Cryo-EM structure of Mycobacterium smegmatis DyP-loaded encapsulin.

Encapsulins containing dye-decolorizing peroxidase (DyP)-type peroxidases are ubiquitous among prokaryotes, protecting cells against oxidative stress. However, little is known about how they interact and function. Here, we have isolated a native cargo-packaging encapsulin from Mycobacterium smegmatis and determined its complete high-resolution structure by cryogenic electron microscopy (cryo-EM). This encapsulin comprises an icosahedral shell and a dodecameric DyP cargo. The dodecameric DyP consists of two hexamers with a twofold axis of symmetry and stretches across the interior of the encapsulin. Our results reveal that the encapsulin shell plays a role in stabilizing the dodecameric DyP. Furthermore, we have proposed a potential mechanism for removing the hydrogen peroxide based on the structural features. Our study also suggests that the DyP is the primary cargo protein of mycobacterial encapsulins and is a potential target for antituberculosis drug discovery.

Expression of the Cyanidioschyzon merolae stromal ascorbate peroxidase in Arabidopsis thaliana enhances thermotolerance.

The ability of the primitive red alga Cyanidioschyzon merolae to adapt to high temperatures was utilized to produce thermotolerant transgenic plants. C. merolae inhabits an extreme environment (42 degrees C, pH 2.5) and the nuclear, mitochondrial, and plastid genomes have been sequenced. We analyzed expressed sequence tag (EST) data to reveal mechanisms of tolerance to high temperatures. The stromal ascorbate peroxidase (CmstAPX) that scavenges reactive oxygen species (ROS) was expressed at high levels (4th of 4,479 entries), thus, it offers clues to understanding high-temperature tolerance. CmstAPX has a chloroplast transit peptide (cTP) and a peroxidase domain. The peroxidase domain of CmstAPX has deletions and insertions when compared with that of Arabidopsis thaliana stromal APX (AtstAPX). To clarify aspects of tolerance to oxidative and high-temperature stress, we produced transgenic A. thaliana plants overexpressing CmstAPX and AtstAPX. CmstAPX plants showed higher activities of soluble APX than those of wild-type and AtstAPX plants. Fluorescence signals of a GFP fusion protein, immuno-fluorescence, and immunogold electron microscopy showed that CmstAPX was localized in the stroma of chloroplasts. Compared with wild-type plants and AtstAPX plants, CmstAPX plants were more tolerant to oxidative stress induced by methylviologen (MV, 0.4 muM) and high-temperature stress (33 degrees C). CmstAPX plants retained the highest chlorophyll content when treated with MV and high temperature, and their stroma and chloroplasts remained intact in their chloroplasts, whereas they disintegrated in wild-type plants. Our results suggest that the increased activity of APX in the chloroplasts of CmstAPX plants increased thermotolerance by increasing ROS-scavenging capacity at high temperatures.

Peroxidase catalytic cycle of MCM-41-entrapped microperoxidase-11 as a mechanism for phenol oxidation.

The encapsulation of microperoxidases (MPs) into molecular sieves with controlled pore size, such as the mesoporous silica MCM-41, represents a nanotechnology strategy to control the catalytic properties of MPs and mimic the enzymatic activity of hemoproteins. In this work, the ferric microperoxidase-11 (MP-11), obtained from trypsin-catalyzed hydrolysis of horse-heart cytochrome c, was entrapped in MCM-41, thus resulting in a catalyst (Fe(III)MP11MCM41) with catalase and monooxygenase properties. The entrapment of MP-11 inside MCM-41 was confirmed by elemental analysis and UV-visible spectrum, with a red shift in the Soret band indicating that the heme group was in a hydrophobic microenvironment. Similarly to catalase, the catalyst Fe(III)MP11MCM41 exhibited specificity for hydrogen peroxide to be converted to a high-valence oxidized intermediate, Compound II. Also mimicking catalase, the cleavage of hydrogen peroxide by MP11MCM41 resulted in O2 production detected by a Clark electrode. Phenol was able to act as reducing agent of MP11MCM41 Compound II leading to the completion of a peroxidase cycle, as confirmed by UV-visible spectrometry and EPR measurements. The analysis of the reaction products by high performance liquid chromatogram coupled to tandem mass spectrometry (HPLC/MS) revealed 2,4-dihydroxyphenol as the product of phenol oxidation by MP11MCM41. Therefore, in addition to catalase activity, the catalyst MP11MCM41 also displayed monooxygenase properties, which was possible because the MP-11 heme iron promotes homolytic cleavage of the hydrogen peroxide generating hydroxyl radicals. With such characteristics, MCM-41-entrapped MP-11 is a promising catalyst for nanobiotechnological devices.

