Thesis (Ph. D.)--University of Texas at Austin, 2006. / Vita. Includes bibliographical references.

Thesis (M.Phil.)--Hong Kong University of Science and Technology, 2008. / Includes bibliographical references.

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Orientadora: Maysa Furlan / Banca: Nivaldo Boralle / Banca: Marcos Pivatto / Resumo: Cromanos e cromenos são metabólitos secundários comumente encontrados em espécies dos gêneros Piper e Peperomia, pertencentes à família Piperaceae. São caracterizados pela presença de um núcleo benzopirânico (um anel benzeno fundido a um anel pirano). Essa classe de substâncias é importante do ponto de vista farmacológico, uma vez que apresenta vasta gama de atividades biológicas, incluindo antifúngica, tripanocida, antioxidante e antiparasitária. Os benzopiranos isolados de espécies de Piper e Peperomia apresentam diversidade quanto aos substituintes da unidade aromática de suas estruturas químicas. Baseado no exposto, rotas biossintéticas distintas foram propostas. Em espécies de Piper essas rotas envolveriam a via do ácido chiquímico pela atuação do ácido para-hidroxibenzóico, enquanto que em espécies de Peperomia estaria operando a via do acetato. O presente trabalho teve como objetivo estudar a relação biossintética dos benzopiranos presentes nas espécies Piper aduncum e Peperomia obtusifolia, bem como a determinação da dinâmica metabólica envolvida na formação dos mesmos, tanto em nível metabólico como enzimático, uma vez que os cromenos isolados de Piper aduncum descrevem ritmo circadiano bem determinado. Estudos de variação circadiana realizados em Peperomia obtusifolia com o objetivo de acompanhar a formação do cromano ácido 3,4-diidro-5-hidróxi-2,7-dimetil-8-(3-metil-2-butenil)-2-(4-metil-1,3-pentadienil)-2H-1-benzopirano carboxílico (4) não demonstraram ritmo uniforme, do tipo sigmoidal, comum aos cromenos isolados de P. aduncum. O acúmulo do cromano 4 mostrou um máximo às 18h00, mas outros picos de concentração do mesmo foram observados às 06h00 e 15h00 e corroboram para o estabelecimento de um ritmo aleatório. Para a avaliação da origem biossintética de 4, foram realizados experimentos de incorporação utilizando precursor enriquecido... / Abstract: Chromanes and chromenes are secondary metabolites commonly found in species of the genera Piper and Peperomia, belonging to the Piperaceae family. They are characterized by the presence of a benzopyran core showing a benzene ring fused to a pyran ring. This class of compounds is pharmacologically important, since they from shown a broad range of biological activities including antifungal, trypanocidal, antioxidant and anti-parasitic. The benzopyrans isolated from Piper and Peperomia species showed diversity biosynthetic pathways, mainly related to the aromatic moieties. The biosynthesis of Piper species involve the shikimic pathway showing as the first precursor the p-hydroxybenzoic acid, whereas in Peperomia species would be operating the route of acetate. The present work aimed to study the biosynthetic relationship of benzopyrans present in Piper aduncum and Peperomia obtusifolia as well as to determine the metabolic dynamics involved in their formation related to metabolic and enzymatic levels, since the chromenes isolated from Piper aduncum describe well-defined circadian rhythm. Studies of circadian rhythm performed in Peperomia obtusifolia, aiming to follow the formation of chromane 3,4 -dihydro- 5 -hydroxy -2 ,7- dimethyl-8- (3-methyl -2- butenyl) -2 - (4 -methyl -1 ,3- pentadienyl )-2H -1- benzopyran carboxylic acid (4) from P. obtusifolia showed no uniform sigmoidal curve, common to the chromenes isolated from Piper aduncum. The accumulation of the chromane 4 showed a maximum at 18:00 pm, but others peaks of the same concentration were observed at 06:00 am and 15:00 pm, corroborating to establish a random pace. To evaluate the biosynthetic origin of the chromane 4, feeding experiments were conducted using a precursor enriched with stable isotopes (ethyl [2-13C ]-sodium acetate) in the leaves of P. obtusifolia. Experiments were performed using seedlings of P. obtusifolia. The enriched extracts... / Mestre

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This thesis is devoted to the evolution of the heme biosynthetic pathway in eukaryotic phototrophs with particular emphasis on algae possessing secondary and tertiary red and green derived plastids. Based on molecular biology and bioinformatics approaches it explores the diversity and similarities in heme biosynthesis among different algae. The core study of this thesis describes the heme biosynthesis in Bigelowiella natans and Guillardia theta, algae containing a remnant endosymbiont nucleus within their plastids, in dinoflagellates containing tertiary endosymbionts derived from diatoms called dinotoms, and in Lepidodinium chlorophorum, a dinoflagellate containing a secondary green plastid. The thesis further focusses on new insights in the heme biosynthetic pathway and general origin of the genes in chromerids the group of free-living algae closely related to apicomplexan parasites.

