Thesis (Ph. D.)--University of Virginia, 2001. / Includes bibliographical references (leaves 187-202). Also available online through Digital Dissertations.

Orientador: Michel Georges Albert Vincentz / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-11T18:45:34Z (GMT). No. of bitstreams: 1 DelBem_LuizEduardoVieira_M.pdf: 9371325 bytes, checksum: 4720605c3fed6784b51b26b99feff19c (MD5) Previous issue date: 2008 / Resumo: Introdução: Os xiloglucanos são os polímeros de açúcar mais abundantes na hemicelulose da maioria das espécies de plantas terrestres, em especial nas eudicotiledôneas. Possuem papel estrutural na parede celular vegetal, interagindo com os filamentos de celulose, e podem ser utilizados como reserva em sementes de várias espécies de eudicotiledôneas, como o Jatobá (Hymenaea courbaril), onde correspondem a quase 50% do peso seco da semente. Este polímero é formado por uma cadeia central de ß-glucano com ramificações que contêm xilose, galactose e fucose. O mecanismo de degradação deste polímero é realizado por cinco hidrolases: XTH, ß-Galactosidase, ß-Glucosidase,? a-Xilosidase e? a-Fucosidase. Estas enzimas são codificadas por genes que constituem famílias multigênicas nos genomas de plantas, e sua atividade na degradação seletiva de xiloglucano têm papel central na regulação do crescimento e morfogênese da célula vegetal. O Jatobá (Leguminosae) é uma árvore tropical, nativa do Brasil, que vem sendo utilizada como modelo vegetal para estudos de impacto ambiental por efeito estufa e estresses abióticos oriundos do aquecimento global. Foi observado que mudas de Jatobá, crescidas numa atmosfera com 720 PPM de CO2 (dobro da concentração atual), apresentam até 50% de aumento de biomassa aos 100 dias. O entendimento das respostas transcripcionais desta planta, em resposta a estes estresses, pode levar a conclusões à cerca de como as florestas tropicais responderão ao aumento inexorável na concentração de CO2, num quadro de aquecimento global. Resultados: Construímos bibliotecas de cDNA de folhas, caule, cotilédones e raízes de plântulas de 45 dias de Jatobá. Um seqüenciamento amostral dos ESTs levou à obtenção de 103 seqüências, parciais ou completas, de proteínas de Jatobá. São os primeiros dados de ESTs numa árvore tropical brasileira. Análises filogenéticas das enzimas que constituem o mecanismo de degradação de xiloglucano foram conduzidas ao longo de 13 genomas completos e 27 bancos de ESTs de espécies dos mais diversos grupos no reino Viridiplantae. Isso nos permitiu organizar a diversidade destas cinco famílias multigênicas em possíveis grupos de ortólogos (PoGOs). As XTHs foram divididas em seis grupos de genes homólogos e 19 PoGOs. As ß-Galactosidases foram divididas em dois grupos de genes homólogos e 10 PoGOs. As ß-Glucosidases foram divididas em dois grupos de genes homólogos e dois PoGOs. As? a-Xilosidase foram divididas em três PoGOs e as a-Fucosidase em dois PoGOs não relacionados evolutivamente. Conclusões e Perspectivas: As 103 seqüências peptídicas obtidas de Jatobá foram anotadas por comparação e serão disponibilizadas nos bancos de dados internacionais. A perspectiva de seqüenciar mais clones poderá levar à montagem do transcriptoma do Jatobá, algo inédito para uma árvore tropical. Concluímos, com as análises filogenéticas, que as XTHs, que formam um grupo monofilético de genes em Streptophyta, surgiram antes da conquista do ambiente terrestre. Estes genes foram progressivamente amplificados ao longo da evolução das plantas terrestres, o que sugere um ganho progressivo de complexidade, que teve seu auge nas Angiospermas. Apresentamos evidências que podem unir evolutivamente as XTHs exclusivas de plantas a enzimas transglicosiladoras de cadeias de ß -glucano em fungos, o que sugere uma origem comum do processo de transglicosilação de cadeias de ß-glucano como mecanismo de controle do crescimento e formato celular em eucariotos com parede celular. As ß-Galactosidases formam um grupo monofilético em Embryophytas com nove PoGOs, no entanto sua grande diversificação (seis PoGOs) ocorreu apenas em Angiospermas. As ß -Glucosidases formam um grupo monofilético em Embryophytas, seqüências similares em bactérias fotossintetizantes podem sugerir uma origem no ancestral dos cloroplastos. As a -Xilosidase, que são monofiléticas nas Spermatophytas, derivaram das ?a-Glucosidases que se encontram dispersas entre todos os eucariotos, é um caso de neofuncionalização. Duas linhagens distintas evolutivamente de a-Fucosidases foram encontradas, uma delas é monofilética em Embryophytas e a outra pertence a uma grande família multigênica (GDSL-motif) da qual pouco se sabe. Mostramos que o mecanismo completo (cinco hidrolases) de degradação de xiloglucano existia no ancestral comum das Spermatophytas (plantas com semente). Como perspectivas este trabalho permite a racionalização de estudos funcionais destas hidrolases o que, em longo prazo, pode