Abstract Prostate cancer is the most frequently diagnosed cancer in men in industrialized countries. Despite the substantial clinical importance of the disease, the mechanisms underlying the development and progression of prostate cancer are poorly understood. In the present study, fragment analysis of chromosome arm 16q was carried out with the aim of searching for sites of consistent chromosomal deletion, possibly uncovering the location of target genes that become inactivated in prostate carcinogenesis. The highest percentage of loss of heterozygosity (LOH) was found at chromosomal region 16q24.1-q24.2, including the gene for 17β-hydroxysteroid dehydrogenase/17-ketosteroid reductase (17HSD/KSR) type 2, HSD17B2. The data further indicated an association between loss of the most commonly deleted region and clinically aggressive features of the disease. A fragment analysis performed using sequential primary and locally recurrent prostate cancer specimens suggested the location of the genes related to prostate cancer progression to be at 16q24.3 and, further, gave rise to a hypothesis of the potential role of locus HSD17B2 as a prognostic marker for prostate cancer progression. Quantitative real-time polymerase chain reaction (PCR) revealed a decreased HSD17B2 gene copy number in prostate cancer specimens compared to their normal counterparts. A diminished HSD17B2 gene copy number was significantly associated with poor differentiation of the tumor. The progression of prostate cancer during androgen deprivation is a serious clinical problem, the molecular mechanisms of which largely remain to be clarified. The present data of enzyme activity measurements performed using high-performance liquid chromatography (HPLC) provided evidence of a substantial decrease in oxidative and an increase in reductive 17HSD/KSR activity during the transition of prostate cancer LNCaP cells into an androgen-independent state. Further, the changes detected in the activities largely coincided with the changes in the relative expression levels of genes for the potential 17HSD/KSR isoenzymes; 17HSD/KSR types 2, 5, and 7, as evidenced by relative quantitative reverse transcription PCR (RT-PCR). The data on the expression analysis of mRNA for 17HSD/KSR types 5 and 7 in prostate tissue specimens performed using in situ hybridization showed a moderately low but constitutive level for 17HSD/KSR7 mRNA in tissues of cancerous as well as hyperplastic origin. The expression of mRNA for 17HSD/KSR type 5, instead, varied considerably between different specimens, the highest expressions being strongly associated with aggressive and metastatic prostate cancer. Interestingly, furthermore, the intense expression of 17HSD/KSR5 was significantly associated with the androgen deprivation achieved either surgically or medically. Since 17HSD/KSRs critically contribute to the control of the bioavailability of active sex steroid hormones locally in the prostate, the variation in intraprostatic 17HSD/KSR activity might be crucially involved in the regulation of the growth and function of the organ.

Pyridine nucleotide transhydrogenase catalyzes the reversible transfer of hydride ion equivalents between NADP(H) and NAD(H). In this study, the activity of the enzyme was measured by following the rate of reduction of an analogue of NAD⁺ , 3-acetylpyridxne-NAD⁺ (APNAD⁺ ) by NADPH. The enzyme was solubilized by detergents such as lysolecithin, sodium cholate (in the presence of ammonium sulphate) or Triton X-100. The molecular size of the solubilized enzyme was examined using sucrose density gradient centrifugation in the presence of Brij 58. These detergents gave soluble fragments of different sizes. That solubilized by Triton X-100 or sodium cholate (in the presence of ammonium sulphate) existed as large aggregates with sedimentation coefficients of 24.5 to 25.4S, whereas that obtained with lysolecithin consisted mainly of a species with a sedimentation coefficient of 7.3 to 16.5S. The fragment resulting from the solubilization with Triton X-100 could be cleaved into a smaller species (8.4S) by lysolecithin. Analysis by chromatography on Sepharose 6B of the enzyme preparation solubilized by sodium cholate (in the presence of ammonium sulphate), revealed the presence of other constituents of the membrane, such as succinate dehydrogenase, ATPase and cytochrome b₁. The molecular weight of the aggregate was estimated to be between 0.25 x 10⁶ and 4 x 10⁶. The enzyme in this preparation could not be further disaggregated by Tween 80, Brij 3 5 or Triton X-100. Chromatography of this preparation on DEAE-Sepharose CL-6B yielded a maximum purification of 37 to 68-fold over that of the membrane particle suspension. The specific activity of the enzyme was 8.8 to 15.7 umol per min per mg protein. Analysis of the partially purified enzyme on poly-acrylamide gels in the presence of sodium dodecyl sulphate revealed enrichment of several major polypeptide bands of molecular weights 90 000, 57 000, 50 000 and 40 000, coinciding with the transhydrogenase activity. The partially purified enzyme could be activated by detergents of the Tween or Brij series and by lysolecithin, palmitic acid and phospholipid extracts from E. coli. Measurements of the steady-state kinetics of the membrane-bound enzyme gave values of 45.6 and 106.7 uM for the substrates APNAD+ and NADPH, and dissociation constants of 3.6 and 16.2 uM, respectively. Lineweaver-Burk plots for each substrate at different fixed concentrations of the other substrate revealed a unique pattern of lines that is characteristic of rapid equilibrium random bireactant mechanisms with two dead-end products. In this type of mechanism each substrate is able to interact at the binding site of the other substrate to cause inhibition of enzyme activity. This mechanism was confirmed by kinetic studies using the alternate substrates deamino-NADPH and NAD⁺ , as well as by product inhibitxon studies. The adenine nucleotides 5’-AMP and ADP were competitive inhibitors of the APNAD+-binding site, while 2'-AMP was a competitive inhibitor of the NADPH-binding site on the enzyme. Studies on the active site using 2,3-butanedione or phenyl glyoxal revealed the presence of one modifiable arginyl residue per active site on the enzyme. Protection against modification by 2,3-butanedione was afforded by 2'-AMP, 5'-AMP, NAD+ and NADP+. Inhibition by 2,3-butanedione was enhanced in the presence of low concentrations of NADH or NADPH suggesting that binding of the reduced pyridine nucleotides, possibly at an allosteric site, causes a conformational change in the enzyme. Enhancement of in-activation of the enzyme by TPCK-trypsin was also observed in the presence of reduced pyridine nucleotides. NAD(P)H was oxidized by 2,3-butanedione in the presence of light. The rate of photooxidation was greatest at pH 7 and when the wavelength of incident light was 410 nm. This indicates that absorption of light by the diketone was necessary for the occurrence of the photooxidation reaction. The stochiometry of the reaction between NADH and 2,3-butanedione was 1:1. The possible nature of the reaction product is discussed in the thesis. / Medicine, Faculty of / Biochemistry and Molecular Biology, Department of / Graduate

