Amidation of peptidoglycan in Staphylococcus aureus

Staphylococcus aureus is one of the most important contemporary human pathogens. The evolutionary “success” of this species is closely related to its remarkably capacity to acquire antibiotic resistance traits. In this perspective, it is important to extend our knowledge concerning the mechanisms of antibiotic resistance in S. aureus and to identify new antimicrobials targets.(...)

Improving the early diagnostic of prostate cancer by multiple biomarker detection with new biosensing devices

Prostate cancer (PCa) is the most common form of cancer in men, in Europe (World Health Organization data). The most recent statistics, in Portuguese territory, confirm this scenario, which states that about 50% of Portuguese men may suffer from prostate cancer and 15% of these will die from this condition. Its early detection is therefore fundamental. This is currently being done by Prostate Specific Antigen (PSA) screening in urine but false positive and negative results are quite often obtained and many patients are sent to unnecessary biopsy procedures. This early detection protocol may be improved, by the development of point-of-care cancer detection devices, not only to PSA but also to other biomarkers recently identified. Thus, the present work aims to screen several biomarkers in cultured human prostate cell lines, serum and urine samples, developing low cost sensors based on new synthetic biomaterials. Biomarkers considered in this study are the following: prostate specific antigen (PSA), annexin A3 (ANXA3), microseminoprotein-beta (MSMB) and sarcosine (SAR). The biomarker recognition may occurs by means of molecularly imprinted polymers (MIP), which are a kind of plastic antibodies, and enzymatic approaches. The growth of a rigid polymer, chemically stable, using the biomarker as a template allows the synthesis of the plastic antibody. MIPs show high sensitivity/selectivity and present much longer stability and much lower price than natural antibodies. This nanostructured material was prepared on a carbon solid. The interaction between the biomarker and the sensing-material produces electrical signals generating quantitative or semi-quantitative data. These devices allow inexpensive and portable detection in point-of-care testing.

Peroxisomal beta-oxidation--a metabolic pathway with multiple functions.

Fatty acid degradation in most organisms occurs primarily via the beta-oxidation cycle. In mammals, beta-oxidation occurs in both mitochondria and peroxisomes, whereas plants and most fungi harbor the beta-oxidation cycle only in the peroxisomes. Although several of the enzymes participating in this pathway in both organelles are similar, some distinct physiological roles have been uncovered. Recent advances in the structural elucidation of numerous mammalian and yeast enzymes involved in beta-oxidation have shed light on the basis of the substrate specificity for several of them. Of particular interest is the structural organization and function of the type 1 and 2 multifunctional enzyme (MFE-1 and MFE-2), two enzymes evolutionarily distant yet catalyzing the same overall enzymatic reactions but via opposite stereochemistry. New data on the physiological roles of the various enzymes participating in beta-oxidation have been gathered through the analysis of knockout mutants in plants, yeast and animals, as well as by the use of polyhydroxyalkanoate synthesis from beta-oxidation intermediates as a tool to study carbon flux through the pathway. In plants, both forward and reverse genetics performed on the model plant Arabidopsis thaliana have revealed novel roles for beta-oxidation in the germination process that is independent of the generation of carbohydrates for growth, as well as in embryo and flower development, and the generation of the phytohormone indole-3-acetic acid and the signal molecule jasmonic acid.

Febuxostat, an Inhibitor of Xanthine Oxidase, Suppresses Lipopolysaccharide-Induced MCP-1 Production via MAPK Phosphatase-1-Mediated Inactivation of JNK.

