Toluene / o-xylene monooxyenase (ToMO) from Pseudomonas sp. OX1 is a multimeric metalloenzyme enzyme that efficiently catalyzes the hydroxylation of aromatic hydrocarbons with high specificity. Though included in a larger group of conserved bacterial multicomponent monooxygenases (BMMs) studied as potential biocatalysts for industrial hydrocarbon chemistry, the substrate specificity and oxygenated intermediates of ToMO differ greatly from its well-characterized, alkane-hydroxylating analog sMMO. Despite a shared global topology and near identical active sites, sMMO can cleave inert C-H bonds in alkanes while ToMO cannot - two seemingly similar structures give rise to vastly different chemistries. This work seeks to determine a structural basis for this difference by mutational analysis of residues thought to conformationally constrain the active site in ToMO, with the goal of replicating the terminal alkane hydroxylating activity of sMMO. To this end, a library of potential alkane-hydroxylating mutants was generated and kinetically characterized, revealing a range of novel behaviors including significant reaction rate enhancements. In combination with low-level computational modeling to quantify the bulk and local rigidity of both sMMOH and ToMOH, we propose a broader strategy for BMM scaffolds to achieve a variety of specific and efficient hydrocarbon chemistries.

Nesse trabalho avaliamos o potencial enzimático de diferentes linhagens de fungos, visando determinar a presença de mono-oxigenases capazes de oxidar cetonas aromáticas e cíclicas. Todas as linhagens empregadas apresentaram atividade de álcool desidrogenase e Baeyer-Villiger mono-oxigenases. Adicionalmente foram sintetizadas oito moléculas bi-funcionalizadas com grupos sulfeto, seleneto e carbonila (cetona). Os produtos das reações biocatalisadas foram isolados e caracterizados. / In this work, we evaluated the enzymatic potential of different Aspergillus strains, through the biotransformations of two substrates: 2- and 4-methylcyclohexanone (1a e 1b). All the strains employed showed alcohol dehydrogenase and Baeyer-Villiger monooxygenase (CPMO and CHMO) activities. These enzymes can perform ketone biorreduction and oxidation. Using the A. terreus SSP 1498 selected from the screening study, we prepared alcohols and lactones in good enantiosselectivity. In this way, other fungal strains were studied aiming to determine the presence of monooxygenase activity by means of the biotransformation of aromatic ketones. Like the Aspergillus, we observed that all strains used in this study showed alcohol dehydrogenase and Baeyer-Villiger monooxygenase (APMO) activities. We selected 1-phenyl-etanone and its para substituted derivates as substrates. Additionally, we synthesized eight examples of bi-functionalized compounds with sulfide, selenide and ketone groups. These compounds were submitted to the action of enzymatic system of different fungi which were selected from the initial screening. The products from the biotransformation were isolated and characterized.

NADPH-cytochrome P450 reductase (CPR) is a flavoprotein containing both FAD and FMN and functions as the electron donor protein for several oxygenase enzymes found on the endoplasmic reticulum of eukaryotic cells, including cytochrome P450s involved in drug metabolism and cholesterol biosynthesis. As many as three enzymes in the cholesterol biosynthetic pathway have been demonstrated, or proposed, to use CPR as a redox partner: squalene monooxygenase, which converts squalene to 2,3-oxidosqualene; lanosterol demethylase, a cytochrome P450 (CYP51); and 7-dehydrocholesterol reductase, the final step in cholesterol synthesis. In yeast CPR can be replaced by the NADH-cytochrome b5 pathway, but this has not been demonstrated in animals or plants. My studies with hepatic cytochrome P450 reductase-null mice have revealed a second microsomal reductase for squalene monooxygenase that was not previously detected. Studies carried out with hepatocytes from CPR-null mice demonstrate that this second reductase is active in whole cells and leads to the accumulation of 24-dihydrolanosterol, indicating that lanosterol demethylation, catalyzed by CYP51, is blocked. These results demonstrate that this second reductase plays a significant role in supporting squalene monooxygenase but not cytochrome P450-mediated reactions. 7-Dehydrocholesterol reductase (E.C. 1.3.1.21) catalyzes the reduction of the 7-8 double bond of 7-dehydrocholesterol to yield cholesterol. It has been suggested that cytochrome-P450 reductase is required for this reaction. My studies show that 7-dehydrocholesterol reductase is enzymatically active in CPR-null microsomes, with activity equal to or greater than that found in preparations from wild-type mice. Mammalian cytochrome b5, which can accept electrons from either cytochrome P450 reductase or NADH-cytochrome b5 reductase, is known to be involved in augmenting some P450-dependent monooxygenase reactions. Cytochrome P450 2E1 has been found to exhibit reasonable rates of turnover via an NADHcytochrome b5 pathway in reconstituted enzyme systems and in heterologous hosts. Using microsomes from hepatic CPR-null mice, I have determined that NADH-dependent CYP2E1 activity in the absence of NADPH-dependent activity constituted approximately 10% of CYP2E1 activity observed in microsomal preparations with NADPH from wild-type mice. However, little or no CYP2E1 activity could be detected in primary hepatocytes isolated from CPR-null mice.