In acetone/butanol-producing clostridia, the metabolic intermediate acetoacetyl-CoA can be directed toward butyrate or butanol formation by the reaction catalyzed by 3-hydroxybutyryl-CoA dehydrogenase, or toward acetone formation by the reaction catalyzed by acetoacetate:acetate/butyrate CoA-transferase. 3-Hydroxybutyryl-CoA dehydrogenase (EC 1.1.1.35 or 1.1.1.157) has been purified 45-fold to apparent homogeneity from the solvent-producing anaerobe Clostridium beijerinckii strain NRRL B593. The identities of 34 of the 35 N-terminal amino acid residues have been determined. The enzyme exhibited a native M_r of 213,000 and a subunit M_r of 30,800. It is specific for the (S)-enantiomer of 3-hydroxybutyryl-CoA. Michaelis constants for NADH and acetoacetyl-CoA were 8.6 and 14 µM, respectively. The maximum velocity of the enzyme was 540 µmol/(min mg) for the reduction of acetoacetyl-CoA with NADH. The enzyme could use either NAD(H) or NADP(H) as cosubstrate; however, NAD(H) appeared to be the physiological substrate. In the presence of 9.5 µM NADH, the enzyme was inhibited by acetoacetyl-CoA at concentrations as low as 20 µM, but the inhibition was relieved as the concentration of NADH was increased, suggesting a possible mechanism for modulating the energy efficiency during growth. Acetoacetate:acetate/butyrate CoA-transferase (EC 2.8.3.9) has been purified 308-fold to apparent homogeneity from the same organism. The enzyme exhibited a native M_r of 89,100. The subunits of the enzyme were separated by preparative SDS-PAGE, and exhibited M, values of 28,400 and 25,200. The identities of the 34 N-terminal amino acids of the large subunit and 38 of the 39 N-terminal amino acids of the small subunit were determined. The N-terminal region of the two subunits showed significant similarity with several other CoA transferase enzymes. Michaelis constants for butyrate and acetoacetyl-CoA were 11.7 mM and 107 µM, respectively, while those for acetate and acetoacetyl-CoA were 424 mM and 118 µM, respectively. The value of k_cat/K_m was approximately 100 times higher with butyrate than with acetate. Implications of the properties of these two enzymes for the acetone-butanol fermentation are discussed, and a model for the induction of the enzymes responsible for solvent production is suggested. / Ph. D.

