Arginine decarboxylase is a key enzyme involved in the polyamine pathway of organisms. Pyruvoyl-dependent arginine decarboxylases are expressed in the form of proenzymes that self-cleave to form N-terminal [beta] and C-terminal [alpha] subunits generating an active pyruvoyl group at the [alpha] terminus. We have identified an archaeal homolog of a pyruvoyl-dependent arginine decarboxylase in Chlamydophila pneumoniae that could play a role in the persistence of the organism in the host. The recombinant enzyme showed highest activity at pH 3.4, which is the lowest optimum pH ever reported for a pyruvoyl dependent arginine decarboxylase. The proton-consuming decarboxylation raises intracellular pH, and thereby plays a role in acid-resistance. It could inhibit the pro-inflammatory nitric oxide synthase resulting in asymptomatic infection. A variant protein Thr⁵²Ser at the predicted cleavage site showed less pro-enzyme cleavage and activity compared to the wild-type. The homologs of arginine decarboxylase and flanking arginine-agmatine antiporter were also found in different biovariants of Chlamydia trachomatis. In the invasive L2 strain of C. trachomatis, the presence of a nonsense codon in the gene encoding arginine decarboxylase enzyme prevented the expression of an active enzyme. The variant protein with tryptophan replacing nonsense codon restored arginine decarboxylase activity. The non-invasive D strain of C. trachomatis had an intact arginine decarboxylase gene, but it was recombinantly expressed as a proenzyme that was uncleaved. The arginine-agmatine antiporters from both the strains were active and transported tritiated arginine into their cells. The polyamine pathway of the crenarchaeon Sulfolobus solfataricus uses arginine to make putrescine, but the organism lacks homologs of arginine decarboxylase. However, it has two paralogs of pyruvoyl dependent S-adenosylmethionine decarboxylase − SSO0536 and SSO0585. These enzymes were recombinantly expressed as pro-enzymes that self-cleaved into [beta] and [alpha] subunits. Even with a 47% amino acid sequence identity, the SSO0536 protein exhibited significant arginine decarboxylase activity whereas SSO0585 protein had significant S-adenosylmethionine decarboxylase activity. This is the first report of an S-adenosylmethionine decarboxylase enzyme showing alternative decarboxylase activity. The chimeric protein with the [alpha]-subunit of SSO0585 and [beta]-subunit of SSO0536 had arginine decarboxylase activity, suggesting that the residues responsible for substrate recognition are located in the amino terminus. / text

No description available.

No description available.

Rhizopus oryzae is a filamentous fungi which produces lactic acid and ethanol in fermentations. R. oryzae has numerous advantages for use industrial production of L-(+)-lactic acid but the yield of lactic acid produced on the basis of carbon consumed is low. Metabolic flux analysis of R. oryzae has shown that most of the pyruvate produced at the end of the glycolysis is channelled to ethanol, acetyl-CoA and oxaloacetate production. This study aimed to answer some questions addressed on the regulation of pyruvate branch point in R. oryzae and for this purpose biochemical characterisation of the enzymes acting at this branch point and cloning the genes coding for these enzymes have been done. Pyruvate decarboxylase was purified and characterised for the first time from R. oryzae. The purified enzyme has a Hill coefficient of 1.84 and the Km of the enzyme is 8.6 mM for pyruvate at pH 6.5. The enzyme is inhibited at pyruvate concentrations higher than 30 mM. The optimum pH for enzyme activity shows a broad range from 5.7 and 7.2. The monomer molecular weight was estimated as 59&plusmn / 2 kDa by SDS-PAGE analysis. Pyruvate decarboxylase (pdcA and pdcB) and lactate dehydrogenase (ldhA and ldhB) genes of R. oryzae have been cloned by PCR-cloning approach and the filamentous fungi Aspergillus niger was transformed with these genes. The A. niger transformed with either of the ldh genes of R. oryzae showed enhanced production of lactic acid compared to wild type. Citric acid production was also increased in these transformants while no gluconate production was observed Cloning of hexokinase gene from R. oryzae using degenerate primers was studied by the use of GenomeWalker kit (Clontech). The results of this study were evaluated by using some bioinformatics tools depending on the unassembled clone sequences of R. oryzae genome.

Diss. med. dent. Zürich. / Literaturverz.