Excess reactive oxygen species (ROS) formation can trigger various pathological conditions such as inflammation, in which xanthine oxidase (XO) is one major enzymatic source of ROS. Although XO has been reported to play essential roles in inflammatory conditions, the molecular mechanisms underlying the involvement of XO in inflammatory pathways remain unclear. Febuxostat, a selective and potent inhibitor of XO, effectively inhibits not only the generation of uric acid but also the formation of ROS. In this study, therefore, we examined the effects of febuxostat on lipopolysaccharide (LPS)-mediated inflammatory responses. Here we show that febuxostat suppresses LPS-induced MCP-1 production and mRNA expression via activating MAPK phosphatase-1 (MKP-1) which, in turn, leads to dephosphorylation and inactivation of JNK in macrophages. Moreover, these effects of febuxostat are mediated by inhibiting XO-mediated intracellular ROS production. Taken together, our data suggest that XO mediates LPS-induced phosphorylation of JNK through ROS production and MKP-1 inactivation, leading to MCP-1 production in macrophages. These studies may bring new insights into the novel role of XO in regulating inflammatory process through MAPK phosphatase, and demonstrate the potential use of XO inhibitor in modulating the inflammatory processes.

Malt1 protease inactivation efficiently dampens immune responses but causes spontaneous autoimmunity.

The protease activity of the paracaspase Malt1 has recently gained interest as a drug target for immunomodulation and the treatment of diffuse large B-cell lymphomas. To address the consequences of Malt1 protease inactivation on the immune response in vivo, we generated knock-in mice expressing a catalytically inactive C472A mutant of Malt1 that conserves its scaffold function. Like Malt1-deficient mice, knock-in mice had strong defects in the activation of lymphocytes, NK and dendritic cells, and the development of B1 and marginal zone B cells and were completely protected against the induction of autoimmune encephalomyelitis. Malt1 inactivation also protected the mice from experimental induction of colitis. However, Malt1 knock-in mice but not Malt1-deficient mice spontaneously developed signs of autoimmune gastritis that correlated with an absence of Treg cells, an accumulation of T cells with an activated phenotype and high serum levels of IgE and IgG1. Thus, removal of the enzymatic activity of Malt1 efficiently dampens the immune response, but favors autoimmunity through impaired Treg development, which could be relevant for therapeutic Malt1-targeting strategies.

Structure of the glycosyl-phosphatidylinositol membrane anchor of the Leishmania major promastigote surface protease.

In common with many other plasma membrane glycoproteins of eukaryotic origin, the promastigote surface protease (PSP) of the protozoan parasite Leishmania contains a glycosyl-phosphatidylinositol (GPI) membrane anchor. The GPI anchor of Leishmania major PSP was purified following proteolysis of the PSP and analyzed by two-dimensional 1H-1H NMR, compositional and methylation linkage analyses, chemical and enzymatic modifications, and amino acid sequencing. From these results, the structure of the GPI-containing peptide was found to be Asp-Gly-Gly-Asn-ethanolamine-PO4-6Man alpha 1-6Man alpha 1-4GlcN alpha 1-6myo-inositol-1-PO4-(1-alkyl-2-acyl-glycerol). The glycan structure is identical to the conserved glycan core regions of the GPI anchor of Trypanosoma brucei variant surface glycoprotein and rat brain Thy-1 antigen, supporting the notion that this portion of GPIs are highly conserved. The phosphatidylinositol moiety of the PSP anchor is unusual, containing a fully saturated, unbranched 1-O-alkyl chain (mainly C24:0) and a mixture of fully saturated unbranched 2-O-acyl chains (C12:0, C14:0, C16:0, and C18:0). This lipid composition differs significantly from those of the GPIs of T. brucei variant surface glycoprotein and mammalian erythrocyte acetylcholinesterase but is similar to that of a family of glycosylated phosphoinositides found uniquely in Leishmania.

