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Title: Enzymology and structural enzymology of dye-decolorizing peroxidases and a primary study of encapsulin
Author: Rahman Pour, Rahman
ISNI:       0000 0004 5368 0003
Awarding Body: University of Warwick
Current Institution: University of Warwick
Date of Award: 2015
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The aim of this project is to provide a detailed comparative study in enzymology of dye-decolorising peroxidases, DyP, from Pseudomonas fluorescens and from Thermobifida fusca, a thermophile bacterium. Another objective is a primary study of encapsulin, a recently discovered icosahedral nanocompartment protein from Rhodococcus jostii Rha1. Three peroxidase genes from P. fluorescens and one from T. fusca were cloned, expressed, and their products were purified and the enzymes kinetically characterized with different substrates, lignin model compounds and lignocellulose. In addition, encapsulin has been purified, its assembly/disassembly under different pH conditions was studied and finally, its presence or absence in the extracellular fraction of R. jostii investigated. DyP type peroxidases from Gram-positive bacteria have been studied recently and showed oxidation activity toward Mn (II) and lignin model compounds. Gram-negative pseudomonads, also show activity for lignin oxidation and contain DyP-type peroxidase genes. P. fluorescens Pf-5 contains three DyP-type peroxidases (35, 40 and 47 kDa). In this study each of them was overexpressed in Escherichia coli, purified, and characterised by different substrates, Kraft lignin and lignocellulose. Each of the aforementioned enzymes shows activity for oxidation of most of the substrates, but the 35 kDa DyP1B and 40 kDa DyP2B enzymes show activity for oxidation of Mn (II). Only in the presence of Mn (II) and hydrogen peroxide, incubation of finely powdered lignocellulose with DyP1B leads to the release of a low molecular weight lignin fragment that was identified by mass spectrometry as a ß-aryl ether lignin dimer that contains one G unit and one H unit bearing a benzylic ketone. A mechanism for releasing of the -aryl ether lignin dimer fragment from the lignin molecule via oxidation is proposed. A DyP-type peroxidase enzyme from the thermophilic cellulose degrader Thermobifida fusca was investigated for its catalytic ability for lignin oxidation. TfuDyP was found to oxidise a ß-aryl ether lignin model compound, forming an oxidised tetramer. A crystal structure of TfuDyP was determined, to 1.7 Å resolution, which was found to contain a diatomic oxygen ligand bound to the heme centre, hydrogen-bonded to active site residues Asp-203 and Arg-315. For three amino acid residues present in distal heme pocket, site directed mutagenesis was performed and the effect of each mutation on enzyme activity was measured by three different substrates. Recently DyPB peroxidase from Rhodococcus jostii RHA1 has been recognised as a bacterial lignin peroxidase enzyme. The dypB gene is next to a gene that encodes an encapsulin protein that previously was shown in Thermotoga maritima to assemble and form into a nano-compartment comprised of 60-subunits. DyPB protein contains a C-terminal sequence motif that is supposed to lead the protein to the encapsulin nanocompartment. In this study, R. jostii RHA1 encapsulin gene was overexpressed in R. jostii RHA1, and the encapsulin protein was extracted as a high molecular weight native assembly (Mr >106 kDa). It was shown that by treatment of the purified nanocompartment at pH 3.0, it is able to be denatured to form a low molecular weight species and most importantly it is able to be re-assembled to form the native nanocompartment at pH 7.0. Dynamic light scattering showed that DyPB peroxidase in vitro could be assembled with encapsulin in a monomeric state to form an assembly of encapsulated DyPB in similar size and shape compared to the encapsulin-only nanocompartment. By using a nitrated lignin UV-Vis assay method, it was shown that the assembled complex of DyPB-encapsulin exhibited enhanced lignin degradation activity per mg DyPB present, compared with native DyPB. The stoichiometry of encapsulin/µmol DyPB in the assembled complex was measured, 8.6 mol encapsulin/mol DyPB, that was comparable to the predicted value of 10 obtained from the crystal structure.
Supervisor: Not available Sponsor: Not available
Qualification Name: Thesis (Ph.D.) Qualification Level: Doctoral
EThOS ID:  DOI: Not available
Keywords: QD Chemistry