Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / The rice is one of the cereals more cultivated in the world, however its production can be limited by several plant pathogenics agents, among them the rootknot nematode (Meloidogyne spp.). The present work was accomplished in three stages. In the first, twenty and one populations of root-knot nematode of eight districts of the central area of Rio Grande do Sul State, were biochemical characterized through the isoenzyme esterase and morphological characterized through the microscopic observations of nematode females perineal patterns. In the second stage of the work, they were appraised the penetration and the development of M. graminicola in the roots of the irrigated rice (BR-IRGA 410, IRGA 417, IRGA 420, IRGA 422CL, BRS 7 "Taim", BRS Atalanta, BRS Fronteira, BRS Firmeza, BRS Pelota and BRS Querência) cultivars recommended for the South of Brazil, as well as the reaction of these materials to the nematode. In the third stage of the work the effect of ten essential oils of bioactives plants were evaluated in the control of M. graminicola "in vitro", as well as the efficiency essential oils in the control of the irrigated rice plant nematode. The isoenzymatic characterization of root-knot nematode in the area studied revealed the presence of the phenotype esterase VS1 (Rm 0,70), typical of M. graminicola. Among the cultivars tested, most were independently susceptible of the irrigation regime. The cultivar IRGA 422CL was what provided a smalest penetration of nematodes for the evaluated conditions behaving as moderately resistant under condition of saturation of soil. The oregano, eucalyptus and mint oils presented the highest nematostatic effect "in vitro ", while the alfazema, cidrão and alecrim oils presented highest effect nematicida "in vitro" also reducing the multiplication of nematode "in vivo", demonstrating its potential in the control of M. graminicola. / O arroz é um dos cereais mais cultivados no mundo, entretanto sua produção pode ser limitada por vários agentes fitopatogênicos, dentre eles o nematóide das galhas (Meloidogyne spp.). O presente trabalho foi realizado em três etapas. Na primeira, vinte e uma populações do nematóide das galhas provenientes de oito municípios da região central do Estado do Rio Grande do Sul foram caracterizadas bioquimicamente através da isoenzima esterase e morfologicamente através de observações microscópicas de configurações perineais das fêmeas do nematóide. Na segunda etapa do trabalho, foram avaliados a penetração e os estádios de desenvolvimento de M. graminicola nas raízes dos cultivares de arroz irrigado (BRIRGA-410, IRGA-417, IRGA-420, IRGA-422CL, BRS 7- Taim , BRS Atalanta, BRS Fronteira, BRS Firmeza, BRS Pelota e BRS Querência) recomendados para o Sul do Brasil, bem como a reação destes materiais ao nematóide. Na terceira etapa do trabalho foi avaliado o efeito de dez óleos essenciais de plantas bioativas no controle de M. graminicola in vitro , bem como a eficiência dos óleos ssenciais no controle do nematóide em plantas de arroz irrigado. A caracterização isoenzimática do nematóide das galhas na região de estudo revelou apenas a presença do fenótipo esterástico VS1 (Rm 0,70), típico de M. graminicola. Dentre os cultivares testados, a maioria foi suscetível independentemente do regime de irrigação. Apenas o cultivar IRGA-422CL foi o que proporcionou uma menor penetração dos nematóides para as condições avaliadas, comportando-se como moderadamente resistente sob condição de saturação do solo. Os óleos de orégano, eucalipto e hortelã foram os que apresentaram o maior efeito nematostático sobre os ovos de M. graminicola in vitro , enquanto que os óleos de alfazema, cidrão e alecrim além de terem apresentado maior efeito nematicida in vitro , também reduziram a multiplicação do nematóide in vivo , demonstrando seu potencial no controle do nematóide.