Fundação de Amparo a Pesquisa no Estado do Rio Grande do Sul / Gout attack is characterized severe joint pain and inflammation with concomitant accumulation of monosodium urate (MSU) crystals. However, gout and the mechanisms responsible for the acute attacks are poorly understood, leading to improper treatment of the patient and reducing the quality of life. Polyamines (putrescine, spermidine and spermine) are involved in inflammatory nociceptive processes and have not been investigated to date. Therefore, the aim of the present study was to investigate the involvement of polyamines in the development of acute gout attack. Arthritis score, a compound measure of joint compromise that considers edema formation, erythema and paw position, mechanical hyperalgesia and inflammatory parameters were measured in an acute gout attack model in male mice induced by intra-articular (i.a.) injection of MSU, H2O2, phorbol 12-myristate 13-acetate (PMA), L-ornithine or polyamines (putrescine, spermidine, spermine). All these algogenic agents increased arthritis score in a dose-dependent manner with ED50 of 0.73 (0.4-1.1) mg/site for MSU, 2.3 (1.5-3.5) μmol/site for H2O2, 3.5 (2.1-5.6) nmol/site for PMA, 0.6 (0.3-1.1) μmol/site for L-ornithine, 0.8 (0.4-1.7) μmol/site for putrescine, 3.6 (2.6-5.1) μmol/site for spermidine and 0.1 (0.06-0.2) μmol/site for spermine. All tested algogenic agents caused joint edema and nociception, except putrescine, which increased only arthritis score. α-Difluoromethylornithine (DFMO; ornithine decarboxylase ODC - inhibitor, i.a.) prevented MSU-, H2O2-, PMA-, L-ornithine-induced nociception, but not edema. On the other hand, DFMO did not prevent spermine-induced edema and nociception. DFMO prevented MSU-induced increase of ODC activity. Our results indicate that polyamines contribute to acute gout attacks, suggesting that inhibitors of polyamine synthesis may be potential therapeutic agents for the treatment and prophylaxis of gout. / O ataque agudo de gota é caracterizado por dor intensa e inflamação combinados com o acúmulo de cristais de urato monossódico (MSU). No entanto, a gota e os mecanismos responsáveis pelos ataques agudos ainda estão mal compreendidos, levando ao tratamento inadequado dos pacientes e reduzindo a qualidade de vida. As poliaminas (putrescina, espermidina e espermina) estão envolvidas em processos nociceptivos inflamatórios, e não foram investigadas até o momento, por conseguinte, o objetivo do presente estudo foi investigar o envolvimento das poliaminas no desenvolvimento do ataque de gota aguda em camundongos. Para isso, o escore de artrite (conjunto de somatórios de medidas que considera a formação de edema, eritema e posição da pata tratada do animal), hiperalgesia mecânica e parâmetros inflamatórios foram medidos em um modelo de ataque agudo de gota em camundongos machos, induzidos por uma injeção intra-articular de (i.a.) MSU, H2O2, forbol 12-miristato 13-acetato (PMA), L-ornitina ou poliaminas (putrescina, espermidina, espermina). Todos os agentes algogênicos aumentaram o escore de artrite de um modo dose dependente com um DE50 de 0,73 (0,4-1,1) mg/sitio de MSU, 2,3 (1,5-3,5) μmol/sitio de H2O2, 3,5 (2,1-5,6) nmol/sitio para PMA, 0,6 (0,3-1,1) μmol/sitio para a L-ornitina, 0,8 (0,4-1,7) μmol/sitio para a putrescina, 3,6 (2,6-5,1) μmol/sitio para a espermidina e 0,1 (0,06-0,2) μmol/sitio para espermina. Todos os agentes algogênicos testados causaram edema articular e nocicepção, exceto a putrescina, que aumentou apenas o escore de artrite. α-Difluorometilornitina (DFMO; inibidor da ornitina descarboxilase - ODC) preveniu a nocicepção induzida por: MSU, H2O2, PMA, L-ornitina, mas não o edema. Por outro lado, DFMO não preveniu a nocicepção e o edema induzido por espermina. DFMO preveniu o aumento da atividade da ODC induzido por MSU. Os nossos resultados indicam que as poliaminas estão envolvidas no ataque agudo de gota, sugerindo que os inibidores da síntese de poliaminas podem ser potenciais agentes terapêuticos para o tratamento e profilaxia da gota.