La géosmine est un terpénoïde, provoquant un goût moisi-terreux associée à des flaveurs atypiques dans l'eau et le vin. Chez les bactéries, la voie de biosynthèse de la géosmine est bien caractérisée, mais peu de connaissance sont disponibles au sujet de sa biosynthèse chez les eucaryotes, en particulier dans les champignons filamenteux. L'origine de la géosmine dans la vigne est en grande partie attribuable à la présence de Penicillium expansum sur les raisins. Dans cette thèse, afin de mieux comprendre la voie de biosynthèse de la géosmine chez Penicillium expansum, nous avons décrit la caractérisation et l'analyse de "gpe1", un gène codant pour une cytochrome P450 monooxygénase impliquée dans la biosynthèse de la géosmine. Nous avons démontré que les deux fragments d'ADN: p450-1 et p450-2 appartiennent à un seul gène du cytochrome p450 (gpe1). La séquence d'acides aminés déduite de gpe1 a une identité moyenne de 40 % avec les enzymes PbP450-2 et P450-4 qui ont été trouvées impliquées respectivement dans la synthèse d'indole diterpène et dans la synthèse des gibbérellines. Les amplifications par PCR effectuée sur quatorze espèces de Penicillium ont montré que seules les espèces producteurices de la géosmine ont donné le même fragment de ~1,2 kb que gpe1. L'analyse du gène gpe1 nous a permis d'identifier la présence de certains domaines conservés de cytochromes P450 monooxygénases. Ensuite, la caractérisation fonctionnelle du gène gpe1 chez P. expansum M2230 a été décrite. Nous avons montré que les mutants de gpe1 ont perdus leur pouvoir de produire la géosmine alors que les révertants de gpe1 ont rétablis leur pouvoir de production. Enfin, nous avons démontré qu'une polykétide synthase putative et une putative NRPS sont présentes sur le côté droit du gène gpe1 proposant que le gène gpe1 pourrait être une partie d'un «Cluster» codant pour la biosynthèse de métabolites secondaires. / Geosmin is a terpenoid, an earthy-musty compound associated with off-flavors in water and wine. In bacteria, the biosynthesis pathway of geosmin is well characterized, but little is known about its biosynthesis in eukaryotes, especially in filamentous fungi. The origin of geosmin in grapevine is largely attributable to the presence of Penicillium expansum on grapes. In this thesis, we have described the characterization and analysis of "gpe1", a gene encoding a cytochrome P450 monooxygenase probably involved in the biosynthesis of geosmin in P. expansum M2230, in order to better understand of the biosynthesis pathway of geosmin in this species. We demonstrated that the two DNA fragments i.e. p450-1 and p450-2 belong to a single cytochrome p450 gene (gpe1). We showed that the deduced amino acid sequence of gpe1 has an average identity of 40 % with PbP450-2 and P450-4 enzymes which have been found involved in indole diterpene synthesis and in gibberellin synthesis respectively. Then, the results of PCRs performed on the fourteen Penicillium species showed that only Penicillium species which were producers of geosmin gave the same fragment of ~1.2 kb like gpe1. Analysis of the gpe1 gene enabled us to identify the presence of some conserved domains of cytochromes P450 monoxygenases in the amino acid sequence of gpe1. Then, the functional characterization of the gpe1 gene in P. expansum M2230 was described. We illustrated that the mutants of gpe1 lost their potential to produce geosmin whereas the reverse complements of gpe1 restored their potential to produce geosmin. Finally, we demonstrated that a putative polyketide synthase and a putative NRPS-like enzyme are present on the right side of the gpe1 gene suggesting that gpe1 gene might be the part of a gene cluster encoding the biosynthesis of secondary metabolites.

