Marcela Ayala

Suicide Inactivation of Peroxidases and the Challenge of Engineering More Robust Enzymes

As the number of industrial applications for proteins continues to expand, the exploitation of protein engineering becomes critical. It is predicted that protein engineering can generate enzymes with new catalytic properties and create desirable, high-value, products at lower production costs. Peroxidases are ubiquitous enzymes that catalyze a variety of oxygen-transfer reactions and are thus potentially useful for industrial and biomedical applications. However, peroxidases are unstable and are readily inactivated by their substrate, hydrogen peroxide. Researchers rely on the powerful tools of molecular biology to improve the stability of these enzymes, either by protecting residues sensitive to oxidation or by devising more efficient intramolecular pathways for free-radical allocation. Here, we discuss the catalytic cycle of peroxidases and the mechanism of the suicide inactivation process to establish a broad knowledge base for future rational protein engineering.

Biocatalytic chlorination of aromatic hydrocarbons by chloroperoxidase of Caldariomyces fumago.

Chloroperoxidase from Caldariomyces fumago was able to chlorinate 17 of 20 aromatic hydrocarbons assayed in the presence of hydrogen peroxide and chloride ions. Reaction rates varied from 0.6 min(-1) for naphthalene to 758 min(-1) for 9-methylanthracene. Mono-, di- and tri-chlorinated compounds were obtained from the chloroperoxidase-mediated reaction on aromatic compounds. Dichloroacenaphthene, trichloroacenaphthene, 9,10-dichloroanthracene, chloropyrene, dichloropyrene, dichlorobiphenylene and trichlorobiphenylene were identified by mass spectral analyses as products from acenaphthene, anthracene, pyrene and biophenylene respectively. Polycyclic aromatic hydrocarbons with 5 and 6 aromatic rings were also substrates for the chloroperoxidase reaction. The importance of the microbial chlorination of aromatic pollutants and its potential environmental impact are discussed.

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.

Biocatalytic oxidation of fuel as an alternative to biodesulfurization

A biotechnological method for fuel desulfurization is described. The method includes the steps of biocatalytic oxidation of organosulfides and thiophenes, contained in the fuel, with hemoproteins to form sulfoxides and sulfones, followed by a distillation step in which these oxidized compounds are removed from the fuel. Straight-run diesel fuel containing 1.6% sulfur was biocatalytically oxidized with chloroperoxidase from Caldariomyces fumago in the presence of 0.25 mM hydrogen peroxide. The reaction was carried out at room temperature and the organosulfur compounds were effectively transformed to their respective sulfoxides and sulfones which were then removed by distillation. The resulting fraction after distillation contained only 0.27% sulfur. Biocatalytic oxidation of fuels appears as an interesting alternative to biodesulfurization.

Biocatalysis Based on Heme Peroxidases

1.-Introduction MOLECULAR AND STRUCTURAL ASPECTS OF PEROXIDASES 2.- Molecular phylogeny of heme peroxidases (Marcel Zamocky and Christian Obinger) 3.- Structural and functional features of peroxidases with a potential as industrial biocatalysts (Francisco J. Ruiz-Duenas and Angel T. Martinez) 4.-Redox potential of heme peroxidases (Marcela Ayala) 5.- Catalytic mechanisms of heme peroxidases (Paul R. Ortiz de Montellano) PROSPECTIVE USAGE OF PEROXIDASES IN INDUSTRY 6.- Potential applications of peroxidases in the fine chemicals industry (Luigi Casella, Enrico Monzani and Stefania Nicolis) 7.- Grafting of functional molecules: insights into peroxidase-derived materials (Gibson S. Nyanhongo, Endry Nugroho Prasetyo, Tukayi Kudanga and Georg Guebitz ) 8.- Applications and prospective of peroxidase biocatalysis in the environmental field (Cristina Torres-Duarte and Rafael Vazquez-Duhalt) CHALLENGES IN THE APPLICATION OF PEROXIDASES 9.-Enzyme technology of peroxidases: immobilization, chemical and genetic modification (Adriana Longoria, Raunel Tinoco and Eduardo Torres). 10.- Reactor engineering (Juan M. Lema, Carmen Lopez, Gemma Eibes, Roberto Taboada-Puig, M. Teresa Moreira and Gumersindo Feijoo) 11.- Deactivation of heme peroxidases by hydrogen peroxide: focus on Compound III (Brenda Valderrama) 12.- Heterologous expression of peroxidases (Sandra de Weert and B. Christien Lokman) 13.- A compendium of bio-physical-chemical properties of peroxidases (Humberto Garcia-Arellano)

Cross-linked crystals of chloroperoxidase

Chloroperoxidase from Caldariomyces fumago was crystallized. The crystals were modified with several cross-linkers, but only glurataldehyde was able to produce catalytically active and insoluble crystals. Unlike other immobilized chloroperoxidase preparations, these catalytic crystals are more thermostable than the unmodified soluble enzyme. The enhanced stability is probably due to the structure conservation in the crystalline matrix. In addition, non-cross-linked chloroperoxidase crystals retained more activity than the soluble enzyme after incubation in an organic solvent with low water content. Although the cross-linked crystals were catalytically active, they showed lower specific activity than the soluble enzyme. This low activity may be due to non-specific reactions between the cross-linker and essential residues for catalysis. Alternative cross-linking strategies are discussed.

