Pc reducer reduced the hydroxyl radical HO and the stable nitroxide radical under certain conditions. It inhibited the repolymerization of the products from the oxidation of phenolic lignin-model compounds by reducing certain intermediate radicals. The activity of manganese peroxidases was promoted by Pc reducer at certain concentrations. Pc reducer could also weaken the repolymerization of fragments from the oxidation of Na-lignosulfonate by lignin peroxidases and manganese peroxidases. It has potential ability to improve the ligninolytic efficiency of peroxidases in P. chrysosporium.     

Possible functions of extracellular peroxidases in stress-induced generation and detoxification of active oxygen species

Extracellular peroxidases are classified as free, or ionically or covalently bound to the cell wall. In addition, peroxidase-like activities have often been demonstrated at the outer surface of protoplasts and plasma membrane preparations. Under certain conditions apoplastic peroxidases have been shown to contribute to the formation of superoxide and hydrogen peroxide during the `oxidative burst' through the oxidation of a reductant. However, the identity of this reductant remains unclear. It has been suggested that the production of these active oxygen species may play important roles in plant responses to biotic and abiotic stress. Extracellular release of pre-existing and de novo synthesis of apoplastic peroxidases is regulated by changing environmental conditions. While the oxidative burst could potentially be harmful to a plant's own cells, tissues can rapidly metabolize even high concentrations of hydrogen peroxide. Recent work has shown that when extracellular hydrogen peroxide exceeds the supplies of reductants, class II and class III peroxidases can display catalase-like activity. Under these conditions, hydrogen peroxide is able to act as both oxidizing and reducing substrate. It seems likely therefore, that a further role of extracellular peroxidases is to protect plants from the consequences of the oxidative burst that they themselves are responsible for producing.     

Structural determinants of plant peroxidase function

The classical plant peroxidases are a well-studied group of heme-containing enzymes for which many different functions have been proposed. In the majority of plant species investigated they occur as distinctive isoenzymes which can be constitutive or induced in response to external factors such as wounding, stress and attack by pathogens. More than 70 peroxidase isoenzymes are predicted to occur in Arabidopsis thaliana alone, according to recent analysis of the complete peroxidase gene family of this model plant. Understanding this enzymatic diversity and its functional significance is a major focus of structural and mechanistic studies of plant peroxidases. The three-dimensional structures of plant peroxidases from Arabidopsis, barley, horseradish, peanut and soybean have now been determined by X-ray crystallography together with the structures of several catalytic intermediates and substrate complexes that are relevant to enzyme function. On this basis, specific roles for particular amino acid residues and structural motifs or regions have been proposed or in some cases, confirmed. Some of these have been investigated experimentally using site-directed mutagenesis and other techniques. An overview of recent developments will be presented that reflects our current understanding of structure and function in this important group of enzymes.     

Hormonal regulation and distribution of peroxidase isoenzymes in the Cucurbitaceae

Ethylene enhanced the levels of peroxidases in the roots, stems, leaves, and cotyledons of 2-week-old cucumber Cucumis sativus cv Poinsett 76 seedlings. Antibodies to the isoelectric point (pl) 9 and pl 4 isoenzymes were used in a radial immuno-diffusion assay to demonstrate that ethylene induced similar peroxidases in other cultivars of C. sativus, other species of Cucumis and other genera of Cucurbitaceae. Examination of ethylene-induced peroxidases, using isoelectric focusing gels, demonstrated the presence of a series of other peroxidases, mostly slightly acidic, whose isoelectric focusing pH was approximately 6. These pl 6 peroxidases were partially purified on a cation exchange column. Ouchterlony double diffusion gels indicated that these proteins cross-reacted with antibodies to both the pl 9 and pl 4 peroxidase. The data presented here suggest that the induction of peroxidase isoenzymes during ethylene-induced senescence is a common response in this family of plants. In addition, antibody and isoelectric focusing studies indicate that both acidic and basic peroxidase are highly conserved in members of this family.     

Peroxidases of Solanum melongena leaves

Three major peroxidases, designated as A, B₂ and B₂ from Solanum melongena leaves have been reported. Peroxidases-A, -B₂ and -B₂ were considered to be true peroxidases on the basis of k₁:k₄ ratio. The pH optima for the three enzymes were found to be 7·0, 6·0 and 6.0 respectively. These peroxidases differ in their k₁:k₄ ratio, in the effect of pH on this ratio and in the uric acid/guaiacol and o-dianisidine/guaiacol activity ratio.     