La bactérie phytopathogène Dickeya dadantii est responsable de la pourriture molle de nombreux végétaux. Elle sécrète dans le milieu extérieur toute une batterie d’enzymes capables de dégrader les constituants des parois végétales. La première partie de mon travail concerne les féruloyl estérases FaeD et FaeT. Les féruloyl estérases sont responsables de l’hydrolyse de liaisons ester entre l’acide férulique et les chaînes de xylane ou de pectine. En clivant ces liaisons, elles favorisent une dégradation complète de la paroi végétale. L'importance de ces enzymes nous a conduit à rechercher si D. dadantii produit de telles estérases. Le criblage d’une banque de gènes par un test de détection de l’activité féruloyl estérase a permis d’identifier deux gènes qui ont été caractérisés. Alors que faeT est faiblement transcrit dans toutes les conditions, la transcription de faeD est fortement induite en présence d’acide férulique et contrôlée par le régulateur FaeR. Alors que FaeT est une protéine cytoplasmique, FaeD est sécrétée par le système Out qui permet la sécrétion de nombreuses pectinases. Les enzymes FaeD et FaeT ont été surproduites dans E. coli et leurs principales propriétés biochimiques ont été déterminées. La connaissance de la séquence complète du génome de D. dadantii permet d’aborder des études de génomique fonctionnelle. Cette séquence confirme la présence des gènes codant les pectinases déjà caractérisées et révèle que ce génome code de nouvelles pectinases potentielles. La deuxième partie de mon travail concerne le gène pelN identifié par analyse du génome. Les pectate lyases coupent les liaisons glycosidiques du polygalacturonate par une réaction de β-élimination, générant des produits insaturés. Leur mécanisme d’action nécessite des cations comme cofacteur, en général Ca2+. Après clonage du gène pelN, la protéine PelN a été surproduite dans E. coli. Son activité pectate lyase a été prouvée en montrant sa capacité à produire des dérivés insaturés à partir de polygalacturonate ou de pectines plus ou moins méthylées. Cette étude démontre que PelN est la première pectate lyase utilisant les ions Fe2+ comme cofacteur préférentiel. Chez D. dadantii, l’expression du gène pelN dépend de divers régulateurs affectant la synthèse des pectinases, comme PecS ou GacA. PelN est une protéine extracellulaire sécrétée par le système Out. Ces études contribuent à mieux comprendre le rôle respectif des différentes enzymes impliquées dans la dégradation de la paroi végétale et le fonctionnement coopératif de ce système pluri-enzymatique. / The phytopathogenic bacterium Dickeya dadantii is responsible for soft rot diseases of various plants. It secretes in the external medium a large array of enzymes which are able to degrade the constituents of the plant-cell wall. The first part of my work was related to the féruloyl esterases FaeD and FaeT. Feruloyl esterases are responsible for the hydrolysis of ester linkages between ferulic acid and the xylan or pectin chains. By cleaving these linkages, they improve the complete degradation of the plant-cell wall. The importance of these enzymes led us to search whether D. dadantii produces such esterases. A gene bank screening using a specific detection test for the feruloyl esterase activity allowed us to identify two genes which were characterized. While faeT is weakly transcribed in all the conditions, the faeD transcription is strongly induced in the presence of ferulic acid and it is controlled by the regulator FaeR. Whereas FaeT is a cytoplasmic protein, FaeD is secreted by the Out system responsible for the secretion of several pectinases. The enzymes FaeD and FaeT were overproduced in E. coli and their main biochemical properties were determined. The determination of the complete sequence of the D. dadantii genome makes it possible to develop functional genomic studies. This sequence confirms the presence of genes encoding the previously characterized pectinases and it reveals that this genome encodes new potential pectinases. The second part of my work was related to the gene pelN identified by genome analysis. Pectate lyases cleave the glycosidic bounds in the polygalacturonate chain by a β-elimination reaction, generating unsaturated products. This reaction mechanism requires cations as cofactor, generally Ca2+. After cloning of the gene pelN, the protein PelN was overproduced in E. coli. Its pectate lyase activity was demonstrated by its capacity to produce unsaturated derivatives from polygalacturonate or pectins. This study showed that PelN is the first pectate lyase that uses Fe2+ ions as the preferential cofactor. In D. dadantii, the pelN expression depends on various regulators controlling the pectinase synthesis, such as PecS or GacA. PelN is an extracellular protein secreted by the Out system. These studies contribute to increase the knowledge on the respective role of the different enzymes involved in the degradation of the plant-cell wall and the cooperative interactions in this pluri-enzymatic system.