Nucleic acids are ubiquitous in nature and modified nucleosides are present in a wide range of anti-viral, anti-cancer drugs and antibiotics. Although a variety of naturally occurring nucleoside analogues exist, few include modifications to the ribose or deoxyribose ring. Intriguingly, the uridyl peptide antibiotics (UPAs), such as pacidamycin, contain a biosynthetically unique 3'-deoxyuridine which resembles synthetic anti-retrovirals. Elucidation of the biosynthesis of this structuraly unique nucleoside motif suggests a degree of substrate flexibility, making it a highly attractive prospect for biosynthetic approaches to nucleoside modification. In order to fully exploit the biotransformative potential, a detailed mechanistic understanding of the individual enzymes involved in the biosynthesis of the nucleoside moiety, and especially the enzyme employed at the installation of the 3'-deoxy modification, is required. Chapter 1, the introduction the thesis, discusses the importance of nucleosides for Chemistry and Biology. The section describes the biosynthesis of the nucleoside antibiotics and reviews the recent advances relating to the synthesis and biosynthesis of 3'-deoxy-nucleosides. The Chapter proceeds to describes the biosynthesis of deoxy-sugars, deoxy-nucleosides and nucleotides, reviewing the most common dehydratase mechanisms in addition to examining unusual dehydratases involved in carbohydrate metabolism. Chapter 2, the study of Pac13, the uridine-5'-aldehyde dehydratase of the pacidamyicin nucleoside cluster, is reported. Through detailed functional, structural and kinetic analysis of the wild-type enzyme as well a series of mutants, Chapter 2 provides insight into the mechanism emplyed by this unusual enzyme. Chapter 3 describes the structural and functional analysis of Pac11, the flavin-dependent oxidoreductase of the nucleoside biosynthetic cluster, while Chapter 4 revolves around Pac5, the PLP-dependent aminotransferase. In Chapter 5, the chemical synthesis of fluorinated nucleosides, as probes for exploring the enzymes' mechanism is investigated. Chapter 7 reports the experimental procedures for the research described in this document. The work described in this thesis broadens the understanding of the biosynthesis of deoxy-nucleosides and constitutes the first structural and mechanistic study of the biosynthesis of the biosynthesis of the valuable yet, synthetically challenging 3'-deoxy nucleosides.