contribuir com processos biotecnológicos que passem pela modificação seletiva da parede celular vegetal. / Abstract: Introduction: Xyloglucans are the main hemicelulose in most of land plants, especially in eudicots. It is a structural compound of plant cell-wall that interacts with cellulose and can be used as seed's energy storage of many species, like Jatoba (Hymenaea courbaril). Xyloglucan structure is composed of a ß-glucan backbone that it branched with xylose, galactose and fucose. Its degradation machinery is composed by five glycosil hydrolases: XTH, ß-Galactosidase, ß-Glucosidase,?a-Xylosidase and? a- Fucosidase. These enzymes are codified by multigenic families in plant's genomes and it plays a central role in key processes like growth and morphogenesis of plant cells. Jatoba (Leguminosae) is a tropical tree, native of Brazil. It's been used as a model tree in researches of plant's responses to stresses caused by global warming and high atmospheric CO2 concentration. It was observed a 50% increase in biomass of a 100 days Jatoba seedling when grown in a 720 PPM of CO2 atmosphere (two times bigger than today's atmospheric concentration). Understand the transcriptional responses to these stresses can lead to conclusions about how tropical forests will respond to high concentrations of CO2 and global warming. Results: We made cDNA libraries of leaves, stem, cotyledons and roots of 45 days seedlings of Jatoba. A preliminary sequencing of these libraries reveled 103 predict protein sequences (most partial sequences). Phylogenetic analyses of xyloglucan hydrolytic enzymes were conducted using 13 completed genomes and 27 ESTs assemblies, from a wild range of taxonomic groups in the Viridiplantae kingdom. It allowed us to divide XTH's diversity of genes into six homology groups and 19 possible groups of orthologues (PoGOs). ß-Galactosidases were divided into two groups of homologues and 10 PoGOs. ß -Glucosidases were divided into two groups of homologues and two PoGOs. a-Xylosidase were divided into three PoGOs and a-Fucosidase into two PoGOs evolutionarily unrelated. Conclusions and Perspectives: The 103 protein sequences of Jatoba were annotated by comparison to known proteins and will be deposited in international sequences assemblies. As a perspective, the sequencing of Jatoba ESTs will lead to the assembly of its transcriptome, something never done before in a tropical tree. We concluded that XTHs are monophyletic group o genes in Streptophyta, what means they emerged before lands conquest by plants. These genes were progressively amplified in land plants evolution, especially in Angiosperms, what suggests a progressive gain in complexity. We showed evidences of a possible evolutionary relation between plant's XTHs and fungus hydrolases/transglycosylases enzymes. It suggests a eukaryotic ancestral mechanism to control cell expansion and shape based in ß -glucan transglycosylation and its interaction to cellulose (in plants) or chitin (in fungus). The ß -Galactosidases are a monophyletic group in Embryophytas that were divided into nine PoGOs, six PoGOs only appeared in Angiosperms. The ß -Glucosidases belongs to a monophyletic group in Embryophytas that has sequence similarity to bacterial proteins, especially ones from photosynthetic bacteria species. The a-Xylosidases are a PoGO in Spermatophyta that probably emerged from a-Glucosidases presents in all eukaryotes. It's probably a neofunctionalization process. Two evolutionary distinct lineages of a-Fucosidases where found, one monophyletic in Embryophytas and another that belongs to the poorly understood multigenic family "GDSL-motif proteins". We showed that the complete machinery (all the five hydrolases) of Xyloglucan degradation already exists in Spermatophytas common ancestor. As a perspective, we expect to rationalize the functional characterization works among these multigenic families and to contribute in biotechnology processes that pass through cell-wall modification and selective control. / Mestrado / Genetica Vegetal e Melhoramento / Mestre em Genética e Biologia Molecular

A proteína recombinante inibidora de serinoprotease denominada de Amblyomin-X foi obtida a partir de uma biblioteca de cDNA das glândulas salivares do carrapato Amblyomma cajannense, construída e utilizada para identificar um gene que codifica um inibidor de serinoprotease do tipo Kunitz. O Amblyomin-X inibe a formação da massa tumoral in vivo, no entanto o mecanismo envolvido neste efeito não está totalmente esclarecido. Visto que um dos mecanismos anti-carcinogênicos dos inibidores de serinoproteases é a inibição do processo de angiogênese, este trabalho foi delineado para avaliar as ações do Amblyomin-X sobre a angiogênese in vivo e sobre funções da célula endotelial envolvidas neste processo. A angiogênese in vivo foi estudada em modelo de câmara dorsal por microscopia intravital. Quarenta e oito horas após a