Comparison of the decameric structure of peroxiredoxin-II by transmission electron microscopy and X-ray crystallography.

The decameric human erythrocyte protein torin is identical to the thiol-specific antioxidant protein-II (TSA-II), also termed peroxiredoxin-II (Prx-II). Single particle analysis from electron micrographs of Prx-II molecules homogeneously orientated across holes in the presence of a thin film of ammonium molybdate and trehalose has facilitated the production of a >/=20 A 3-D reconstruction by angular reconstitution that emphasises the D5 symmetry of the ring-like decamer. The X-ray structure for Prx-II was fitted into the transmission electron microscopic reconstruction by molecular replacement. The surface-rendered transmission electron microscopy (TEM) reconstruction correlates well with the solvent-excluded surface of the X-ray structure of the Prx-II molecule. This provides confirmation that transmission electron microscopy of negatively stained specimens, despite limited resolution, has the potential to reveal a valid representation of surface features of protein molecules. 2-D crystallisation of the Prx-II protein on mica as part of a TEM study resulted in the formation of a p2 crystal form with parallel linear arrays of stacked rings. This latter 2-D form correlates well with that observed from the 2.7 A X-ray structure of Prx-II solved from a new orthorhombic 3-D crystal form.

Low pH crystal structure of glycosylated lignin peroxidase from Phanerochaete chrysosporium at 2.5 A resolution.

The heme-containing glycoprotein lignin peroxidase (pI 4.15) has been crystallized at pH 4.0. The structure of the peroxidase from the orthorhombic crystals has been determined by multiple isomorphous replacement. The model comprises all 343 amino acids, one heme molecule, and three sugar residues. It has been refined to an R-factor of 20.3%. The chain fold of residues 15 to 275 is in general similar to those of cytochrome c peroxidase. Despite binding of the heme to the same region and a similar arrangement of the proximal and distal histidine as in cytochrome c peroxidase a significantly larger distance of the iron ion to the proximal histidine is observed. Distinct electron density extending from Asn-257 and at the distal side of the heme indicates ordered sugar residues in the crystal.

In silico studies on tryparedoxin peroxidase of Leishmania infantum: structural aspects.

Tryparedoxin peroxidase (TryP) is a key enzyme of the trypanothione-dependent metabolism for removal of oxidative stress in leishmania. These enzymes function as antioxidants through their peroxidase and peroxynitrite reductase activities. Inhibitors of this enzyme are presumed to be antilesihmania drugs and structural studies are prerequisite of rational drug design. We have constructed three dimensional structure of TryP of Leishmania infantum using comparative modeling. Structural analysis reveals several interesting features. Moreover, it shows remarkable structural difference with human host glutathione peroxidase, an enzyme involved in similar function and TryP from Leishmania major.

Ultrastructure of the proteoliaisin-ovoperoxidase complex and its spatial organization within the Strongylocentrotus purpuratus fertilization envelope.

Ovoperoxidase is a cortical granule-derived enzyme that hardens the sea urchin fertilization envelope by catalyzing the formation of dityrosine residues. Ovoperoxidase works in concert with a second protein, proteoliaisin, which anchors ovoperoxidase to the nascent fertilization envelope in a divalent cation-dependent manner. In this study, we examined the Ca(2+)-dependent interaction of proteoliaisin with ovoperoxidase in rotary-shadowed Pt replicas. Ovoperoxidase, a uniformly sized globular molecule, binds to a distal portion of rod-shaped proteoliaisin when low concentrations of Ca2+ are present. Higher Ca2+ concentrations lead to the formation of extended proteoliaisin strands that are decorated along their lengths with ovoperoxidase. Using immunogold labeling, we also examined the assimilation of these two proteins into the fertilization envelope in quick-frozen, deeply etched samples. Both proteins are abundant in the fertilization envelope as early as one minute after fertilization. Coincident with paracrystalline coating of the envelope, the labeling density is markedly reduced, suggesting that antigenic sites may be masked by the paracrystalline coat. This suggests that the ovoperoxidase-proteoliaisin complex resides within the central portion of the fertilization envelope, rather than in the paracrystalline coat.