A parede celular vegetal, estrutura essencial para as plantas, é extremamente importante para a economia humana, já que apresenta diversas utilidades, como por exemplo, fabricação de papel, fibras de vestuário, construção civil, entre outras. A maior parte da parede celular vegetal primária (aproximadamente 90%), é formada por polissacarídeos como celulose, hemiceluloses e pectinas. Os monossacarídeos, unidades formadoras dos polissacarídeos, são sintetizados, nas plantas, a partir de diferentes açúcares nucleotídeos, sendo que, o suprimento desses, pode afetar a biossíntese dos polissacarídeos da parede celular. Visando analisar o impacto da alteração do fluxo metabólico do carbono na composição da parede celular, o presente projeto de pesquisa teve como objetivo alterar a composição dos polissacarídeos da parede celular de Nicotiana tabcum, através da modulação da expressão do gene uxs, responsável pela codificação da enzima UDP-D-glucuronato descarboxilase (UDPGlcADC, EC 4.1.1.35) que converte UDP-D-glucuronato em UDP-D-xilose, importante açúcar nucleotídeo, precursor do monossacarídeo xilose. Para isso, após a clonagem do gene uxs de ervilha, foram obtidas plantas transgênicas de tabaco superexpressando esse gene. Diversas análises foram realizadas para determinação da composição química da parede celular primária e secundária dessas plantas. Pela análise de FTIR da parede celular primária, verificou-se que três linhagens transgênicas apresentaram espectrotipos consistentes, indicando uma redução na quantidade de pectinas e ligações ésteres carboxílica nessas linhagens transgênicas. Apesar de não terem sido detectadas alterações na proporção dos monossacarídeos ramnose, xilose, arabinose, manose e galactose, e na quantidade de celulose, na parede celular primária das plantas transgênicas, foram observadas diferenças na proporção de galactose não esterificada, nas linhagens que apresentaram espectrotipo. Com relação à parede celular secundária, observou-se que algumas linhagens transgênicas apresentaram maior concentração de lignina solúvel relacionada a uma redução no conteúdo de lignina insolúvel. / The plant cell wall is not only an essential structure for plants, but also an extremely important raw material in human economy. The plant cell wall has diverse utilities, for example, papermaking, textile fiber, civil construction. Polysaccharides, such as cellulose, hemicelluloses and pectins, are the major components of the primary plant cell wall (approximately 90%). These polysaccharides are formed by monosaccharides, which are synthesized in the plant from different nucleotide sugars. The suppliment of the nucleotide sugars can affect plant cell wall polysaccharides biosynthesis. Aiming at analyzing the impact of the alteration in the metabolic carbon flux on cell wall composition, the objective of this research project was to alterate the plant cell wall polysaccharides composition by the modulation of the uxs gene. This gene encodes the UDP-D-glucuronic acid decarboxylase enzyme (UDPGlcADC, EC 4.1.1.35) that promotes the conversion of UDP-D-glucuronic acid to UDP-D-xylose, an important sugar nucleotide precursor of xylose monosaccharide. To achieve this goal, the pea uxs gene was cloned and transgenic tobacco plants overexpressing this gene were obtained. Several analyses were performed to determinate the primary and secondary cell wall composition of those transgenic plants. The primary cell wall analysis by FTIR identified three transgenic lines that show different spectrotypes compared to wild type and those transgenic spectrotypes had the same features. The results indicate a reduction of pectin and ester carbonyl binding in the transgenic plants. No alterations were detected in the monosaccharide (rhamnose, xylose, arabinose, manose and galactose) proportions and the amount of cellulose in the primary cell wall of the transgenic plants. Nevertheless, differences in the proportion of unesterified galactose were observed in the same transgenic lines that showed spectrotypes. With regard to secondary cell wall, some transgenic lines showed an increase in soluble lignin which is related to a reduction in insoluble lignin.

The sterol biosynthetic pathway is essential for growth of all eukaryotic cells and the main target of antifungal agents. The emergence of resistance to these antifungals in an already ill patient population indicates a need to develop drugs that have a broad spectrum of activity among pathogenic fungi and have minimal patient toxicity. Squalene synthase is the first committed step in the sterol pathway and has been studied intensively for development of antifungal agents. While the overall architecture of this enzyme is identical throughout eukaryotes, it was shown that plant and animal genes cannot complement a squalene synthase knockout mutation in yeast unless the carboxy-terminal domain is swapped for one of fungal origin. This implies that there is a component of the fungal carboxy-terminal domain that is responsible for the complementation phenotype and that is unique to the fungal kingdom of life. To determine the role of the carboxy-terminal domain of squalene synthase in the sterol pathway, we used the yeast Saccharomyces cerevisiae with a squalene synthase knockout mutation and expressed squalene synthases originating from fungi, plants, and animals. In contrast to previous observations, all enzymes tested could partially complement the knockout mutation when the genes were weakly expressed. When induced, non-fungal squalene synthases could not complement the knockout mutation and instead led to the accumulation of carboxysterol intermediates, suggesting an interaction between squalene synthase and the downstream sterol C4-decarboxylase. Overexpression of a sterol C4-decarboxylase from any kingdom of life both decreased the accumulation of carboxysterol intermediates and allowed non-fungal squalene synthases to complement the squalene synthase knockout mutation. Using chimeric squalene synthases from each kingdom of life, the motif in the C-terminal domain responsible for preventing this toxicity was mapped to a kingdom-specific 26-amino acid hinge motif adjacent to the catalytic domain. Furthermore, over-expression of the carboxy-terminal domain alone containing a hinge motif from fungi, not from animals or plants, led to growth inhibition of wild-type yeast. Since this hinge region is unique to and highly conserved within each kingdom of life, this data provides evidence for the development of an antifungal therapeutic as well as for tools to develop an understanding of triterpene catalytic activity and identify similar motifs in other biosynthetic pathways.

