Note:

Evolution has provided vast genetic diversity, enabling plants to surmount many biotic pressures. Plants have evolved various morphological and biochemical adaptations to cope with herbivores attacks. Despite that, yearly, around 40 % of worldwide crop production is lost due to pests and pathogens, with 13 % due to insects. Tuta absoluta has become a major pest threatening tomato crops worldwide and without the appropriated management it can cause production losses between 80 to 100 %. To cope with this threat, we need to strengthen plant defense arsenals. The incorporation to plants of defensive genes like proteinase inhibitors by means of genetic engineering is a promising alternative. In the first chapter of this work we investigated the inhibitory activity of two trypsin inhibitors from barley; BTI-CMe and BTI-CMc. Besides, we succeeded to increase the BTI-CMc in vitro inhibitory activity by introducing a single mutation in its putative reactive site. In the second chapter, we investigated the in vivo effect of (a serine proteinase inhibitor) BTI-CMe and a (cysteine proteinase inhibitor) Hv-CPI2 isolated from barley on Tuta absoluta and we examined the effect of their expression on the tomato defensive response. We found that larvae fed on the double transgenic plants showed a notable reduction in weight. Moreover, only 56% of the larvae reached the adult stage. The emerged adults showed wings deformities and reduced fertility. We also investigated the effect of proteinase inhibitors ingestion on the insect digestive enzymes. Our results showed a decrease in larval trypsin activity. Proteinase inhibitors had no harmful effect on Nesidiocoris tenuis; a predator of Tuta absoluta, despite transgenic tomato plants attracted the mirid. We investigated whether or not plant defensive mechanisms were activated in the transgenic tomato plants and found that, interestingly, the expression of the barley cysteine proteinase inhibitor promoted plant defense, inducing the tomato endogenous wound inducible proteinase inhibitor 2 (Pin2) gene. Moreover, glandular trichomes production was increased and the emission of volatile organic compounds was altered. Our results demonstrate the usefulness of the co-expression of different proteinase inhibitors for the enhancement of plant resistance to pests. / La evolución ha proporcionado una gran diversidad genética, permitiendo a las plantas superar muchas presiones bióticas. Las plantas han desarrollado diversas adaptaciones morfológicas y bioquímicas para hacer frente a los ataques de los herbívoros. A pesar de ello, anualmente, alrededor del 40 % de la producción mundial de cultivos se pierde debido a plagas y patógenos, siendo un 13 % debido a insectos. Tuta absoluta se ha convertido en una de las principales plagas que amenazan los cultivos de tomate en todo el mundo y sin la gestión adecuada puede causar pérdidas de producción entre el 80 y el 100 %. Para hacer frente a esta amenaza, necesitamos fortalecer los arsenales de defensa de las plantas. La incorporación a las plantas, mediante ingeniería genética, de genes defensivos como los inhibidores de proteinasas es una alternativa prometedora. En el primer capítulo de este trabajo se investigó la actividad inhibitoria de dos inhibidores de tripsina procedentes de cebada; BTI-CMe y BTI-CMc. Además, se logró aumentar la actividad inhibitoria in vitro de BTI-CMc mediante la introducción de una única mutación en su putativo centro reactivo. En el segundo capítulo, se investigó el efecto in vivo de un inhibidor de serin proteinasa (BTI-CMe) y un inhibidor de cisteín proteinasa (Hv-CPI2) aislado de cebada en Tuta absoluta y se examinó el efecto de su expresión en la respuesta defensiva del tomate. Se encontró que las larvas alimentadas con las plantas transgénicas dobles mostraron una notable reducción de peso. Además, sólo el 56 % de las larvas alcanzó la etapa adulta. Los adultos emergentes mostraron deformidades de las alas y reducción de la fertilidad. También se investigó el efecto de la ingesta de inhibidores de proteinasa en las enzimas digestivas de los insectos. Nuestros resultados mostraron una disminución en la actividad tripsina larvaria. Los inhibidores de proteinasas no tuvieron efectos nocivos sobre Nesidiocoris tenuis(depredador de Tuta absoluta) a pesar de que las plantas transgénicas de tomate atrajeron al mirido. Se investigó si los mecanismos defensivos de las plantas se activaban en las plantas de tomate transgénico y se encontró que, curiosamente, la expresión de la cistatina de cebada promovía la defensa de la planta, induciendo el gen del inhibidor de proteasa 2 endógeno del tomate, inducible por herida (Pin2). Además, aumentó la producción de tricomas glandulares y se alteró la emisión de compuestos orgánicos volátiles. Nuestros