Identification of a specific manganese peroxidase among ligninolytic enzymes secreted by Phanerochaete chrysosporium during wood decay.

The specific enzymes associated with lignin degradation in solid lignocellulosic substrates have not been identified. Therefore, we examined extracts of cultures of Phanerochaete chrysosporium that were degrading a mechanical pulp of aspen wood. Western blot (immunoblot) analyses of the partially purified protein revealed lignin peroxidase, manganese-dependent peroxidase (MnP), and glyoxal oxidase. The dominant peroxidase, an isoenzyme of MnP (pI 4.9), was isolated, and its N-terminal amino acid sequence and amino acid composition were determined. The results reveal both similarities to and differences from the deduced amino acid sequences from cDNA clones of dominant MnP isoenzymes from liquid cultures. Our results suggest, therefore, that the ligninolytic-enzyme-encoding genes that are expressed during solid substrate degradation differ from those expressed in liquid culture or are allelic variants of their liquid culture counterparts. In addition to lignin peroxidase, MnP, and glyoxal oxidase, xylanase and protease activities were present in the extracts of the degrading pulp.

NADH binding site and catalysis of NADH peroxidase.

The structure of the complex between cofactor NADH and the enzyme NADH peroxidase from Streptococcus faecalis 10C1 (Enterococcus faecalis) has been determined by crystal soaking, X-ray data collection, model building of NADH and refinement at 0.24-nm resolution based on the known enzyme structure [Stehle, T., Ahmed, S. A., Claiborne, A. & Schulz, G. E. (1991) J. Mol. Biol. 221, 1325-1344]. Apart from NADH, the catalytic center of the enzyme contains FAD and a cysteine that shuttles between thiolate and sulfenic acid states. Unfortunately, this cysteine was irreversibly oxidized to a cysteine sulfonic acid in the established enzyme structure. Based on the geometry of the catalytic center, we discuss the stabilization of the oxidation-sensitive sulfenic acid and propose a reaction mechanism.

Vesicular transport of peroxidase in human eosinophilic myelocytes.

We performed ultrastructural cytochemistry to detect peroxidase in developmentally arrested human eosinophilic myelocytes. Human umbilical cord blood mononuclear cells were cultured for 21 days in the presence of murine-derived conditioned media, resulting in the development of eosinophilic myelocytes. Unlike normally developing eosinophilic myelocytes, which contain peroxidase in synthetic organelles (i.e. cisterns surrounding the nucleus and bounded by the rough endoplasmic reticulum and Golgi structures) and in immature and mature granules, the developmentally arrested cells showed ultrastructural evidence of decreased synthesis and secretory transport of peroxidase. Thus, peroxidase was generally absent in the perinuclear and rough endoplasmic cisterns, in Golgi structures, in immature granules and in the matrix compartment of most mature granules. Rather, biocompartmental specific granules displayed empty, peroxidase-negative matrix and central, peroxidase-negative core material. Peroxidase was present in perigranular vesicles, some of which were attached to granules. Such peroxidase-loaded transport vesicles are similar to those that effect piecemeal degranulation of mature human eosinophils cultured in rhIL-5-containing media [1]. These findings establish vesicle-mediated piecemeal degranulation in the secretory repertoire of immature human eosinophils and suggest the possibility that eosinophilic myelocytes may participate in vivo in important physiological and/or pathological events that require selective secretion from the specific granule matrix compartment.

Production and characterization of monoclonal antibodies to wall-localized peroxidases from corn seedlings.

A library of 22 hybridomas, which make antibodies to soluble wall antigens from the coleoptiles and primary leaves of etiolated corn (Zea mays L.) seedlings, was raised and cloned three times by limit dilution to assure monoclonal growth and stability. Two of these hybridomas made immunoglobulin G antibodies, designated mWP3 and mWP19, which both effectively immunoprecipitated peroxidase activity from crude and partially purified preparations of wall peroxidases. Direct peroxidase-binding assays revealed that both antibodies bound enzymes with peroxidase activity. As judged by immunoblot analyses, mWP3 recognized a Mr 98,000 wall peroxidase with an isoelectric point near 4.2, and mWP19 recognized a Mr 58,000 wall peroxidase. Immunogold localization studies showed both peroxidases are predominately in cell walls.