First evidence of mineralization of petroleum asphaltenes by a strain of Neosartorya fischeri

A fungal strain isolated from a microbial consortium growing in a natural asphalt lake is able to grow in purified asphaltenes as the only source of carbon and energy. The asphaltenes were rigorously purified in order to avoid contamination from other petroleum fractions. In addition, most of petroporphyrins were removed. The 18S rRNA and β‐tubulin genomic sequences, as well as some morphologic characteristics, indicate that the isolate is Neosartorya fischeri. After 11 weeks of growth, the fungus is able to metabolize 15.5% of the asphaltenic carbon, including 13.2% transformed to CO2. In a medium containing asphaltenes as the sole source of carbon and energy, the fungal isolate produces extracellular laccase activity, which is not detected when the fungus grow in a rich medium. The results obtained in this work clearly demonstrate that there are microorganisms able to metabolize and mineralize asphaltenes, which is considered the most recalcitrant petroleum fraction.

Peroxidase activity stabilization of cytochrome P450BM3 by rational analysis of intramolecular electron transfer

Combined quantum mechanical and molecular mechanical (QM/MM) calculations were used to explore the electron pathway involved in the suicide inactivation of cytochrome P450BM3 from Bacillus megaterium. The suicide inactivation is a common phenomenon observed for heme peroxidases, in which the enzyme is inactivated as a result of self-oxidation mediated by highly oxidizing enzyme intermediates formed during the catalytic cycle. The selected model was a mutant comprising only the heme domain (CYPBM3 21B3) that had been previously evolved to efficiently catalyze hydroxylation reactions with hydrogen peroxide (H2O2) as electron acceptor. An extensive mapping of residues involved in electron transfer routes was obtained from density functional calculations on activated heme (i.e. Compound I) and selected amino acid residues. Identification of oxidizable residues (electron donors) was performed by selectively activating/deactivating different quantum regions. This method allowed a rational identification of key oxidizable targets in order to replace them for less oxidizable residues by site-directed mutagenesis. The residues W96 and F405 were consistently predicted by the QM/MM electron pathway to hold high spin density; single and double mutants of P450BM3 on these positions (W96A, F405L, W96A/F405L) resulted in a more stable variants in the presence of hydrogen peroxide, displaying a similar reaction rate than P450BM3 21B3. Furthermore, mass spectrometry confirmed these oxidation sites and corroborated the possible routes described by QM/MM electron transfer (ET) pathways.

Heme destruction, the main molecular event during the peroxide-mediated inactivation of chloroperoxidase from Caldariomyces fumago

Heme peroxidases are subject to a mechanism-based oxidative inactivation. During the catalytic cycle, the heme group is activated to form highly oxidizing species, which may extract electrons from the protein itself. In this work, we analyze changes in residues prone to oxidation owing to their low redox potential during the peroxide-mediated inactivation of chloroperoxidase from Caldariomyces fumago under peroxidasic catalytic conditions. Surprisingly, we found only minor changes in the amino acid content of the fully inactivated enzyme. Our results show that tyrosine residues are not oxidized, whereas all tryptophan residues are partially oxidized in the inactive protein. The data suggest that the main process leading to enzyme inactivation is heme destruction. The molecular characterization of the peroxide-mediated inactivation process could provide specific targets for the protein engineering of this versatile peroxidase.

Xenobiotic Compounds Degradation by Heterologous Expression of a Trametes sanguineus Laccase in Trichoderma atroviride

Fungal laccases are enzymes that have been studied because of their ability to decolorize and detoxify effluents; they are also used in paper bleaching, synthesis of polymers, bioremediation, etc. In this work we were able to express a laccase from Trametes (Pycnoporus) sanguineus in the filamentous fungus Trichoderma atroviride. For this purpose, a transformation vector was designed to integrate the gene of interest in an intergenic locus near the blu17 terminator region. Although monosporic selection was still necessary, stable integration at the desired locus was achieved. The native signal peptide from T. sanguineus laccase was successful to secrete the recombinant protein into the culture medium. The purified, heterologously expressed laccase maintained similar properties to those observed in the native enzyme (Km and kcat and kcat/km values for ABTS, thermostability, substrate range, pH optimum, etc). To determine the bioremediation potential of this modified strain, the laccase-overexpressing Trichoderma strain was used to remove xenobiotic compounds. Phenolic compounds present in industrial wastewater and bisphenol A (an endocrine disruptor) from the culture medium were more efficiently removed by this modified strain than with the wild type. In addition, the heterologously expressed laccase was able to decolorize different dyes as well as remove benzo[α]pyrene and phenanthrene in vitro, showing its potential for xenobiotic compound degradation.