Characterization of the chitinolytic system during the mycoparasitic interaction between Trichoderma aggressivum f. aggressivum and different host strains of Agaricus bisporus /

Green mould is a serious disease of commercially grown mushrooms, the causal agent being attributed to the filamentous soil fungus Triclzodenna aggressivum f. aggressivu11l and T. aggressivum f. ellropaellm. Found worldwide, and capable of devastating crops, this disease has caused millions of dollars in lost revenue within the mushroom industry. One mechanism used by TricllOdenlla spp. in the antagonism of other fungi, is the secretion of lytic enzymes such as chitinases, which actively degrade a host's cell wall. Therefore, the intent of this study was to examine the production of chitinase enzymes during the host-parasite interaction of Agaricus bisporus (commercial mushroom) and Triclzodemza aggressivum, focusing specifically on chitinase involvement in the differential resistance of white, off-white, and brown commercial mushroom strains. Chitinases isolated from cultures of A. bisporus and T. aggressivu11l grown together and separately, were identified following native PAGE, and analysis of fluorescence based on specific enzymatic cleavage of 4-methylumbelliferyl glucoside substrates. Results indicate that the interaction between T. aggressivulll and A. bisporus involves a complex enzyme battle. It was determined that T. aggressivum produces a number of chitinases that appear to correlate to those isolated in previous studies using biocontrol strains of T. Izarziallilm. A 122 kDa N-acetylglucosaminidase of T. aggressivu11l revealed the highest and most variable activity, and is therefore believed to be an important predictor of antifungal activity. Furthermore, results indicate that brown strain resistance of mushrooms may be related to high levels of a 96 kDa N-acetylglucosaminidase, which showed elevated activity in both solitary and dual cultures with T. aggressivum. Overall, each host-parasite combination produced unique enzyme profiles, with the majority of the differences seen between day 0 and day 6 for the extracellular chitinases. Therefore, it was concluded that the antagonistic behaviour of T. aggressivli1ll does not involve a typical response, always producing the same types and levels of enzymes, but that mycoparasitism, specifically in the form of chitinase production, may be induced and regulated based on the host presented.

Hydration, conformational states and kinetics of yeast hexokinase PII /

The kinetic study of the coupled enzymatic reaction involving monomeric yeast hexokinase PII (HK) and yeast glucose-6-phosphate dehydrogenase (G-6-PDH) yields a Michaelis constant of 0.15 ± 0.01 mM for D-glucose. At pH 8.7 HK is present in monomeric form. The addition of polyethylene glycol (PEG), to the reaction mixture increased the affinity of HK for glucose, independent ofMW of the PEG from 2000 to 10000. The osmotic stress exerted by PEG can be used to measure the change in number of water molecules that accompany enzyme conformational changes (Rand, et al., 1993). Results indicate that the G-6-PDH is not osmotically sensitive and thus, the change in the number of PEG-inaccessible water molecules (ANw) measured in the coupled reaction is only the difference between the glucose-bound and glucosefree conformations of HK. ANw ~ 450 with PEGs of MW > 2000 under conditions for both binding (Reid and Rand, 1997) and kinetic assays. The contribution water may play in the binding of ATP (Km = 0.24 + 0.02 mM) has also been examined. It was found that in this case ANw = (for osmotic pressures < 2.8x10* dynes/cm^), suggesting no additional numbers of waters are displaced when ATP binds to HK. Osmotic pressure experiments were also performed with dimeric HK. It was determined that both the monomeric and dimeric forms of HK give the same ANw under low pressures. If this large ANw is due to conformational flexibility, it would appear that the flexibility is not reduced upon dimerization ofthe enzyme.

Metabolic, biochemical and molecular profiling of Catharanthus roseus flower cultivars and transformed hairy roots for monoterpenoid indole alkaloid accumulation /