Ellipticine, an alkaloid isolated from Apocynaceae plants, exhibits significant antitumor and HIV activities. Ellipticine is a pro-drug, whose pharmacological and genotoxic effects depend on activation by cytochromes P450 (CYP) and peroxidases (Px) to a reactive species generating DNA adducts. To elucidate contribution of CYPs (and which of them) and Px to ellipticine activation, we used rat and mouse models, mice with deleted gene of NADPH:CYP reductase in the liver, thus absenting this enzyme in the liver (HRNTM ) and a control mouse line (WT), rats treated with ellipticine, and microsomal systems isolated from the liver of mouse lines and from the liver, kidney and lung of rats. The purified enzymes, CYP1A1 and 3A4, reconstituted with NADPH:CYP reductase were also used. The effect of cytochrome b5, a facultative component of the mixed function monooxygenase system, on ellipticine oxidation by CYP1A1 and 3A4 was also investigated. Carcinogenic benzo(a)pyrene (BaP), known to covalently bind to DNA after its activation with CYPs, was investigated for its potential to generate DNA adducts and to induce CYP and NADPH:CYP reductase enzymes in mouse livers. We investigated an influence of each of components of the mixed function oxidases (MFO) system on metabolism of BaP. CYP1A1 is widely accepted to be the...

Chen, Tingting. / Thesis (Ph.D.)--Chinese University of Hong Kong, 2013. / Includes bibliographical references (leaves 100-109). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstract also in Chinese.

There is an important need to immobilise enzymes for use in industry, to do this I have the promising idea that by conjugating the enzyme to a hydrogel network, thus fabricating a stable biocatalytic network would be a potential method for immobilising enzymes for the manufacture of fine chemicals, this has not been done before for octapeptide systems. Hydrogels have been previously shown as a viable way of immobilising and stabilising enzymes. In this thesis the octapeptide VKVKVEVK (V is valine, K is lysine and E is glutamic acid) is used to immobilise enzymes tagged with VKVKVEVK. This peptide sequence is chosen as it forms stable hydrogels at enzyme appropriate conditions (pH 7). The enzymes chosen are; PETNR as it is well understood and is therefore a good starting point, CDH and CHMO were also chosen as they could combine with PETNR to form a cascade reaction. PETNR was both chemically conjugated to VKVKVEVK (SpepPETNR) and also genetically modified to express the peptide tag (CpepPETNR), whilst CDH and CHMO were genetically modified to express the tag (NpepCDH and CpepCHMO respectively). For S/CpepPETNR retention within the hydrogels was superior to retention for untagged PETNR. NpepCDH was found to not precipitate within the hydrogel whilst untagged was found to do so. CpepCHMO functionalised hydrogels were found to be heterogeneous. Characterisation of CpepPETNR functionalised hydrogels was undertaken using micro differential scanning calorimetry (µDSC), rheology, small angle neutron scattering (SANS) and atomic force microscopy (AFM). From the µDSC evidence of 'protective immobilisation' was observed by the increase in denaturation energy (+253 kJ mol-1) in the hydrogel in comparison to in solution (+18 kJ mol-1). The ability of S/CpepPETNR functionalised hydrogels to perform the ketoisophorone to levodione biotransformation reaction was explored with yields of 86%. S/CpepPETNR within VKVKVEVK hydrogels was found to retain ~90% conversion for at least 9 months at room temperature. Incubation overnight at 90°C resulted in a yield of 84% of levodione. These two results added more evidence for 'protective immobilisation'. Hydrogels functionalised with NpepCDH or CpepCHMO were characterised using rheology and atomic force microscopy. The biotransformation ability of NpepCDH was elucidated; the overall yield of carvone was a maximum of 54% from the hydrogel phase. NpepCDH was used alongside CpepPETNR for the cascade reaction producing dihydrocarvone in low yields; however, an improvement from 2% to 13% in yield is presented. The yield of lactone products from CpepCHMO functionalised hydrogel was low at 15%. The CpepPETNR/ CpepPETNR cascade reaction proceeded with a yield of 36%. The initial activities of CpepPETNR, NpepCDH and CpepCHMO were assayed in both solution and in gel phase using a modified method. The activities were assessed with varying conditions; temperature, pH, quantity of ethanol and incubation at high and low temperatures. Generally, it was found that immobilisation within the hydrogel phase resulted in 'protective immobilisation' against non-optimal conditions. This work will be of benefit to those who are interesting immobilising enzymes within hydrogels in the future.