The use of slower acid-producing starter bacteria for the production of lower fat Cheddar cheese has lead to milder flavor Cheddar cheeses that lack intense Cheddar notes. The metabolism of methionine leads to the production of methanethiol, which is one of the desirable Cheddar cheese flavor compounds. The influence of NaCl and reduced pH was determined for aminopeptidase, lipase/ esterase, and methanethiol-producing capability in selected lactic acid bacteria and brevibacteria in simulated cheese-like conditions. The activity of each enzyme decreased with NaCl addition and pH reduction to approximate a Cheddar cheese environment (5% NaCl and pH 5.2). The mechanism for methanethiol production by the starter and adjunct bacteria was also investigated. Different enzyme systems were found to be responsible for methanethiol production in starter lactococci, lactobacilli, and brevibacteria. In the lactococci, enzymes that acted primarily on cystathionine were responsible for methanethiol production from methionine. Lactobacilli also contained cystathionine-degrading enzymes, but these enzymes have properties different from the lactococcal enzymes. Brevibacterium linensBL2 lacked cystathionine-degrading enzymes, but was capable of the direct conversion of methionine to methanethiol. L-Methionine γ-lyase from B. linens BL2 was purified to homogeneity, and was found to catalyze the α, γ elimination of methionine resulting in the production of methanethiol, α-ketobutyrate, and ammonia. Characterization of the pure enzyme demonstrated that it is pyridoxal phosphate dependent, which is active at salt and pH conditions existing in ripening Cheddar cheese. The addition of either B. linens BL2 or L-methionine γ-lyase to aseptic cheese curd slurries increased methanethiol and total volatile sulfur compound production. In an attempt to increase methanethiol production and Cheddar cheese flavor in reduced-fat Cheddar cheese, B. linens BL2 was added as a starter adjunct to 60% reduced-fat cheese. Sensory evaluation of the cheese indicated that B. linens BL2 improved the flavor of 60% reduced-fat Cheddar cheese. This suggests that the addition of B. linens BL2 is an alternative to the addition of lactic acid bacteria to improve Cheddar cheese flavor via the metabolism of methionine.

<p>The metagenomic approach to gene discovery circumvents conventional gene and gene product acquisition by exploiting the uncultured majority of microorganisms in the environment. It was demonstrated in this study that metagenomic methods are suitable for gene mining in extreme environments that harbor very high levels of unculturable microorganisms. DNA was extracted from Antarctic mineral soil samples taken from the Miers Valley, Antarctica. The metagenomic DNA was also used to construct a fosmid library comprising over 7900 clones with an average insert size of 29 kb. PCR amplification using bacterial and archaeal 16S rRNA gene specific primers and subsequent denaturing gradient gel electrophoresis (DGGE) of bacterial 16S rDNA amplicons showed that a small percentage of bacterial diversity (&gt / 1%) was captured in the metagenomic fosmid library. Activity-based screening for lipase and esterase genes using a tributyrin plate assay yielded twelve positive clones. LD1, a putative, novel cold-active GDSL lipase/esterase was identified and sequenced. The C-terminal domain of the ORF was found to be an autotransporter similar to those associated with type V secretion systems in Gram negative bacteria. Sub-cloning of the gene resulted in lipolytic activity in E. coli. Preliminary enzyme assays have determined that LD1 hydrolyses p-nitrophenyl esters with chain lengths shorter than C10, an indication that the enzyme is an esterase. Complete purification and characterisation of this enzyme is subject to further study.</p>