Enzymatic pathways have evolved over billions of years to carry out essential cellular processes and ensure the survival of their host species. These reaction pathways rely on the interconnectedness of multiple enzymes and substrate, encouraging cross-talk and, at times, competition. In many cases, enzymes require the assistance of a diffusible secondary biomolecule, known as a cofactor, to participate in catalytic reactions. This network of reactions is unfavorable when trying to optimize the production of a specific product. In order to circumvent surrounding reactions, researchers have been engineering orthogonal enzymatic pathways that operate independently from endogenous reactions within a cell. Orthogonal pathways can be created by utilizing biomimetics molecules; most enzymes have not naturally evolved affinity and activity with these are non-canonical cofactors. Nicotinamide adenine dinucleotide (NAD(H) and nicotinamide adenine dinucleotide 2’-phosphate (NADP(H)) are vital cofactors that participate in redox reactions within cells. NAD(P)(H) have been the target of enzymatic research for several decades due to their extensive involvement in reactions across species and their utility in the biotechnology industry. Creation of orthogonal pathways dependent on NAD(P)(H) analogs has massive potential in various industries, such as biofuels and biopharmaceuticals. Nicotinamide mononucleotide (NMN(H)) is a precursor molecule in the biosynthesis of NAD(H); it currently exists within cells but, in general, does not participate as a cofactor. Nicotinamide adenine dinucleotide 3’-phosphate (3’-NADP(H)) is another analog that closely resembles NAD(P)(H) for which most enzymes have not evolved natural affinity and activity. Computation and structural inspection techniques were used in an attempt to engineer formate dehydrogenase from Candida boidinii (CbFDH) for activity with the non-canonical cofactors NMN(H) and 3’-NADP(H). Amino acid positions proximal to the NAD(H) binding site were input into a PyRosetta algorithm, which then outputted a list of recommended mutations ranked by their Rosetta energy scores. Structural alignment and visual inspection were also used to design mutations. The mutations were recombinantly expressed, and the purified enzymes were assays with NAD+, NADP+, NMN+ and 3’-NADP+. None of the designed single mutations led to CbFDH activity gain with NMN+ to any meaningful degree; however, various mutations led to the removal of NAD+ activity. A strength of PyRosetta was identifying key mutations that would lead to activity removal. The single mutants D195A and D195G attained the largest specific initial rates with 3’-NADP+ under the screening assay conditions. Kinetics parameters of a simplified ordered bi bi model were calculated for these mutants. Double mutants were created in an attempt to further enhance activity. The double mutations resulted in decreased activity but enhanced the specificity for 3’-NADP+ over NAD+. To complete the 3’-NADP(H) enzymatic cycle, a non-specific cofactor oxidizer, xenobiotic reductase A (XenA), was expressed and assayed with 3’-NADPH. It was found that XenA is able to oxidize 3’-NADPH back to 3’-NADP+. The avirulence factor AvrRxo1 from a rice plant pathogen was explored since it specifically catalyzes NAD+ phosphorylation at the 3’ position. The AvrRxo1 gene was expressed in LysY/IQ competent E. coli cells and it was found that the presence of AvrRxo1 caused a longer lag phase, but the bacteria were later able to recover. Co-expressing AvrRxo1, XenA, and D195A CbFDH has the potential to create an orthogonal pathway depending on biosynthesized 3’-NADP(H) in vivo. Another in vivo non-canonical cofactor source is NAD(H)-capped RNA, which have recently captured researchers’ attention. NAD+-RNA was synthesized using the polymerase chain reaction, and it was shown that D195A and D195G CbFDH were able to reduce the NAD+ cap.

No description available.

No description available.

The ammonium inducible nicotinamide phosphate-specific glutamate dehydrogenase from Chlorella sorokiniana has been purified 260-fold to homogeneity. Depending on the technique used, the native enzyme appeared to have a molecular mass of 290,000 to 400,000 daltons and to be composed of subunits with an identical molecular weight of 58,000. Differences in the molecular weight of the native enzyme, as determined by sedimentation equilibrium, Sephadex G-200 gel filtration and gradient polyacrylamide gel electrophoresis, indicate that the native enzyme may be elliptical in shape. The amino acid composition of the enzyme is high in glycine, glutamate, and asparate. Moreover, the arginine to lysine ratio is similar to those measured in other glutamate dehydrogenases. The Nterminal amino acid is unavailable to dansylation. All six cysteines in the enzyme are in the free sulfhydryl form. The enzyme is very specific for the reduced and oxidized forms of nicotinamide adenine dinucleotide phosphate and has less than 0.5 percent of maximal activity, using the oxidized and reduced forms of nicotinamide adine dinucleotide. With low concentrations of the substrates, no cooperativity was seen; however severe substrate inhibition was observed with a-ketoglutarate. Antiserum produced to the subunits of the enzyme yielded a single precipitin band against purified enzyme in Ouchterlony double diffusion analysis. "Rocket" immunoelectrophoresis has been used to quantify the amount of antigen present in samples of the purified enzyme. / Master of Science