implantação da câmara dorsal, os animais receberam tratamento tópico de salina ou de Amblyomin-X por 8 dias, com intervalos de 48 horas a cada dose (10, 100 ou 1000ng/mL). Os efeitos foram avaliados em condições basais e na vigência do crescimento tumoral (injeção de 1x105 células B16-F10 de melanoma murino no tecido subcutâneo). Adicionalmente, os efeitos do Amblyomin-X sobre a permeabilidade vascular foram avaliados pela mensuração espectrofotométrica da quantidade de corante extravasado no tecido dos animais após injeção intradérmica do fator de crescimento do endotélio vascular (VEGF) ou do Amblyomin-X. Uma série de estudos in vitro foram realizados em células endoteliais de linhagem de microcirculação (t-End) para avaliar os efeitos do Amblyomin-X (10, 100 e 1000ng/mL) sobre: 1) a migração destas células, usando modelos bidimensional (2D) de cicatrização in vitro e tridimensional (3D) em câmara de Boyden modificada, na ausência e frente ao fator de crescimento do endotélio vascular (VEGF; 100 ng/mL); 2) sobre a aderência em Matrigel® e 3) sobre a secreção de prostaglandina E2 (PGE2) e a produção de óxido nítrico (NO) por ensaio imunoenzimático e reação de Griess, respectivamente. Ademais, foram avaliados os efeitos do Amblyomin-X sobre a viabilidade das células B16-F10 (1x105) por citometria de fluxo. Os resultados obtidos mostram que a aplicação tópica de Amblyomin-X reduziu o número de vasos no tecido subcutâneo dorsal (10ng/mL = 21,7%; 100ng/mL= 35,7%; 1000ng/mL= 36,8% vs 1° dia de tratamento). O mesmo efeito foi observado na presença de células B16-F10 (1000ng/mL= 44,3% vs 1° dia de tratamento), além de uma redução no desenvolvimento da massa tumoral (1000ng/mL= 88% vs controle). O tratamento com Amblyomin-X reduziu a migração basal das células t-End no modelo 2D (10ng/mL=16,4%; 1OOng/mL=23, 1%; 1000ng/mL=26,8% vs controle) e 3D (10ng/mL=39,2%; 100ng/mL=49,4%; 1000ng/mL=50,4% vs controle); inibiu a adesão destas células endoteliais em Matrigel® (100ng/mL=46,4%; 1000ng/mL=48,4% vs controle); não alterou produção os mediadores químicos NO e PGE2 pelas células endoteliais; não modificou a permeabilidade vascular e não alterou a viabilidade das células de melanoma murino B16-F10. Em conjunto, os dados obtidos mostram que o Amblyomin-X inibe a formação de novos vasos em condições basais e na vigência de crescimento tumoral in vivo que este efeito pode estar relacionado à redução do desenvolvimento tumoral, uma vez que a concentração de Amblyomin-X que inibe a angiogênese não causou citotoxicidade às células tumorais in vitro. Além disso, os mecanismos envolvidos no processo de angiogênese podem ser decorrentes, pelo menos em parte, de prejuízos na migração e adesão das células endoteliais. / The recombinant serine protease inhibitor protein called Amblyomin-X was obtained from a cDNA library of the Amblyomma cajennense salivary glands constructed and used to identify a gene encoding a kunitz type serine protease inhibitor. Amblyomin-X presents inhibitory effect on tumoral mass formation in vivo. Nevertheless, the mechanisms involved in the effects have not been clarified. Considering that interference on angiogenesis process is one of the mechanisms responsible for the antitumor activity displayed by serine protease inhibitors, this project was undertaken to study the Amblyomin-X actions on this process and on related endothelial cell functions. In vivo angiogenesis was studied using dorsal chamber model associated to intravital microscopy. Forty eight hours after dorsal chamber implantation, the animals were topically treated with saline or Amblyomin-X during 8 days, with intervals at each 48hs (10, 100 ou 1000ng/mL). The effects were evaluated at basal conditions or during tumoral development (1x105 B16-F10 murine melanoma cells injected into subcutaneous tissue). In addition, the effects of Amblyomin-X on vascular permeability were evaluated by measuring the dye leakage into dorsal intradermic tissue after local injection of vascular endothelial growth factor (VEGF) or Amblyomin-X, or both. In vitro assays were also performed using endothelial cells from microcirculation (t-End) and the effects of Amblyomin-X (10, 100 e 1000ng/mL) were studied on: 1) cell migration, using bidimensional (2D) and tridimensional (3D) models in modified Boyden chamber using chemotatic factor (VEGF100 ng/mL); 2) Matrigel® adherence and, 3) prostaglandin E2 (PGE2) and nitric oxide (NO) secretion by enzymatic assay and Griess reaction, respectively. In addition, the Amblyomin-X toxicity was evaluated on the B16-F10 cells (1x105), using flow citometry. Results obtained show that topic application of Amblyomin-X reduced the number of vessels in the subcutaneous dorsal tissue (10ng/mL = 21,7%; 100ng/mL= 35,7%; 1000ng/mL= 36,8% vs 1st day of treatment). The same effect was observed in the presence of B16-F10 cells (1000ng/mL= 44,3% vs 1st day of treatment), simultanesouly to a