Thyronamine (TAM) sind eine neue Molekülklasse, die endokrinologische und metabolische Prozesse miteinander vereinen. Der biologisch aktive Metabolit 3-Iod-L-Thyronamin (3-T1AM) wird durch eine kombinierte Deiodierung und Decarboxylierung von Schilddrüsenhormonen (TH) gebildet. Existierende Methoden zum Nachweis und zur Quantifizierung von 3-T1AM im menschlichen Serum sind immer noch umstritten. Auch die an der Biosynthese vermutlich beteiligte TH-Decarboxylase konnte noch nicht identifiziert werden. Für die Identifizierung und Quantifizierung von TH und TAM Profilen wurde die Flüssigchromatographie-Tandem-Massenspektrometrie (LC-MS/MS) verwendet. In der bisherigen präanalytischen Aufarbeitung liefern weder Flüssig-Flüssig- noch Festphasenextraktionen reproduzierbare Ergebnisse des 3-T1AM-Gehalts im Serum. Mit der Entwicklung eines spezifischen Extraktionsverfahrens und nachfolgender Detektion mittels LC-MS/MS gelang der gleichzeitige Nachweis der häufigsten TH im humanen Serum. Parallel dazu wurden monoklonale Antikörper gegen 3-T1AM entwickelt, auf deren Basis ein quantitativer 3-T1AM Chemilumineszenz-Immunoassay entstand. Ergebnisse aus klinischen Kollektiven zeigen, dass 3-T1AM im Serum im nM Konzentrationsbereich vorkommt und dass 3-T1AM bei Patienten außerhalb der Schilddrüse produziert wird. Viele Forscher gehen davon aus, dass die aromatische L-Aminosäure Decarboxylase (AADC) die Synthese von TAM über Decarboxylierung von TH katalysiert. Diese Hypothese wurde durch Inkubation von rekombinanter humaner AADC mit TH getestet. In keinem der Experimente konnte AADC die Decarboxylierung von TH katalysieren. Zusammenfassend ist die Bestimmung von 3-T1AM im Serum mittels LC-MS/MS aufgrund der nicht reproduzierbaren präanalytischen Probenaufbereitung problematisch. In dieser Arbeit wird der erste MAb-basierte 3-T1AM assay vorgestellt, der 3-T1AM zuverlässig in humanem Serum quantifiziert. Die AADC ist wahrscheinlich nicht an der Biosynthese von TAM beteiligt. / Thyronamines (TAM) are a new class of molecules linking endocrinology and metabolism. Combined deiodination and decarboxylation of thyroid hormones (TH) generates a biologically active ‘cooling’ metabolite, 3-iodo-L-thyronamine (3-T1AM).. It remains controversial, which methods are able or not to reliably detect 3-T1AM in human serum, and the presumed TH decarboxylase is still elusive. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used for the simultane-ous identification and quantification of TH and TAM profiles in biological samples. Several preanalytical methods were tested for complete extraction of 3-T1AM in human serum. Thus far, neither liquid-liquid nor solid-phase extraction methods allowed reproducible extraction of 3-T1AM from human serum samples in the preanalytical sample workup. Nevertheless, a rapid and sensitive extraction procedure was developed for detection of the major TH by LC-MS/MS in a single human serum sample. In parallel, monoclonal antibodies (MAb) targeting 3-T1AM were developed and characterized, and a highly specific quantitative 3-T1AM MAb-based chemiluminescence immunoassay was developed. Studies in clinical cohorts provide evidence that 3-T1AM is present in human serum in the nM concentration range and that 3-T1AM is produced extrathyroidally. Many researchers have reasoned that the aromatic L-amino acid decarboxylase (AADC) mediates TAM synthesis via decarboxylation of TH. This hypothesis was tested by incubating recombinant human AADC with several TH. In all tested conditions, AADC failed to catalyze the decarboxylation of TH. These in vitro observations are supported by the finding that 3-T1AM is also present in plasma samples of patients with AADC deficiency. In summary, 3-T1AM detection in serum using LC-MS/MS encounters preanalytical problems. The first MAb-based 3-T1AM CLIA is presented, which reliably quantifies 3-T1AM in human serum. AADC is likely not involved in TAM biosynthesis.