Made available in DSpace on 2014-06-11T19:35:09Z (GMT). No. of bitstreams: 0 Previous issue date: 2011-11-28Bitstream added on 2014-06-13T20:46:07Z : No. of bitstreams: 1 silva_fc_dr_araiq.pdf: 3716542 bytes, checksum: 39496f4900491cbbebdf1e1fc94be6e5 (MD5) / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / Três espécies de Piper foram escolhidas como modelos para estudos biossintéticos, transcriptômicos e proteômicos: P. tuberculatum, P. nigrum e P. crassinervium. As duas primeiras espécies acumulam principalmente metabólitos secundários da classe das amidas e essas substâncias foram alvo de experimentos biossintéticos. Foram monitoradas as atividades de diversas enzimas envolvidas na via fenilpropanoídica, dentre elas a fenilalanina amônia liase (PAL) e a cinamato 4-hidroxilase (C4H). Observou-se também atividade de uma enzima que catalisa a conversão do ácido ferúlico ao ácido 3,4-metilenodioxicinâmico, denominada 3,4- metilenodioxicinâmico sintase. Esta é provavelmente uma enzima monooxigenase-dependente do citocromo P450. A principal questão biossintética está centrada na sequência na qual as reações ocorrem: o grupo metilenodioxílico pode ser formado antes ou depois da porção amídica. Para elucidar esta questão, sintetizou-se dois possíveis precursores contendo o grupo 4-hidróxi-3- metóxifenílico: o ácido ferupérico e a feruperina. No entanto, experimentos de atividade enzimática in vitro utilizando estes dois precursores não foram esclarecedores, devido a existência de piperina endógena no extrato enzimático proveniente de folhas de P. nigrum, o que impediu observar a formação de produto. Foi avaliado também a participação de ácido malônico e L-valina na biossintese destas amidas: incorporou-se precursores isotopicamente marcados em plântulas de P. tuberculatum: ácido 2-[13C]-malônico, ácido malônico-U-2H e 15N-L-valina). Após análise por CLAEEM, conclui-se que o ácido malônico participa da reação de condensação com fenilpropanóides, gerando os derivados C6-C5 e L-valina é precursor do grupo isobutilamina. Considerando todos as evidências... / Three Piper species were chosen as a models for biosynthetic, transcriptomic and proteomics studies: P. tuberculatum, P. nigrum and P. crassinervium. The first two species accumulate mainly amides as secondary metabolites. This class of compounds was targeted by biosynthetic experiments. It was monitored the enzymatic activities of several enzymes involved in the phenylpropanoid pathway, including phenylalanine ammonia-lyase and cinnamate 4-hydroxylase. It was also observed the activity of an enzyme that catalyzes the conversion of ferulic acid to 3,4- methylenedioxycinnamic acid, named 3,4 methylenedioxycinnamic acid synthase. The main question was centered on the biosynthetic sequence: whether the methylenedioxy group can be formed before or after the amide portion. In order to elucidate this question, two possible precursors containing the group 4-hydroxy-3-methoxyphenyl were synthesized: feruperic acid and feruperine. However, experiments of in vitro enzymatic activity using these two precursors were not enlightening, due to the existence of piperine as endogenous in the enzymatic extract from leaves of P. nigrum, which prevented observe the formation of product. It was also evaluate the participation of malonic acid and L-valine in the biosynthesis of these amides, by incorporating isotopically labeled precursors in plants of P. tuberculatum: 2-[13C]-malonic acid, malonic-U-2H acid and 15N-Lvaline. After analysis by HPLC-MS, it was concluded that the malonic acid participates in the condensation reaction with phenylpropanoids, generating the C6-C5 derivatives and L-valine is the putative precursor of the isobutylamine group. Considering all the experimental evidence, the biosynthetic pathway proposed was that in which the methylenedioxy group is formed before the amide. In the second step, it carried out the ... (Complete abstract click electronic access below)