significant reduction on tumoral mass development (1000ng/mL= 88% vs control). Amblyomin-X treatment impaired basal migration of tEnd in the 2D (10ng/mL=16,4%; 100ng/mL=23, 1%; 1000ng/mL=26,8% vs control) and 3D model (10ng/mL=39,2%; 100ng/mL=49,4%; 1000ng/mL=50,4% vs controle); inhibited the adhesion of t-End in Matrigel® (100ng/mL=46,4%; 1000ng/mL=48,4% vs control); did not alter the production of chemical mediators (PGE2 and NO); did not modify the vascular permeability and did not affect the B16-F10 cells viability. Taken together, data here obtained show that Amblyomin-X inhibited the new vessels formation under basal conditions, and during tumoral development. The effect could be related to the reduction of tumoral progress also detected in vivo, asthe schedule of treatment employed did not induce cancer cell toxicity. The mechanisms involved in the reduced angiogenesis may be related, at least in part, to the impaired endothelial cell migration and adhesion.

Biological sulph ate reduction has been identi fied as a potentially valuable process for removing sulphate and heavy metals from indllstrial effluents. The role of sulphate reducing bacteria (SRB) in this process has attracted the attention of biotechnologists and recently of enzymologists due to its fundamental properties and possible role in AMD bioremediation. These obligatory anaerobic sulphate-reducing bacteria are commonly known to dissimilate sulphate for energy. Under anaerobic conditions SRB oxidize simple organic compounds such as lactic acid with the sulphate and thereby generate hydrogen sulphide (a stTong reducing agent) and bicarbonate ions. The hydrogen sulphide in turn reacts with contaminant metals contained in AMD and precipitates them out of solution as metal sulphides. Bicarbonate ions neutralize AMD by reaction with protons to form carbon dioxide and water. Organic matter in the municipal sewage sludge has been identified as a potential source of electron donors for su lphate reduction. However, this organic matter is in the polymeric form that cannot be util ised by SRB. The latter depend on the activities of other hydrolytic bacteria for the degradation of complex polymers. Hence the availability of these monomeric substrates is a major factor, which may constrain further process development and is considered a rate-limiting step. Thi s study is therefore undertaken to investigate the bacterial glucohydrolase enzymes involved in the digestion of the polysaccharides present in the sewage sludge with specific interest in cellulases and/or p-glucosidase enzymes. The goals of the research are to: isolate, identify, purify and quantify these enzymes; study their distribution with respect to time, pH, and temperature; maximize and quantify the hydrol ys is products; study whether sulphide and sulphate have an enhancing or an inhibitory effect on the activity of enzymes; optimize the enzyme activity against substrate and/or product inhibition and soluble heavy metal salts. / KMBT_363 / Adobe Acrobat 9.54 Paper Capture Plug-in

Self-immobilisation enzyme technologies, such as SphereZyme™, suffer from the lack of applicability to hydrolyse large substrates. Solid support immobilisation is usually a method of choice, to produce a stable biocatalyst for large substrates hydrolysis in the industry. In order to investigate this limitation, a commercial protease called Alcalase® was chosen as a model enzyme due to its natural activity (hydrolysis of large substrates-proteins). Prior to immobilising through the SphereZyme™ technology, Alcalase® was partially purified through dialysis followed by CM Sepharose™ FF cation exchanger. Sample contaminants, such as salts and stabilisers can inhibit protein crosslinking by reacting with glutaraldehyde. Alcalase® was successfully separated into 3 proteases with the major peak correlating to a positive control run on native PAGE, indicating that it was likely subtilisin Carlsberg. A 16% alkaline protease activity for azo-casein hydrolysis was retained when 5% v/v PEI: 25% v/v glutaraldehyde solution was used as a crosslinking agent in Alcalase® SphereZyme™ production. An increase in activity was also observed for monomeric substrates (PNPA) where the highest was 55%. The highest % activities maintained when 0.33 M EDA: 25% v/v glutaraldehyde solution was initially used as crosslinking agent were 4.5% and 1.6% for monomeric and polymeric substrates, respectively. PEI is a hydrophilic branched polymer with an abundance of amine groups compared to EDA. A comparison study of immobilisation efficiencies of SphereZyme™, Eupergit® and Dendrispheres was also performed for large substrate biocatalysis. The two latter technologies are solid-support immobilisation methods. Dendrispheres reached its maximum loading capacity in the first 5 minute of the one hour binding time. Twenty minutes was chosen as a maximum binding time since there was constant protein