resultados demuestran la utilidad de la co-expresión de diferentes inhibidores de proteinasas para el aumento de la resistencia de las plantas a plagas. / L'evolució ha proporcionat una gran diversitat genètica, permetent a les plantes superar moltes pressions biòtiques. Les plantes han desenvolupat diverses adaptacions morfològiques i bioquímiques per fer front als atacs dels herbívors. Tot i això, anualment, al voltant del 40 % de la producció mundial de cultius es perd a causa de plagues i patògens, amb un 13 % a causa de insectes. Tuta absoluta s'ha convertit en una de les principals plagues que amenacen els cultius de tomaca a tot el món i sense la gestió adequada pot causar pèrdues de producció entre el 80 i el 100 %. Per fer front a aquesta amenaça, necessitem enfortir els arsenals de defensa de les plantes. La incorporació a les plantes de gens defensius com els inhibidors de proteïnases per mitjà de l'enginyeria genètica és una alternativa prometedora. En el primer capítol d'aquest treball es va investigar l'activitat inhibitòria de dos inhibidors de tripsina aïllats a partir d'ordi; BTI-CMe i BTI-CMC. A més, es va aconseguir augmentar l'activitat inhibitòria in vitro de BTI-CMC mitjançant la introducció d'una única mutació en el seu lloc reactiu putatiu. En el segon capítol, es va investigar l'efecte in vivo d'un inhibidor de serin proteinasa (BTI-CMe) i un inhibidor de cisteïn proteinasa (Hv-CPI2) aïllats d'ordi en Tuta absoluta i es va examinar l'efecte de la seva expressió en la resposta defensiva del tomaca. Es va trobar que les larves alimentades amb les plantes transgèniques dobles van mostrar una notable reducció de pes. A més, només el 56 % de les larves va aconseguir l'etapa adulta. Els adults emergents van mostrar deformitats de les ales i reducció de la fertilitat. També es va investigar l'efecte de la ingesta d'inhibidors de proteinasa en els enzims digestius dels insectes. Els nostres resultats van mostrar una disminució en l'activitat tripsina larvària. Els inhibidors de proteïnases no van tenir efectes nocius sobre Nesidiocoris tenuis, un depredador de Tuta absoluta, tot i les plantes transgèniques de tomaca van atreure al mirid. Es va investigar si els mecanismes defensius de les plantes s'activaven a les plantes de tomaca transgènic i es va trobar que, curiosament, l'expressió de cistatina d'ordi promovia la defensa de la planta, induint el gen de l'inhibidor de proteasa 2 endogen de la tomaca, induïble per ferida (Pin2). A més, va augmentar la producció de tricomes glandulars i es va alterar l'emissió de compostos orgànics volàtils. Els nostres resultats demostren la utilitat de la co-expressió de diferents inhibidors de proteïnases per a l'augment de la resistència de les plantes a plagues. / Hamza, R. (2017). Enhancement of tomato resistance to Tuta absoluta by the expression of two barley proteinase inhibitors [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/92723

A linhagem queratinolítica Chryseobacterium sp. Kr6 mostrou-se com possibilidade de aplicação em processos envolvendo queratinólise, principalmente na hidrólise de penas de frango e depilação de couro bovino. No presente trabalho avaliou-se o efeito da composição do meio sobre o crescimento e atividade proteolítica deste isolado e uma protease queratinolítica (queratinase) foi purificada e caracterizada. O microrganismo mostrou-se adaptado à utilização de queratina como substrato durante o crescimento, produziu diferentes proteases dependendo do meio utilizado e a maior atividade proteolítica foi atingida quando utilizado meio de cultivo com penas como única fonte de carbono e nitrogênio. A adição de fonte extra de nutrientes resultou em uma parcial repressão catabólica. Uma protease extracelular (Q1) foi purificada cerca de 14 vezes utilizando cromatografia de interação hidrofóbica em Phenyl-Sepharose CL 4B e gel filtração em Superose H12R. Q1 mostrou ser uma proteína monomérica com peso molecular de 64 KDa determinado por SDS-PAGE e pH e temperatura ótimos de 8,5 e 50°C respectivamente. O perfil de inibição indica tratar-se uma metaloprotease e as seqüências internas dos peptídeos resultantes de digestão tríptica mostraram homologia ao sítio ativo e de ligação ao Zn da família M14 (Carboxipeptidase). A atividade proteolítica foi estimulada pela presença de íons Ca2+ e Mg2+ e inibida por Cu2+, Zn2+, Al2+, Hg 2+ e agentes redutores. Q1 apresentou atividade queratinolítica sobre o substrato keratin azure, mas não foi capaz de hidrolisar penas de frango sugerindo a necessidade de outras enzimas durante o processo de degradação de penas. Utilizando os iniciadores degenerados desenhados com base na seqüência dos peptídeos, foi amplificado um fragmento de 470 pb correspondente a uma região do possível gene desta metaloproteína utilizando DNA e cDNA como molde. A