Made available in DSpace on 2014-12-02T11:16:39Z (GMT). No. of bitstreams: 0 Previous issue date: 2014-01-10Bitstream added on 2014-12-02T11:21:04Z : No. of bitstreams: 1 000748501_20160131.pdf: 701656 bytes, checksum: 493a3dd3a311bf41b1aa17b996230e0a (MD5) Bitstreams deleted on 2016-02-01T10:15:54Z: 000748501_20160131.pdf,. Added 1 bitstream(s) on 2016-02-01T10:16:44Z : No. of bitstreams: 1 000748501.pdf: 2259840 bytes, checksum: 1a6811da169a1eebac336c7d8d838a3a (MD5) / Cromanos e cromenos são metabólitos secundários comumente encontrados em espécies dos gêneros Piper e Peperomia, pertencentes à família Piperaceae. São caracterizados pela presença de um núcleo benzopirânico (um anel benzeno fundido a um anel pirano). Essa classe de substâncias é importante do ponto de vista farmacológico, uma vez que apresenta vasta gama de atividades biológicas, incluindo antifúngica, tripanocida, antioxidante e antiparasitária. Os benzopiranos isolados de espécies de Piper e Peperomia apresentam diversidade quanto aos substituintes da unidade aromática de suas estruturas químicas. Baseado no exposto, rotas biossintéticas distintas foram propostas. Em espécies de Piper essas rotas envolveriam a via do ácido chiquímico pela atuação do ácido para-hidroxibenzóico, enquanto que em espécies de Peperomia estaria operando a via do acetato. O presente trabalho teve como objetivo estudar a relação biossintética dos benzopiranos presentes nas espécies Piper aduncum e Peperomia obtusifolia, bem como a determinação da dinâmica metabólica envolvida na formação dos mesmos, tanto em nível metabólico como enzimático, uma vez que os cromenos isolados de Piper aduncum descrevem ritmo circadiano bem determinado. Estudos de variação circadiana realizados em Peperomia obtusifolia com o objetivo de acompanhar a formação do cromano ácido 3,4-diidro-5-hidróxi-2,7-dimetil-8-(3-metil-2-butenil)-2-(4-metil-1,3-pentadienil)-2H-1-benzopirano carboxílico (4) não demonstraram ritmo uniforme, do tipo sigmoidal, comum aos cromenos isolados de P. aduncum. O acúmulo do cromano 4 mostrou um máximo às 18h00, mas outros picos de concentração do mesmo foram observados às 06h00 e 15h00 e corroboram para o estabelecimento de um ritmo aleatório. Para a avaliação da origem biossintética de 4, foram realizados experimentos de incorporação utilizando precursor enriquecido... / Chromanes and chromenes are secondary metabolites commonly found in species of the genera Piper and Peperomia, belonging to the Piperaceae family. They are characterized by the presence of a benzopyran core showing a benzene ring fused to a pyran ring. This class of compounds is pharmacologically important, since they from shown a broad range of biological activities including antifungal, trypanocidal, antioxidant and anti-parasitic. The benzopyrans isolated from Piper and Peperomia species showed diversity biosynthetic pathways, mainly related to the aromatic moieties. The biosynthesis of Piper species involve the shikimic pathway showing as the first precursor the p-hydroxybenzoic acid, whereas in Peperomia species would be operating the route of acetate. The present work aimed to study the biosynthetic relationship of benzopyrans present in Piper aduncum and Peperomia obtusifolia as well as to determine the metabolic dynamics involved in their formation related to metabolic and enzymatic levels, since the chromenes isolated from Piper aduncum describe well-defined circadian rhythm. Studies of circadian rhythm performed in Peperomia obtusifolia, aiming to follow the formation of chromane 3,4 -dihydro- 5 -hydroxy -2 ,7- dimethyl-8- (3-methyl -2- butenyl) -2 - (4 -methyl -1 ,3- pentadienyl )-2H -1- benzopyran carboxylic acid (4) from P. obtusifolia showed no uniform sigmoidal curve, common to the chromenes isolated from Piper aduncum. The accumulation of the chromane 4 showed a maximum at 18:00 pm, but others peaks of the same concentration were observed at 06:00 am and 15:00 pm, corroborating to establish a random pace. To evaluate the biosynthetic origin of the chromane 4, feeding experiments were conducted using a precursor enriched with stable isotopes (ethyl [2-13C ]-sodium acetate) in the leaves of P. obtusifolia. Experiments were performed using seedlings of P. obtusifolia. The enriched extracts...