Catharanthlls rosellS (L.) G Don is a commercially significant flower species and in addition is the only source of the monoterpenoid indole alkaloids (MIA) vinblastine and vincristine, which are key pharmaceutical compounds that are used to combat a number of different cancers. Therefore, procurement of the antineoplastic agents is difficult but essential procedure. Alternatively, CatharanthllS tissue cultures have been investigated as a source of these agents; however they do not produce vindoline, which is an obligate precursor to vinblastine and vincristine. The interest in developing high MIA cultivars of Catharantlws rosellS has prompted metabolic profiling studies to determine the variability of MIA accumulation of existing flowering cultivars, with particular focus on the vindoline component ofthe pathway. Metabolic profiling studies that used high performance liquid chromatography of MIAs from seedlings and young leaf extracts from 50 different flowering cultivars showed that, except for a single low vindoline cultivar (Vinca Mediterranean DP Orchid), they all accumulate similar levels of MIAs. Further enzymatic studies with extracts from young leaves and from developing seedlings showed that the low vindoline cultivar has a IO-fold lower tabersonine-16-hydroxylase activity than those of CatharanthllS rosellS cv Little Delicata. Additionally, studies aimed at metabolic engineering ofvindoline bios}l1thesis in Catharanthus rosellS hairy root cultures have been performed by expressing the last step in vindoline biosynthesis [Dcacetylvindoline-4-0- acetyltransferase (DAT)]. Enzymatic profiling studies with transformed hairy roots have confirmed that over-expressing DAT leads to lines with high levels of O-acetyltransferase activity when compared to non-expressing hairy roots. One particular DA T over111 expressing hairy root culture (line 7) contained 200 times the OAT activity than leaves of control lines. Additional MIA analyses revealed that DAT over-expressing hairy roots have an altered alkaloid profile with significant variation in the accumulation of h6rhammericine. Further analysis of transformed hairy root line 7 suggests a correlation between the expression of OAT activity and h6rhammericine accumulation with root maturation. These studies show that metabolic and selective enzymatic profiling can enhance our ability to search for relevant MIA pathway mutants and that genetic engineering with appropriate pathway genes shows promise as a tool to modify the MIA profile of Catharanthus roseus.

An investigation into some mechanistic aspects of estrogen biosynthesis

The mechanistic aspects of the 19-hydroxy1ation and aromatization of androgens were investigated. Fungal, bacterial and mammalian enzymatic activities were studied in this regard . The fungus Pell i cular~ fi1amentosa metabolized androst-4-ene-3 , 17-dione to the corresponding 110<' , 11 f and 14 0( hydroxylated derivatives. No ~19- hydroxylated products were isolated, although this transformation was previously observed for the C21-steroids . The intestinal bacterium Clostridi um paraputrific~ had been reported to aromatize androsten-4-ene-3,17-dione. In the present study, however, only the ring A reduced products , 17(3 - hydroxy-5f -andro8tane- 3-one and 5f-androstane-3,17-dione , were recovered . Human placental microsomes contain substantial aromatase activity and were employed in an effort to elucidate some of the mechanistic details of aromatization. Selectively deuterated steroidal substrates were employed as a probe in order to distinguish b'!tween certain of the mechanisms proposed for aromatization . Retention of deuterium at C4 and C6 was observed. It was concluded that no free intermediates allowing for loss of hydrogen from either of these two positions are implicated in this process . The involvement of a Schiff base enzyme-sup strate complex in aromatization was examined using the substrate 17f - hydroxyandrost-4-ene-3-one- 3_ 1BO. Since no loss of label was ob~erved, the implication of a Schiff base was discounted . Mixed label1ir~ studies were performed in order to determine if hydroxylation at C19 is a rate-determining process in aromatization . Isotope effects of 2 .1 and 1.7 were determined for the conversion of 17f - hydroxyandrost-4-ene-J-one-19,19,19-dJ and -19-dl respectively to estrogens. It was concluded from this that 19-hydroxylation is at l east a partially rate-determinjng process in aromatization. A homoenb~ation mechanism for 19-hydroxylation was not supported by the data obtained in this s tudy. In vitro 1JC NMR monitoring using l7f-hydroxyandrost-4-ene-Jone- 19-l3C was found not to be a successful approach in the study of steroid transformations, owing in part t o their low solubility in the incubation medium.