Alkilpirazinų katabolizmas bakterijose yra prastai ištirtas. Nors yra žinomi tarpiniai metabolitai susidarantys skaidant di- ir tri- pakeistus alkilpirazinus, tačiau šių junginių skaidymas prasideda hidroksilinimo reakcija, kuri negalima tetrametilpirazino atveju. Šiame darbe pirmą kartą nustatytas tetrametilpirazino katabolizmo kelias šį junginį skaidančiose Rhodococcus jostii TMP1 bakterijose. MS/MS de novo sekoskaitos būdu identifikavus tetrametilpirazinu indukuojamą baltymą, buvo nustatyta genų sankaupa, koduojanti pradines tetrametilpirazino katabolizmo reakcijas katalizuojančius fermentus ir transkripcijos reguliatorių, dalyvaujantį šių genų aktyvavime. Pradiniame tetrametilpirazino skaidymo etape monooksigenazė TpdAB katalizuoja oksidacinį žiedo atidarymą, susidarant (Z)-N,N'-(but-2-ene-2,3-diil)diacetamidui. Tolesnę skaidymo reakciją katalizuoja amidazė TpdC, kurios produktą N-(3-oksobutan-2-il)acetamidą aminoalkoholių dehidrogenazė TpdE redukuoja iki N-(3-hidroksibutan-2-il)acetamido. Nustačius tarpinius tetrametilpirazino skaidymo metabolitus, reakcijas katalizuojančius fermentus ir juos koduojančius genus buvo rekonstruotas pirmasis alkilpirazinų katabolizmo kelias bakterijose. Darbo metu taip pat parodyta, kad Rhodococcus jostii TMP1 bakterijos modifikuoja daugelį alkilpirazino ir alkilpiridino junginių ir gali būti panaudotos 2,4,6-trimetilpiridin-3-olio biosintezei iš 2,4,6-trimetilpiridino. / The catabolism of alkylpyrazines is poorly described. The pathways for the degradation of di- and tri-substituted pyrazines have been proposed, but these related routes consistently include a hydroxylation step that cannot be performed on tetramethylpyrazine. Here we describe for the first time the catabolic pathway of tetramethylpyrazine in tetramethylpyrazine-degrading Rhodococcus jostii TMP1 strain. MS/MS analysis of the protein primarily upregulated by tetramethylpyrazine led to the identification of the gene locus encoding proteins required for the initial steps of tetrametylpyrazine degradation and for the regulation of this locus. Tetramethylpyrazine degradation starts with oxidative ring cleavage catalysed by monooxygenase TpdAB, which produces (Z)-N,N'-(but-2-ene-2,3-diyl)diacetamide. This compound is further hydrolysed by amidase TpdC to N-(3-oxobutan-2-yl)acetamide. TpdE was confirmed to be an aminoalcohol dehydrogenase yielding N-(3-hydroxybutan-2-yl)acetamide. By determining intermediates, enzymes involved and genes responsible for tetramethylpyrazine degradation we provide the first validated pathway for pyrazine degradation. We also report that Rhodococcus jostii TMP1 is capable of modifying various alkylpyrazines and alkylpyridines and can be employed for the bioconversion of 2,4,6-trimethylpyridine and 2,4,6-trimethylpyridin-3-ol biosynthesis.