maintained on the solid support and no enzyme loss was observed during the 1 hour binding time. PEI at pH 11.5, its native pH, gave the highest immobilisation yield and specific activity over the PEI pH range of 11.5 to 7. SphereZyme™ had the highest ratio for azocasein hydrolysis followed by Dendrispheres and Eupergit®. The SphereZyme™ was also shown to be applicable to biosensors for phenol detection. Different modifications of glassy carbon electrode (GCE) were evaluated as a benchmark for the fabrication of SphereZyme™ modified phenol biosensor. GCE modified with laccase SphereZyme™ entrapped in cellulose membrane was the best modification due to the broad catechol range (<0.950 mM), high correlation coefficient (R2, 0.995) and relative high sensitivity factor (0.305 μA.mM-1). This type of biosensor was also shown to be electroactive at pH 7.0 for which its control, free laccase, lacked electroactivity. From the catalytic constants calculated, GCE modified with laccase SphereZyme™ entrapped in cellulose membrane also gave the highest effectiveness factor (Imax/Km app) of 1.84 μA.mM-1. The modified GCE with Alcalase® SphereZyme™ was relatively more sensitive than GCE modified with free Alcalase®.

PDase II activity was determined using a synthetic substrate, the 2,4-dinitrophenyl ester of thymidine 3'-phosphate. The enzyme activity was estimated in fractions obtained by differential centrifugation of homogenates of epithelial cells fromt.the small intestinal mucosa of guinea pigs and rats. In guinea pig preparations PDase II occurred with highest specific activity in those fractions rich in succinate dehydrogenase and acid phosphatase. A lysosomal location for the guinea pig enzyme was indicated by its structure-linked latency and by its association with particles which underwent a characteristic decrease in equilibrium density when Triton WR-1339 was injected into the animals. With rat preparations a much greater proportion of the PDase II activity was found in the soluble fraction after uult-ra;c;entrifugation. The rat enzyme exhibited a lower degree of latency and administration of Triton WR-1339 had no effect. The rat enzyme activity in these crude preparations further differed from that of the guinea pig in other respects; it was more labile at 60°C, exhibited a slightly lower pH optimum, had a higher molecular weight as determined by gel filtration chromatography and displayed a much smaller tendency to aggregate under Llow salt conditions. Both enzymes were purified by chromatography on DEAE-cellulose, CM-cellulose and agarose, the extensive purification (550 fold) of the rat enzyme being largely due to its behaviour oh the latter material where it was found to bind tenaciously in low ionic strength solutions. On the other hand, only a fifteen-fold purification of the guinea pig enzyme was obtained because of its tendency tofform insoluble aggregatesdduring the chromatographic steps. In the main, the properties of the partially purified enzymes were quite similar. Both displayed pH optima between pH 6 and 7, were inhibited in solutions of high ionic strength, were unaffected' by divalent cations or EDTA, were similarly inactivated by heating at a temperature of 60°G displayed discontinuous Arrhenius plots _5 and exhibited Km values of the order 2-5x10 M for dTpDNP. In most casestfche differences between the enzymes were just differences of degree and could probably be accounted for byethe different extents to which the enzymes were purified. A more extensive characterization of the highly purified rat PDase was carried out. The fall-off in PDase II reaction rate observed at high enzyme levels with dTpDNP as substrate was found to be due to competitive inhibition of the enzyme by dTp, a reaction product which showed a of 2x10 M. The isoelectric point of PDase II was estimated by electrofocusing but since multiple peaks of activity were found at pH 3.4, 4.2-4.5, and pH 7.2 a conclusive result was not obtained. Polyacrylamide gel electrophoresis of purified rat PDase II indicated that the pattern obtained was, in part, dependent on whether the preparation was fresh or not; freshly purified PDase II contained up to 10 bands in gels stained for protein whereas only 1-2 bands were obtained when the preparations were "aged". A molecular weight of 150000-170000 for the enzyme was estimated in experiments performed by gel-filtration chromatography on dextran and agarose gels. Investigation of the interaction with, and hydrolysis by, rat PDase II of a number of possible phosphodiester substrates indicated that'-, the enzyme required a nucleoside 3'-phosphoryl residue for the initiation of hydrolysis which then proceeded in a 5'+3' direction. Finally, the effect of some enzyme inhibitors was investigated. PDase II activity was inhibited in the presence; of NEM, PCMB, PCMPS and iodoacetic acid. It was further found that the inactivation by iodoacetic acid could be prevented by the presence of a PDase substrate or, better still, by dTp. This is good evidence that iodoacetate alkylates an essential residue at the active center of PDase II and is the first time that such an effect has been shown for a PDase. / Medicine, Faculty of / Biochemistry and Molecular Biology, Department of / Graduate