Induction of 33-kD and 60-kD Peroxidases during Ethylene-Induced Senescence of Cucumber Cotyledons

Ethylene enhanced the senescence of cucumber (Cucumis sativus L. cv `Poinsett 76') cotyledons. The effect of 10 microliters per liter ethylene was inhibited by 1 millimolar silver thiosulfate, an inhibitor of ethylene action. An increase in proteins with molecular weights of 33 to 30 kilodaltons and lower molecular weights (25, 23, 20, 16, 12, and 10 kilodaltons) were observed in sodium dodecyl sulfate-polyacrylamide gel electrophoresis gels after ethylene enhanced senescence. The measurement of DNase and RNase activity in gels indicated that these new proteins were not nucleases. Two proteins from ethylene-treated cotyledons were purified on the basis of their association with a red chromaphore and subsequently were identified as peroxidases. The molecular weights and isoelectric points (pI) of two of these peroxidases were 33 kilodaltons (cationic, pI = 8.9) and 60 kilodaltons (anionic, pI = 4.0). The observation that [³⁵S]Na₂SO₄ was incorporated into these proteins during ethylene-enhanced senescence suggests that these peroxidases represent newly synthesized proteins. Antibodies to the 33-kilodalton peroxidase precipitated two in vitro translation products from RNA isolated from ethylene-treated but not from control cucumber seedlings. This indicates that the increase in 33-kilodalton peroxidase activity represents de novo protein synthesis. Both forms of peroxidase degraded chlorophyll in vitro, which is consistent with the hypothesis that peroxidases have catabolic or scavenging functions in senescent tissues.     

Peroxidases of Papaver somniferum

Extracts of Papaver somniferum that had peroxidase activity were ineffective in catalysing oxidation of reticuline. Two peroxidases were purified from young seedlings and their properties examined. Only one of them was active toward indole-3-acetic acid (IAA).     

Homology of Plant Peroxidases: AN IMMUNOCHEMICAL APPROACH

Antisera specific for the basic peroxidase from horseradish (Amoracea rusticana) were used to examine homology among horseradish peroxidase isoenzymes and among basic peroxidases from root plants. The antisera cross-reacted with all tested isoperoxidases when measured by both agar diffusion and quantitative precipitin reactions. Precipitin analyses provided quantitative measurements of homology among these plant peroxidases. The basic radish (Raphanus sativus L. cv. Cherry Belle) peroxidase had a high degree of homology (73 to 81%) with the basic peroxidase from horseradish. Turnip (Brassica rapa L. cv. Purple White Top Globe) and carrot (Daucus carota L. cv. Danvers) basic peroxidases showed less cross-reaction (49 to 54% and 41 to 46%, respectively). However, the cross-reactions of antisera with basic peroxidases from different plants were greater than were those observed with acidic horseradish isoenzymes (30 to 35%). These experiments suggest that basic peroxidase isoenzymes are strongly conserved during evolution and may indicate that the basic peroxidases catalyze reactions involved in specialized cellular functions. Anticatalytic assays were poor indicators of homology. Even though homology among isoperoxidases was detected by other immunological methods, antibodies inhibited only the catalytic activity of the basic peroxidase from radish.     

Peroxidases from the extreme dwarf tomato plant. Identification, isolation, and partial purification

Utilizing starch-gel electrophoresis, 12 discrete peroxidases were identified in purified extracts of the dwarf tomato shoot (Lycopersicon esculentum). Nine of the peroxidases moved toward the anode while 3 moved toward the cathode. In addition, a continuous peroxidase smear was separated from the above 12 peroxidases. This smear moved toward the anode and accounted for 50% of the total peroxidase activity in the crude extract.

Four of the major peroxidases were isolated and partially purified, using acetone and ammonium sulfate precipitations, preparative starch-gel electrophoresis and chromatography on DEAE and CM-cellulose.

     

The catalytic mechanism of Pseudomonas cytochrome c peroxidase

The catalytic mechanism of Pseudomonas cytochrome c peroxidase has been studied using rapid-scan spectrometry and stopped-flow measurements. The reaction of the totally ferric form of the enzyme with H₂O₂ was slow and the complex formed was inactive in the peroxidatic cycle, whereas partially reduced enzyme formed highly reactive intermediates with hydrogen peroxide. Rapid-scan spectrometry revealed two different spectral forms, one assignable to Compound I and the other to Compound II as found in the reaction cycle of other peroxidases. The formation of Compound I was rapid approaching that of diffusion control. The stoichiometry of the peroxidation reaction, deduced from the formation of oxidized electron donor, indicates that both the reduction of Compound I to Compound II and the conversion of Compound II to resting (partially reduced) enzyme are one-electron steps. It is concluded that the reaction mechanism generally accepted for peroxidases is applicable also to Pseudomonas cytochrome c peroxidase, the intramolecular source of one electron in Compound I formation, however, being reduced heme c.     