Aspects of the hemes and modulation of hydrogen donors in catalases from bovine liver, yeast, and escherichia coli

Catalase is the enzyme which decomposes hydrogen peroxide to water and oxygen. Escherichia coli contains two catalases. Hydroperoxidase I (HPI) is a bifunctional catalase-peroxidase. Hydroperoxidase II (HPII) is only catalytically active toward H202. Expression of the genes encoding these proteins is controlled by different regimes. HPJI is thought to be a hexamer, having one heme d cis group per enzymatic subunit. HPII wild type protein and heme containing mutant proteins were obtained from the laboratory of P. Loewen (Univ. of Manitoba). Mutants constructed by oligonucleotidedirected mutagenesis were targeted for replacement of either the His128 residue or the Asn201 residue in the vicinity of the HPII heme crevice. His128 is the residue thought to be analogous to the His74 distal axial ligand of the heme in the bovine liver enzyme, and Asn201 is believed to be a residue critical to the function of the enzyme because of its role in orienting and interacting with the substrate molecule. Investigation of the nature of the hemes via absorption spectroscopy of the unmodified catalase proteins and their derived pyridine hemochromes showed that while the bovine and Saccharomyces cerevisiae catalase enzymes are protoheme-containing, the HPII wild type protein contains heme d, and the mutant proteins contain either solely protoheme, or heme d-protoheme mixtures. Cyanide binding studies supported this, as ligand binding was monophasic for the bovine, Saccharomyces cerevisiae, and wild type HPII enzymes, but biphasic for several of the HPII mutant proteins. Several mammalian catalases, and at least two prokaryotic catalases, are known to be NADPH binding. The function of this cofactor appears to be the prevention of inactivation of the enzyme, which occurs via formation of the inactive secondary catalase peroxide compound (compound II). No physiologically plausible scheme has yet been proposed for the NADPH mediation of catalase activity. This study has shown, via fluorescence and affinity chromatography techniques, that NADPH binds to the T (Typical) and A (Atypical) catalases of Saccharomyces cerevisiae, and that wild type HPII apparently does not bind NADPH. This study has also shown that NADPH is unlike any other hydrogen donor to catalase, and addresses its features as a unique donor by proposing a mechanism whereby NADPH is oxidized and catalase is protected from inactivation via the formation of protein radical species. Migration of this radical to a position close to the NADPH is also proposed as an adjunct hypothesis, based on similar electron migrations that are known to occur within metmyoglobin and cytochrome c peroxidase when reacted with H202. Validation of these hypotheses may be obtained in appropriate future experiments.

Light and electron microscope studies of host-parasite relations in a mycoparasite

Light microscope studies of the mycoparasite Piptocephalis virginiana revealed that the cylindrical spores of the parasite became spherical upon germination and produced 1-4 germ tubes. Generally t"l.vO germ tubes were produced by each spore. When this parasite was inoculated on its potential hosts, Choanephora cucurbitarum and Phascolomyces articulosus, the germ tube nearest to the host hypha continued to grow and made contact with the host hypha. The tip of the parasite's germ tube became swollen to form a distinct appressorium. Up to this stage the behavior of the parasite was similar regardless of the nature of the host. In the compatible host-parasite combination, the parasite penetrated the host, established a nutritional relationship and continued to grow to cover the host completely with its buff colored spores in 3-4 days. In the incompatible host-parasite combination, the parasite penetrated the host but its further advance was arrested. As a result of failure to establish a nutritional relationship with the resistant host, the parasite made further attempts to penetrate the host at different sites producing multiple infections. In the absence of nutrition the parasite weakened and the host outgrew the parasite completely. In the presence of a non-host species, Linderina pennispora the parasite continued to grow across the non-host 1).yp_hae vlithout establishing an initial contact. Germination studies showed that the parasite germinated equally well in the presence of host and non-host species. Further electron microscope studies revealed that the host-parasite interaction between P. virginiana and its host, C. cucurbi tarum, was compatible when the host hyphae were young slender, with a thin cell wall of one layer. The parasite appeared to penetrate mechanically by pushing the host-cell wall inward. The host plasma membrane invaginated along the involuted cell wall. The older hyphae of C. cucurbitarum possessed two distinct layers of cell wall and-showed an incompatible interaction when challenged vlith the parasite. At the point of contact, the outer layer of the host-cell wall dissolved, probably by enzymatic digestion, and the inner layer became thickened and developed a papilla as a result of its response to the parasite. The haustoria of the parasite in the old hyphae were always surrounded by a thick, well developed sheath, whereas the haustoria of the same age in the young host mycelium were devoid of a sheath during early stages of infection. Instead, they were in direct contact with the host protoplast. The incompatible interaction between a resistant host, P. articulosus and the parasite showed similar results as with the old hyphae of C. cucurbitarum. The cell wall of P. articulosus appeared thick-with two or more layers even in the 18-22 h-old hyphae. No contact or interaction was established between the parasite and the non-host L. pennispora. The role of cell wall in the resistance mechanism is discussed.