<p>Lignocellulosic biomass represents an important renewable resource for biofuels production. Lignocellulosic biomass is comprised of cellulose, hemicellulose and lignin. Lignocellulosics are highly recalcitrant to enzymatic degradation and due to its complex nature a range of enzymes are required to synergistically hydrolyse biomass. Many microorganisms are capable of producing these enzymes as part of their hemicellulolytic hydrolysis system(s). The aim of this study was the characterisation of a thermophilic actinobacterial isolate (ORS10), capable of producing hemicellulosic enzymes, and the cloning and characterization of a hemicellulosic enzyme produced by the isolate. Phylogenetic analyses clustered ORS10 with species of the genus Streptomyces. BLAST analysis revealed that ORS10 was most closely related to Streptomyces achromogenes (99% identity). A small-insert genomic library was constructed and a putative acetylxylan esterase (AXEase) gene, axe10, was identified. The enzyme, Axe10, has moderate similarity to &alpha / /&beta / hydrolase proteins, and contains an esterase/lipase superfamily conserved domain and a typical AXEase catalytic triad. The axe10 gene was sub-cloned into an expression vector [pET21a(+)] and a 28.7 kDa protein with demonstrated AXE activity was purified from E. coli Rosetta (DE3) pLysS. Axe10 displayed optimum activity at 37oC and pH 7.0. Despite being derived from a thermophilic Streptomyces species Axe10 was not thermostable. However, given the relative novelty of Axe10, further characterisation and assessment of this enzyme is warranted.</p>

Behavior is a complex process resulting from the integration of genetic and environmental information. Thus, the genetically tractable Drosophila melanogaster was utilized to better understand the interplay between these factors since Drosophila males and females exhibit sex-specific courtship behaviors that are innate yet modifiable. These sex-specific behaviors, as well as sexually dimorphic development, are regulated, in part, by the somatic sex-determination hierarchy. Since reproductive behaviors rely on the rapid integration of multiple sensory cues, it is likely that the perception and integration of such cues and mating-induced physiological changes are mediated in part by changes in gene expression. Therefore, it was hypothesized that assaying gene expression changes in response to courtship or mating in Drosophila males would uncover new targets of the sex-determination hierarchy and other behaviorally important loci. We took a novel approach to find these behaviorally-responsive loci by utilizing microarray technology to assess courtship- or mating-induced gene expression changes in Drosophila male whole bodies or heads. Mutations in candidate loci were tested for effects on reproductive behaviors and present the first data showing that egghead (egh) and female-specific independent of transformer (fit) affect male reproductive behavior. egh is up regulated in male heads 20 min after courting and is required post-developmentally in a subset of neurons for robust male courtship behavior. fit, a fat body-expressed sex-determination hierarchy target gene, is up regulated in male whole bodies after 5 min of courtship. fit is also up regulated in male heads after 20 min of courtship or 2 hrs after mating. Mutations in fit result in male-male courtship; more specifically, fit mutants direct courtship towards males and also elicit courtship from wild-type males. By analyzing fit's role in courtship behavior, we also shed light on the role the fat body plays in modulating behavior. These studies provide the first pieces of evidence that gene expression changes occur in Drosophila males performing reproductive behaviors. This novel approach identified behaviorally important loci that are expressed in the nervous system and the fat body, indicating that both tissues modulate behavior. Also identified were sex-determination hierarchy target genes and it is likely that further analysis of the remaining candidates will reveal more members of this genetic cascade.

<p>The metagenomic approach to gene discovery circumvents conventional gene and gene product acquisition by exploiting the uncultured majority of microorganisms in the environment. It was demonstrated in this study that metagenomic methods are suitable for gene mining in extreme environments that harbor very high levels of unculturable microorganisms. DNA was extracted from Antarctic mineral soil samples taken from the Miers Valley, Antarctica. The metagenomic DNA was also used to construct a fosmid library comprising over 7900 clones with an average insert size of 29 kb. PCR amplification using bacterial and archaeal 16S rRNA gene specific primers and subsequent denaturing gradient gel electrophoresis (DGGE) of bacterial 16S rDNA amplicons showed that a small percentage of bacterial diversity (&gt / 1%) was captured in the metagenomic fosmid library. Activity-based screening for lipase and esterase genes using a tributyrin plate assay yielded twelve positive clones. LD1, a putative, novel cold-active GDSL lipase/esterase was identified and sequenced. The C-terminal domain of the ORF was found to be an autotransporter similar to those associated with type V secretion systems in Gram negative bacteria. Sub-cloning of the gene resulted in lipolytic activity in E. coli. Preliminary enzyme assays have determined that LD1 hydrolyses p-nitrophenyl esters with chain lengths shorter than C10, an indication that the enzyme is an esterase. Complete purification and characterisation of this enzyme is subject to further study.</p>