Bacteroides melaninogenicus strains 2D and K110 were characterized with regard to their pathogenic, collagenolytic, proteolytic, hemagglutinating and metabolic activities. Both strains were members of the subspecies 13. melaninogenicus ss. asaccharolyticus. They possessed a cell-bound oxygen-sensitive collagenase, a cell-bound and a soluble oxygen-sensitive hemagglutinin (HA), and a protease. Both strains produced butyric and phenylacetic acids and were infective in guinea pigs as characterized by their ability to produce necrotic lesions and to be transferred from one animal to another. Strain 2D required hemin for growth and its growth rate was influenced by the addition of free amino acids to the medium. The hemagglutinating and proteolytic activities of strain 2D were investigated further to determine their relationship to infection. The soluble HA was reversibly inhibited by Hg and activity was restored in the presence of reducing agents. Iodoacetic acid caused irreversible inhibition. The HA was sensitive to heat and pronase treatment. Treatment of the red blood cells (RBC) with neuraminidase enhanced HA activity while the presence of galactose in the reaction mixture inhibited it, suggesting the involvement of galactose residues on the RBCs in the reaction.. Adsorption of the HA to RBC followed by elution and gel filtration resulted in the recovery of 50% of the HA activity and a 52-fold purification. Protease production by _B. melaninogenicus strain 2D was dependent on the growth rate of the organism. The protease was reversibly inhibited by HgCl₂ and irreversibly inhibited by iodoacetamide and iodoacetic acid. The enzyme was insensitive to serine protease inhibitors and EDTA. The pH optimum for proteolytic activity was 7.0, which correlates with the pH of its natural environment, the gingival crevice. It is thus classified as a neutral sulfhydryl enzyme. A 774-fold purification of the cellular protease of 2D, with a 160% recovery of activity, was accomplished by precipitation with 60% ethanol, ultracentrifugation and gel filtration through Sephadex G-100 and Sepharose 2B in the presence of urea. Electrophoretic analysis of the protease on SDS-polyacrylamide gels revealed four distinct bands, each of which was shown to be associated with carbohydrate. In the absence of SDS only one band, which did not migrate into the gel, was obtained. Any attempts to further dissociate the protease resulted in the loss of activity. The protease was active against azocoll, azocasein, casein and N,N-dimethylcasein. No glycosidase, lipase, collagenase or HA activities were detected. Protein, carbohydrate and lipid were detected in the preparation. The soluble protease which amounted to 20% of the cellular protease of strain 2D was subjected to gel filtration on Sephadex G-100 and eluted in a single peak at the void volume. The properties of the soluble protease were identical to those of the cell associated enzyme, suggesting the presence of a single proteolytic enzyme which was released into the culture medium with cell lysis or due to shedding of outer membrane fragments. / Science, Faculty of / Microbiology and Immunology, Department of / Graduate

Orientadores: Valéria Maia Merzel, Anete Pereira de Souza / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-27T08:16:52Z (GMT). No. of bitstreams: 1 Ottoni_JuliaRonzella_D.pdf: 14116261 bytes, checksum: f49982ceaff5d9b1dd9c87dcf8c01fcf (MD5) Previous issue date: 2015 / Resumo: Os manguezais são ecossistemas peculiares de alta atividade biológica, considerados um dos ambientes mais ricos do mundo. No Brasil, os manguezais ainda são pouco estudados, tornando o conhecimento e exploração de micro-organismos e seus metabólitos nesses ecossistemas um tópico importante. Os manguezais são ambientes adversos, caracterizados, em muitos casos, pela alta salinidade, variações constantes de pH e temperatura, e condições anóxicas. Micro-organismos adaptados à essas condições podem ser fontes de moléculas bioativas ainda desconhecidas e de interesse ambiental e econômico. Neste contexto, o presente trabalho teve como um dos objetivos analisar a diversidade taxonômica e funcional presente em sedimento de manguezal contaminado com petróleo através do sequenciamento de uma biblioteca metagenômica construída em vetor do tipo fosmídio. As análises taxonômicas da biblioteca metagenômica mostraram predominância do filo Proteobacteria, seguido por Actinobacteria, Planctomycetes, Firmicutes, Cloroflexi e Bacteroidetes. Em nível de classe, a mais abundante foi Gamaproteobacteria, seguida de Alfaproteobacteria