Metabolism of D-amino acids is of considerable interest due to their key importance in cellular functions. The enzymes D-serine dehydratase (DSD) and D-cysteine desulfhydrase (DCyD) are involved in the degradation of D-Ser and D-Cys, respectively. We determined the crystal structure of Salmonella typhimurium DSD (StDSD) by multiple anomalous dispersion method of phasing using selenomethione incorporated protein crystals. The structure revealed a fold typical of fold type II PLP-dependent enzymes. Although holoenzyme was used for crystallization of both wild type StDSD (WtDSD) and selenomethionine labeled StDSD (SeMetDSD), significant electron density was not observed for the co-factor, indicating that the enzyme has a low affinity for the cofactor under crystallization conditions. Interestingly, unexpected conformational differences were observed between the two structures. The WtDSD was in an open conformation while SeMetDSD, crystallized in the presence of isoserine, was in a closed conformation suggesting that the enzyme is likely to undergo conformational changes upon binding of substrate as observed in other fold type II PLP-dependent enzymes. Electron density corresponding to a plausible sodium ion was found near the active site of the closed but not in the open state of the enzyme. Examination of the active site and substrate modeling suggested that Thr166 may be involved in abstraction of proton from the Cα atom of the substrate. Apart from the physiological reaction, StDSD catalyses α, β-elimination of D-Thr, D-Allothr and L-Ser to the corresponding α-keto acids and ammonia. The structure of StDSD provides a molecular framework necessary for understanding differences in the rate of reaction with these substrates. Salmonella typhimurium DCyD (StDCyD) is a fold type II PLP-dependent enzyme that catalyzes the degradation of D-Cys to H2S and pyruvate. We determined the crystal structure of StDCyD using molecular replacement method in two different crystal forms. The better diffracting crystal form obtained in presence of benzamidine illustrated the influence a small molecule in altering protein interfaces and crystal packing. The polypeptide fold of StDCyD consists of a small domain (residues 48-161) and a large domain (residues 1-47 and 162-328) which resemble other fold type II PLP-dependent enzymes. X-ray crystal structures of StDCyD were also obtained in the presence of substrates, D-Cys and βCDA, and substrate analogs, ACC, D-Ser, L-Ser, D-cycloserine (DCS) and L-cycloserine (LCS). The structures obtained in the presence of D-Cys and βCDA show the product, pyruvate, bound at a site 4.0-6.0 Å away from the active site. ACC forms an external aldimine complex while D and L-Ser bind non-covalently suggesting that the reaction with these ligands is arrested at Cα proton abstraction and transimination steps, respectively. In the active site of StDCyD cocrystallized with DCS or LCS, electron density for a pyridoxamine phosphate (PMP) was observed. Crystals soaked in cocktail containing these ligands show density for PLP-cycloserine. Spectroscopic observations also suggested formation of PMP by the hydrolysis of cycloserines. Mutational studies suggested that Ser78 and Gln77 are key determinants of enzyme specificity and the phenolate of Tyr287 is responsible for Cα proton abstraction from D-Cys. Based on these studies, we proposed a probable mechanism for the degradation of D-Cys by StDCyD. The acid-induced arginine decarboxylase (ADC) is part of an enzymatic system in Salmonella typhimurium that contributes to making this organism acid resistant. ADC is a PLP-dependent enzyme that is active at acidic pH. It consumes a proton in the decarboxylation of arginine to agmatine, and by working in tandem with an arginine-agmatine antiporter, this enzymatic cycle protects the organism by preventing the accumulation of protons inside the cell. We have determined the structure of the acid-induced StADC to 3.1 Å resolution. StADC structure revealed an 800 kDa decamer composed as a pentamer of five homodimers. Each homodimer has an abundance of acidic surface residues, which at neutral pH prevent inactive homodimers from associating into active decamers. Conversely, acidic conditions favor the assembly of active decamers. Therefore, the structure of arginine decarboxylase presents a mechanism by which its activity is modulated by external pH.