Naturally-occurring tetrahydro-β-carboline alkaloids derived from tryptophan are oxidized to bioactive β-carboline alkaloids by heme peroxidases

β-Carbolines are indole alkaloids that occur in plants, foods, and endogenously in mammals and humans, and which exhibit potent biological, psychopharmacological and toxicological activities. They form from naturally-occurring tetrahydro-β-carboline alkaloids arising from tryptophan by still unknown way and mechanism. Results in this research show that heme peroxidases catalyzed the oxidation of tetrahydro-β-carbolines (i.e. 1,2,3,4-tetrahydro-β-carboline-3-carboxylic acid and 1-methyl-1,2,3,4-tetrahydro-β-carboline-3-carboxylic acid) into aromatic β-carbolines (i.e. norharman and harman, respectively). This oxidation followed a typical catalytic cycle of peroxidases through redox intermediates I, II, and ferric enzyme. Both, plant peroxidases (horseradish peroxidase, HRP) and mammalian peroxidases (myeloperoxidase, MPO and lactoperoxidase, LPO) catalyzed the oxidation in an efficient manner as determined by kinetic parameters (V_MAX and K_M). Oxidation of tetrahydro-β-carbolines was inhibited by peroxidase inhibitors such as sodium azide, ascorbic acid, hydroxylamine and excess of H₂O₂. The formation of aromatic β-carbolines by heme peroxidases can help to explain the presence and activity of these compounds in biological systems.     

Proteomic analysis of the response of Rhizopus oryzae ENHE to pentachlorophenol: Understanding the mechanisms for tolerance and degradation of this toxic compound

Pentachlorophenol (PCP) is a toxic compound widely distributed in the environment. Rhizopus oryzae ENHE has been shown to possess PCP degradation capacities, peroxidases and phenoloxidases are expected to be involved in the degradation process but no studies have been performed that confirm this hypothesis. We have carried out a proteomic study aiming to understand the mechanisms by which R. oryze tolerates and degrades PCP. After culturing the fungus in media with and without PCP, the secretome and the intracellular proteome were analyzed by shotgun proteomics and 2D-Gel Electrophoresis, respectively. Proteins were identified by LC–MS/MS. In the intracellular proteome, 37 proteins were identified from the spots showing higher intensity or exclusive presence in cultures with PCP. Some redundant identifications of proteins appearing in more than one spot, like proteins belonging to energy metabolism, stress response and cell signaling. Proteins putatively involved in PCP degradation, like peroxidases and a methyltransferase, were also identified. In the secretome, 14 proteins were detected that showed at least 2-fold higher abundance in the broths from cultures with PCP. This work provides new information on the response of R. oryzae to the presence of PCP and allowed the identification of some proteins putatively involved in the degradation of the compound.     

Properties of anionic peroxidases purified from Chinese cabbage roots

Two anionic peroxidases were isolated from Chinese cabbage roots and purified using gel filtration followed by ion-exchange chromatography. Following purification a specific activity of peroxidases was estimated as 50 units.mg^-1 (A1) and 30 units.mg^-1 (A2) compared with that of a crude extract of the peroxidases which was 2.31 units.mg^-1. The pH for its optimum activity was 5.0 and the addition of Ca²⁺ produced a 15 % increase in peroxidase activity. Isoelectric focusing techniques were carried out in order to classify the peroxidases based on their isoelectric point (pI). Two anionic peroxidases, A1 and A2, were found to have pI values of 4.83 and 4.78, respectively. The peroxidases were found to be heat-stable, with 20 % (A1) and 16 % (A2) of the enzymatic activity remaining after heat treatment at 70 °C for 20 min. The heat inactivation rate followed first-order kinetics with the activation energy; Ea, estimated as 38.2 kcal.mol^-1 and 36.4 kcal.mol^-1 for A1 and A2, respectively.     

Characterization of Laccases and Peroxidases from Wood-Rotting Fungi (Family Coprinaceae)

Panaeolus sphinctrinus, Panaeolus papilionaceus, and Coprinus friesii are described as producers of ligninolytic enzymes. P. papilionaceus and P. sphinctrinus both produced a laccase. In addition, P. sphinctrinus produced a manganese peroxidase. C. friesii secreted a laccase and two peroxidases similar to the peroxidase of Coprinus cinereus. The purified laccases and peroxidases were characterized by broad substrate specificities, significant enzyme activities at alkaline pH values, and remarkably high pH optima. The two peroxidases of C. friesii remained active at pH 7.0 and 60°C for up to 60 min of incubation. The peroxidases were inhibited by sodium azide and ethylene glycol-bis(β-aminoethyl ether)-N,N,N′,N′-tetraacetic acid (EGTA), whereas the laccases were inhibited by sodium azide and N,N-diethyldithiocarbamic acid. As determined by native polyacrylamide gel electrophoresis and isoelectric focusing, all three fungi produced laccase isoenzymes.