<p>Lignocellulosic biomass represents an important renewable resource for biofuels production. Lignocellulosic biomass is comprised of cellulose, hemicellulose and lignin. Lignocellulosics are highly recalcitrant to enzymatic degradation and due to its complex nature a range of enzymes are required to synergistically hydrolyse biomass. Many microorganisms are capable of producing these enzymes as part of their hemicellulolytic hydrolysis system(s). The aim of this study was the characterisation of a thermophilic actinobacterial isolate (ORS10), capable of producing hemicellulosic enzymes, and the cloning and characterization of a hemicellulosic enzyme produced by the isolate. Phylogenetic analyses clustered ORS10 with species of the genus Streptomyces. BLAST analysis revealed that ORS10 was most closely related to Streptomyces achromogenes (99% identity). A small-insert genomic library was constructed and a putative acetylxylan esterase (AXEase) gene, axe10, was identified. The enzyme, Axe10, has moderate similarity to &alpha / /&beta / hydrolase proteins, and contains an esterase/lipase superfamily conserved domain and a typical AXEase catalytic triad. The axe10 gene was sub-cloned into an expression vector [pET21a(+)] and a 28.7 kDa protein with demonstrated AXE activity was purified from E. coli Rosetta (DE3) pLysS. Axe10 displayed optimum activity at 37oC and pH 7.0. Despite being derived from a thermophilic Streptomyces species Axe10 was not thermostable. However, given the relative novelty of Axe10, further characterisation and assessment of this enzyme is warranted.</p>

Cocaine is a widely abused and addictive drug, resulting in serious medical and social problems in modern society. Currently, there is no FDA-approved medication specific for cocaine abuse treatment. The disastrous medical and social consequences of cocaine abuse have made the development of an anti-cocaine medication a high priority. However, despite decades of efforts, traditional pharmacodynamic approach has failed to yield a truly useful small-molecule drug due to the difficulties inherent in blocking a blocker like cocaine without affecting the normal functions of the transporters or receptors. An alternative approach, i.e. pharmacokinetic approach, is to interfere with the delivery of cocaine to its receptors/transporters and/or accelerate its metabolism in the body. It would be an ideal anti-cocaine medication to accelerate cocaine metabolism producing biologically inactive metabolites. Two natural enzymes may catalyze hydrolysis of cocaine: human butyrylcholinesterase (BChE) and bacterial cocaine esterase (CocE). However, the wild-type enzymes are not suitable as anti-cocaine therapeutics, due to the low catalytic activity, thermoinstability, or short biological half-life. In this investigation, we performed integrated computational-experimental studies to rationally design and discover mutants of these enzymes in order to improve the catalytic activity, thermostability, and/or biological half-life. To rationally design desirable mutants of the enzymes, we have successfully developed computational models, including those for BChE gating, glycosylated BChE structure, BChE-substrate complex structures, BChE dimer/tetramer structures, CocE monomer/dimer structures, and CocE-substrate complex structures. Development of the computational models enabled us to rationally design new amino-acid mutations that may improve the catalytic activity, thermostability, and/or prolonged biological half-life. The computational design was followed by wet experimental tests, including both in vitro and in vivo experiments, leading to discovery of new enzyme forms with not only a high catalytic efficiency against cocaine, but also an improved thermostability and/or prolonged biological half-life. The identified new mutants of BChE and CocE are expected to be valuable candidates for development of a more efficient enzyme therapy for cocaine abuse. The encouraging outcomes of the present study also suggest that the structure-and-mechanism-based design and integrated computational-experimental approach is promising for rational drug design and discovery.

Diss. (sammanfattning) Stockholm : Karol. inst., 2003. / Härtill 5 uppsatser.