e Deltaproteobacteria. A diversidade taxonômica se reflete na diversidade metabólica, com espécies capazes de degradar hidrocarbonetos, oxidar enxofre em zonas de transição oxica-anóxica costeiras, transformar metais pesados e outros compostos xenobióticos, dentre outras habilidades. Em adição, foram realizadas triagens funcionais com 4.800 clones da biblioteca e 215 isolados bacterianos para esterase e lipase, 5.184 clones para atividade proteolítica e os genomas de duas bactérias foram analisados in silico na busca de genes que codificam para atividade de catalase. As triagens dos clones resultaram em 17 hits positivos para esterases que posteriormente se revelaram falsos-positivos, e 182 hits positivos para proteases nos ensaios com sondas, sendo 60 hits positivos no pH 4,0, 55 no pH 7,0 e 67 no pH 9,0. Nos ensaios com isolados de bactérias foram detectados 42 com atividade de esterase e 20 com atividade de lipase, sendo que a melhor atividade de esterase foi obtida com um isolado de Gordonia sp. e a melhor atividade de lipase foi obtida para um isolado de Bacillus safensis. Estes dois isolados já possuem seus genomas sequenciados e uma análise in silico foi realizada para busca dos respectivos genes de atividade lipolítica. Na busca in silico por catalases foi selecionada uma sequência completa para ensaios de expressão. Foram desenhados pares de primers para amplificação dos genes das três enzimas e, destes, os genes da lipase e da catalase foram expressos, ambos do Bacillus safensis. A caracterização funcional e estrutural foi realizada com a catalase, cujo gene possui 1500 pb, é um tetrâmero composto por 4 monômeros de 59 kDa cada, ativa em intervalo de pH de 6,0 a 12 e temperaturas de 25 ºC a 55 ºC, com atividade ótima em pH 10 e 30 ºC e estável até 40 ºC. Os resultados mostraram que o mangue impactado é composto por populações microbianas adaptadas ao ambiente, e também responsáveis pela degradação de compostos xenobióticos, auxiliando na sua recuperação. A abordagem metagenômica foi bem sucedida nas triagens funcionais para proteases, indicando um grande potencial proteolítico no ambiente. As triagens funcionais com os isolados mostraram a presença de enzimas lipolíticas ativas, e a catalase expressa exibiu características funcionais interessantes, tais como atividade ótima em pH 10 e estabilidade térmica até 40 ºC, com potencial aplicação industrial / Abstract: Mangroves are unique ecosystems of high biological activity and are considered one of the richest environments in the world. In Brazil, mangroves are still poorly studied, making the knowledge of microorganisms and their metabolites in these ecosystems an important topic. Mangroves are harsh environments characterized, in many cases, by high salinity, high pH and temperature variations, and anoxic conditions. Microorganisms adapted to these conditions may be sources of yet unknown bioactive molecules of environmental and economic interest. In this context, one of the objectives of the present study was to analyze the taxonomic and functional diversity present in mangrove sediment contaminated with oil through the sequencing of a metagenomic library constructed using fosmid vector. The taxonomic analysis of the metagenomic library showed predominance of Proteobacteria phylum, followed by Actinobacteria, Planctomycetes, Firmicutes, Chloroflexi and Bacteroidetes. At class level, the most abundant was Gammaproteobacteria, followed by Alphaproteobacteria and Deltaproteobacteria. The taxonomic diversity is reflected in the metabolic diversity, with species capable of degrading hydrocarbons, oxidizing sulfur in oxic-anoxic coastal transition zones, transforming heavy metals and other xenobiotic compounds, among other skills. In addition, functional screenings were performed with 4,800 fosmid clones and 215 bacterial isolates for esterases and lipases, and with 5,184 clones for proteolytic activity and the genomes of two bacteria were analyzed in silico to search for genes encoding catalase activity. The screening of the clones resulted in 17 positive hits for esterases that later proved to be false-positive, and 182 positive hits for proteases using probe-based assays: 60 positive hits at pH 4.0, 55 at pH 7.0 and 67 at pH 9.0. Tests with bacterial isolates yielded 42 positive hits for esterase activity and 20 for lipase activity. The best esterase activity was obtained with one isolate of Gordonia sp. and the best lipase activity was obtained with one isolate of Bacillus safensis. These two isolates have their genomes already sequenced and in silico analyses were performed in the search for the respective genes of lipolytic activity. In silico analysis for catalase genes was performed and a complete sequence was selected for expression assays. Primer pairs were designed to amplify the genes encoding the three enzymes, and of these, lipase and catalase were expressed, both from Bacillus