Enantiodivergent chemoenzymatic synthesis of Balanol and approaches to the synthesis of (+)-Codine

The present thesis reviews the development of a formal enantiodivergent synthesis of the (+)- and (-)-isomers of balanol. This approach commences from a cis-dihydrodiol derived from the enzymatic dihydroxylation of bromobenzene. The stereochemistry of the diol is used to direct the synthesis of two different aziridines, each used in the formal synthesis of one enantiomer of balanol. Also described are several enantioselective approaches to (+ )-codeine. Each strategy begins with the enzymatic dihydroxylation of p-bromoethylbenzene and involves a Mitsunobu inversion and intramolecular Heck reaction as key steps.

Chemoenzymatic synthesis of amaryllidaceae alkaloids and their C-1 analogues : symmetry based approach to total synthesis of thebaine

Described herein is the chemoenzymatic total synthesis of several Amaryllidaceae constituents and their unnatural C-I analogues. A new approach to pancratistatin and related compounds will be discussed along with the completed total synthesis of 7 -deoxypancratistatin and trans-dihydrolycoricidine. Evaluation of all new C-l analogues as cancer cell growth inhibitory agents is described. The enzymatic oxidation of dibromobenzenes by Escherichia coli 1M 109 (pDTG60 1) is presented along with conversion of their metabolites to (-)-conduritol E. Investigation into the steric and functional factors governing the enzymatic dihydroxylation of various benzoates by the same organism is also discussed. The synthetic utility of these metabolites is demonstrated through their conversion to pseudo-sugars, aminocyclitols, and complex bicyclic ring systems. The current work on the total synthesis of some morphine alkaloids is also presented. Highlighted will be the synthesis of several model systems related to the efficient total synthesis of thebaine.

ORGANOSILICON BIOTECHNOLOGY: A BIO-INSPIRED APPROACH TO THE HYDROLYSIS OF ALKOXYSILANES and THE LIPASE-CATALYZED SYNTHESIS OF SILOXANE-CONTAINING POLYESTERS AND POLYAMIDES

The first part of this thesis studied the capacity of amino acids and enzymes to catalyze the hydrolysis and condensation of tetraethoxysilane and phenyltrimethoxysilane. Selected amino acids were shown to accelerate the hydrolysis and condensation of tetraethoxysilane under ambient temperature, pressure and at neutral pH (pH 7±0.02). The nature of the side chain of the amino acid was important in promoting hydrolysis and condensation. Several proteases were shown to have a capacity to hydrolyze tri- and tet-ra- alkoxysilanes under the same mild reaction conditions. The second part of this thesis employed an immobilized Candida antarctica lipase B (Novozym-435, N435) to produce siloxane-containing polyesters, polyamides, and polyester amides under solvent-free conditions. Enzymatic activity was shown to be temperature dependent, increasing until enzyme denaturation became the dominant pro-cess, which typically occurred between 120-130ᵒC. The residual activity of N435 was, on average, greater than 90%, when used in the synthesis of disiloxane-containing polyesters, regardless of the polymerization temperature except at the very highest temperatures, 140-150ᵒC. A study of the thermal tolerance of N435 determined that, over ten reaction cycles, there was a decrease in the initial rate of polymerization with each consecutive use of the catalyst. No change in the degree of monomer conversion after a 24 hour reaction cycle was found.