The carbon monoxide dehydrogenase complex was purified from acetate-grown Methanosarcina thermophila. This complex made up greater than 10% of the cellular protein and the native enzyme formed aggregates with a Mr of approximately 1,000,000. The enzyme contained five subunits of different molecular weight suggesting a multifunctional enzyme complex. Nickel, iron, cobalt, zinc, inorganic sulfide, and a corrinoid were present in the complex. The electron paramagnetic resonance spectrum of CO-reduced enzyme at 113K contained g values of 2.073, 2.049, and 2.028. Isotopic substitution with ⁶¹Ni, ⁵⁷Fe, or ¹³Co resulted in broadening of the spectrum consistent with a Ni-Fe-C spin-coupled complex. Acetyl-CoA caused a perturbation of the signal that was not caused by acetyl-phosphate or mercaptoethanol indicating acetyl-CoA is a physiological substrate. Cell extracts from acetate-grown M. thermophila contained CO-oxidizing:H₂-evolving activity 16-fold greater than extracts of methanol-grown cells. CO-oxidizing:H₂-evolving activity was reconstituted upon combination of: (i) CO dehydrogenase complex, (ii) a ferredoxin, and (iii) purified membranes with associated hydrogenase and b-type cytochrome. The ferredoxin was a direct electron acceptor for the CO dehydrogenase complex. The molecular weight of the isolated protein was 16,400, and the apparent minimum molecular weight was 4,900. The ferredoxin contained 2.8 ± 0.56 Fe atoms and 1.98 ± 0.12 acid-labile sulfide. UV-visible absorption maxima were 395 and 295 nm with a A₃₉₅/A₂₉₅ ratio range of 0.80 to 0.88. The N-terminal amino acid sequence revealed a 4-cysteine cluster, similar to other Fe:S centers that coordinate a Fe:S center. A CH₃-B₁₂:HS-CoM methyltransferase activity was characterized in extracts of acetate- and methanol-grown cells. The activity from extracts of acetate-grown M. thermophila was stable at 70°C for 30 minutes. The activity in cell extracts of acetate- and methanol-grown cells was fractionated with ammonium sulfate treatment and FPLC phenyl superose chromatography. Two peaks of methyltransferase activity were observed in each cell extract sample following phenyl superose fractionation. / Ph. D.

Diss. (sammanfattning) Linköping : Linköpings universitet, 2005. / Härtill 4 uppsatser.

Ph. D. (Department of Biotechnology, Faculty of Applied and Computer Sciences), Vaal University of Technology. / Hydrocarbon pollution is becoming a growing environmental concern in South Africa and globally. This inadvertently supports the need to identify enzymes for their targeted degradation. The search for novel biocatalysts such as monooxygenases, alcohol dehydrogenases and aldehyde dehydrogenases, have relied on conventional culture-based techniques but this allows sourcing of the biomolecules from only 1-10 % of the microbial population leaving the majority of the biomolecules unaccounted for in 90-99 % of the microbial community. The implementation of a metagenomics approach, a culture-independent technique, ensures that more or less than 100 % of the microbial community is assessed. This increases the chance of finding novel enzymes with superior physico-chemical and catalytic traits. Hydrocarbon polluted soils present a rich environment with an adapted microbial diversity. It was thus extrapolated that it could be a potential source of novel monooxygenases, alcohol dehydrogenases (ADH) and aldehyde dehydrogenases (ALDH) involved in hydrocarbon degradation pathways. Therefore, the aim of the study was to extract metagenomic DNA from hydrocarbon contaminated soils and construct a metagenomic fosmid library and screen the library for monooxygenases, alcohol dehydrogenases (ADH) and aldehyde dehydrogenases (ALDH). Accordingly, the fosmid library was constructed from metagenome of hydrocarbon-contaminated soil. Then the library was functionally screened using hexadecane, octadecene and cyclohexane as substrates and fifteen positive clones were selected. The fosmid constructs of the positive clones were sequenced using PacBio next generation sequencing platform. The sequences were de novo assembled and analysed using CLC Genomic Workbench. The open reading frames (ORF) of the contigs were identified by blasting the contigs against uniport database. Accordingly, four novel genes namely amo-vut1, aol-vut3, dhy-sc-vut5 and dhy-g-vut7 that showed close similarity with our target enzymes were further analysed in silico and codon-optimized as per Escherichia coli codon preference. The codon adjusted sequences were synthesised and cloned into pET30a(+) expression vector. However, it is worth noting that expression of amo-vut1 was not successful since it was later identified to be a multi-pass member protein, which made it insoluble despite the use of detergent to the effect. There is a need to meticulously genetically engineer amo-vut1 to remove the signal and other membrane-bound peptides while maintaining its activity. Yet the other three constructs were successfully transformed and expressed in E. coli BL21 (DE3). The enzymes were purified and characterized and cocktail for hydrolysis of hexanol was succesfully engineered based on AOL-VUT3, DHY-SC-VUT5 and DHY-G-VUT7. Therefore, novel enzymes were mined from metagenome of fossil-oil contaminated soil and effective hydrocarbon-degrading enzyme cocktails containing their combination were successfully engineered.