safensis. The functional and structural characterization was carried out with catalase, which gene has 1500 bp, it is a tetramer composed of four monomers of 59 kDa each, active in the pH range from 6.0 to 12 and temperatures of 25 °C to 55 °C, with optimum activity at pH 10 and 30 °C and stable until 40 ºC. The results showed that oil-impacted mangrove is composed by microbial populations adapted to the environment, responsible for the degradation of xenobiotics and assisting in the recovery of the mangrove. The metagenomics approach was successful in the functional screening for proteases, indicating a great proteolytic potential in the environment. Functional screening with the bacterial isolates showed presence of active lipolytic enzymes, and the expressed catalase exhibited unique functional characteristics, such as optimal activity at pH 10 and thermal stability until 40 ºC, with potential industrial application / Doutorado / Genetica de Microorganismos / Doutora em Genética e Biologia Molecular

N-acylethanolamines (NAEs) are a family of signaling lipids derived from a minor membrane lipid constituent N-acylphosphatidylethanolamine (NAPE). In Arabidopsis, NAE mediates physiological functions such as seedling growth, flowering, and response to stress via abscisic acid (ABA) –dependent and –independent signaling pathways. The function of NAEs is terminated by a highly conserved fatty acid amide hydrolase (FAAH). Studies in model plant Arabidopsis showed the significant role of NAEs that makes it relevant to elucidate the conserved metabolic pathway of NAEs in crop species such as tomato. It is hypothesized that there is a functional FAAH in tomato that hydrolyzes NAEs. To test this hypothesis, AtFAAH was used as a template to identify putative FAAH sequences in tomato, using BLASTX. Six SlFAAH sequences with the conserved amidase signature sequence and the catalytic triad, formed by Lys205, Ser281, and Ser305 in AtFAAH, were identified. Phylogenetic analysis of putative SlFAAH homologs and other FAAH family proteins (Arabidopsis, rice and moss), using CLUSTALW, revealed the two sequences that are closely related to the functionally characterized AtFAAH1. Using molecular visualization system (PyMOL), protein structures of putative SlFAAH1and 2 were predicted and compared with AtFAAH; both sequences showed similar domain structure to AtFAAH, with minor differences in spatial arrangement. For further biochemical characterization, full-length coding sequence of SlFAAH1 and SlFAAH2 were isolated and cloned into a heterologous expression system. The expressed protein will be characterized for its hydrolytic activity against radiolabelled NAE substrates. Furthermore, transcript levels for SlFAAH1 and SlFAAH2 will be quantified and correlated with the NAE levels in various tissues to predict their role in tissue-specific NAE hydrolysis. Together, these molecular and biochemical characterization studies in tomato are expected to further validate the conserved nature of NAE metabolic pathway in plants.

N-acylethanolamines(NAEs) are fatty acid amides derived from a minor membrane lipid constituent Nacylphosphatidylethanolamine, structurally consisting the linkage of fatty acid tothe ethanolamines. NAE is hydrolysed by fatty acid amide hydrolase (FAAH) into free fatty acid and ethanolamine in both plants and animals. In plants, FAAH gene has been thus far characterized in Arabidopsis, where it was shown to act as a modulator of endogenous NAE levels, seedling growth and their ability to respond to biotic and biotic stress. Based on the evidence that NAEs occur in tomato (Solanum lycopersicum) seeds, we hypothesized that there is a functional FAAH that hydrolyzes NAEs in tomato. To test this, we performed in silico analysis using AtFAAH sequence as a template and identified six orthologs in tomato. These six S. lycopersicum FAAH homologs have the characteristic amidase signature sequence and conserved catalytic residues. Protein structures of putative SlFAAH1 and 2 were predicted using molecular visualization system (PyMOL). They showed similar domain structure with minor differences in spatial arrangement when compared with that of AtFAAH. Among the six homologs only putative SlFAAH1 and SlFAAH2 expression levels were associated with seedling development. Therefore the study was focused on cloning and characterization of SlFAAH1 and 2. Thus far, full-length coding sequence of putative SlFAAH1 was cloned into a heterologous expression system and its expression was confirmed by Western blot. Biochemical characterization of its hydrolytic activity against radiolabelled NAE substrates is underway. Furthermore, expression of SlFAAH1 and SlFAAH2 will be quantified and correlated with the NAE levels and hydrolytic activity at different developmental stages. This study is expected to reveal how NAE metabolite levels are modulated in tomato plant during its development.