The catabolism of alkylpyrazines is poorly described. The pathways for the degradation of di- and tri-substituted pyrazines have been proposed, but these related routes consistently include a hydroxylation step that cannot be performed on tetramethylpyrazine. Here we describe for the first time the catabolic pathway of tetramethylpyrazine in tetramethylpyrazine-degrading Rhodococcus jostii TMP1 strain. MS/MS analysis of the protein primarily upregulated by tetramethylpyrazine led to the identification of the gene locus encoding proteins required for the initial steps of tetrametylpyrazine degradation and for the regulation of this locus. Tetramethylpyrazine degradation starts with oxidative ring cleavage catalysed by monooxygenase TpdAB, which produces (Z)-N,N'-(but-2-ene-2,3-diyl)diacetamide. This compound is further hydrolysed by amidase TpdC to N-(3-oxobutan-2-yl)acetamide. TpdE was confirmed to be an aminoalcohol dehydrogenase yielding N-(3-hydroxybutan-2-yl)acetamide. By determining intermediates, enzymes involved and genes responsible for tetramethylpyrazine degradation we provide the first validated pathway for pyrazine degradation. We also report that Rhodococcus jostii TMP1 is capable of modifying various alkylpyrazines and alkylpyridines and can be employed for the bioconversion of 2,4,6-trimethylpyridine and 2,4,6-trimethylpyridin-3-ol biosynthesis. / Alkilpirazinų katabolizmas bakterijose yra prastai ištirtas. Nors yra žinomi tarpiniai metabolitai susidarantys skaidant di- ir tri- pakeistus alkilpirazinus, tačiau šių junginių skaidymas prasideda hidroksilinimo reakcija, kuri negalima tetrametilpirazino atveju. Šiame darbe pirmą kartą nustatytas tetrametilpirazino katabolizmo kelias šį junginį skaidančiose Rhodococcus jostii TMP1 bakterijose. MS/MS de novo sekoskaitos būdu identifikavus tetrametilpirazinu indukuojamą baltymą, buvo nustatyta genų sankaupa, koduojanti pradines tetrametilpirazino katabolizmo reakcijas katalizuojančius fermentus ir transkripcijos reguliatorių, dalyvaujantį šių genų aktyvavime. Pradiniame tetrametilpirazino skaidymo etape monooksigenazė TpdAB katalizuoja oksidacinį žiedo atidarymą, susidarant (Z)-N,N'-(but-2-ene-2,3-diil)diacetamidui. Tolesnę skaidymo reakciją katalizuoja amidazė TpdC, kurios produktą N-(3-oksobutan-2-il)acetamidą aminoalkoholių dehidrogenazė TpdE redukuoja iki N-(3-hidroksibutan-2-il)acetamido. Nustačius tarpinius tetrametilpirazino skaidymo metabolitus, reakcijas katalizuojančius fermentus ir juos koduojančius genus buvo rekonstruotas pirmasis alkilpirazinų katabolizmo kelias bakterijose. Darbo metu taip pat parodyta, kad Rhodococcus jostii TMP1 bakterijos modifikuoja daugelį alkilpirazino ir alkilpiridino junginių ir gali būti panaudotos 2,4,6-trimetilpiridin-3-olio biosintezei iš 2,4,6-trimetilpiridino.

Type II polyketide synthase (PKS) produced natural products have proven to be an excellent source of pharmacologically relevant molecules due to their rich biological activities and chemical scaffolds. Type II-PKS manufactured polyketides share similar polycyclic aromatic backbones leaving their diversity to stem from various chemical additions and alterations facilitated by post-PKS tailoring enzymes. Evidence suggests that post-PKS tailoring enzymes form complexes in order to facilitate the highly orchestrated process of biosynthesis. Thus, protein-protein interactions between these enzymes must play crucial roles in their structures and functions. Despite the importance of these interactions little has been done to study them. In the mithramycin (MTM) biosynthetic pathway the Baeyer−Villiger monooxygenase (BVMO) MtmOIV and the ketoreductase MtmW form one such enzyme pair that catalyze the final two steps en route to the final product. MtmOIV oxidatively cleaves the fourth ring of the mithramycin intermediate premithramycin B (PreB) via a Baeyer−Villiger reaction, generating MTM’s characteristic tricyclic aglycone core and highly functionalized pentyl side chain at position 3. This Baeyer−Villiger reaction precedes spontaneous lactone ring opening, decarboxylation, and the final step of MTM biosynthesis, a reduction of the 4′- keto group catalyzed by the ketoreductase MtmW. Another example of co-dependent post-PKS tailoring enzymes from the gilvocarcin biosynthetic pathway is composed of GilM and GilR. These two enzymes form an unusual synergistic tailoring enzyme pair that does not function sequentially. GilM exhibits dual functionality by catalyzing the reduction of a quinone intermediate to a hydroquinone and stabilizes O-methylation and hemiacetal formation. GilM mediates its reductive catalysis through the aid of GilR that provides its covalently bound FADH(2) for the GilM reaction, through which FAD is regenerated for the next catalytic cycle. A few steps later, following glycosylation related events unique to each gilvocarcin derivative, GilR dehydrogenates the hemiacetal moiety created by GilM to establish the formation of a lactone and the final gilvocarcin chromophore. To achieve a better understanding of post-type II PKS tailoring enzymes and their protein-proteininteractions for the benefit of future combinatorial biosynthetic efforts two specific aims were devised. Specific aim 1 was to investigate the structure of MtmOIV and the role of active site residues in its catalytic mechanism. Specific aim 2 was to integrate the function of GilM and its protein-protein interactionswith GilR that lead to their synergistic activity and sharing of GilR’s bicovalently bound FAD moiety.