seqüência do fragmento pode estar sendo expressa, mas não apresentou similaridade e homologia a proteínas conhecidas e portando, indicativa de uma nova metaloprotease. / The strain Chryseobacterium sp. kr6 shown to be useful for biotechnological purposes such as hydrolysis of poultry feathers and de-hairing of bovine pelts. The effect of media composition on the protease production and growth by this strain was studied and a keratinolytic protease (keratinase) was purified and characterized. The strain was adapted to use keratin as substrate to growth, produced different proteases in different media composition and the higher proteolytic activity was reached when used feather as only source of carbon and nitrogen. The addition of sources of nutrients has resulted in partially repressed catabolism. An extracellular protease Q1) was purified 14-fold by chromatography using the hydrophobic interaction Phenyl-Sepharose CL 4B column and gel filtração in Superose 12HR. SDS-PAGE indicated that the Q1 is a monomeric protein with molecular mass of 64 KDa. and optima pH and temperature were 8,5 e 50°C, respectively. The inhibition profile indicates to be a Zn-metalloprotease and analysis of tryptic peptides sequence revealed sequence homology to the conserved active site and Zn binding site, which may characterize keratinase Q1 as a member of M14 metalloprotease family (Carboxipeptidase). The activity was stimulated by of Ca2+ and Mg2+ and inhibited by Cu2+, Zn2+, Al2+, Hg 2+ and reducing agents. Q1 presented keratinolytic activity under substrate keratin azure, but was unable to hydrolyze poultry feather, suggesting the requirement by other enzymes in the feather hydrolysis mechanism. Degenerate primers amplified a 470 bp, corresponding to a probable gene region of this metalloprotein, with DNA and cDNA. The sequence is being expressed but do not showed similarity and homology to known proteins, thus indicating a new metalloprotease.

A linhagem queratinolítica Chryseobacterium sp. Kr6 mostrou-se com possibilidade de aplicação em processos envolvendo queratinólise, principalmente na hidrólise de penas de frango e depilação de couro bovino. No presente trabalho avaliou-se o efeito da composição do meio sobre o crescimento e atividade proteolítica deste isolado e uma protease queratinolítica (queratinase) foi purificada e caracterizada. O microrganismo mostrou-se adaptado à utilização de queratina como substrato durante o crescimento, produziu diferentes proteases dependendo do meio utilizado e a maior atividade proteolítica foi atingida quando utilizado meio de cultivo com penas como única fonte de carbono e nitrogênio. A adição de fonte extra de nutrientes resultou em uma parcial repressão catabólica. Uma protease extracelular (Q1) foi purificada cerca de 14 vezes utilizando cromatografia de interação hidrofóbica em Phenyl-Sepharose CL 4B e gel filtração em Superose H12R. Q1 mostrou ser uma proteína monomérica com peso molecular de 64 KDa determinado por SDS-PAGE e pH e temperatura ótimos de 8,5 e 50°C respectivamente. O perfil de inibição indica tratar-se uma metaloprotease e as seqüências internas dos peptídeos resultantes de digestão tríptica mostraram homologia ao sítio ativo e de ligação ao Zn da família M14 (Carboxipeptidase). A atividade proteolítica foi estimulada pela presença de íons Ca2+ e Mg2+ e inibida por Cu2+, Zn2+, Al2+, Hg 2+ e agentes redutores. Q1 apresentou atividade queratinolítica sobre o substrato keratin azure, mas não foi capaz de hidrolisar penas de frango sugerindo a necessidade de outras enzimas durante o processo de degradação de penas. Utilizando os iniciadores degenerados desenhados com base na seqüência dos peptídeos, foi amplificado um fragmento de 470 pb correspondente a uma região do possível gene desta metaloproteína utilizando DNA e cDNA como molde. A seqüência do fragmento pode estar sendo expressa, mas não apresentou similaridade e homologia a proteínas conhecidas e portando, indicativa de uma nova metaloprotease. / The strain Chryseobacterium sp. kr6 shown to be useful for biotechnological purposes such as hydrolysis of poultry feathers and de-hairing of bovine pelts. The effect of media composition on the protease production and growth by this strain was studied and a keratinolytic protease (keratinase) was purified and characterized. The strain was adapted to use keratin as substrate to growth, produced different proteases in different media composition and the higher proteolytic activity was reached when used feather as only source of carbon and nitrogen. The addition of sources of nutrients has resulted in partially repressed catabolism. An extracellular protease Q1) was purified 14-fold by chromatography using the hydrophobic interaction Phenyl-Sepharose CL 4B column and gel filtração in Superose 12HR. SDS-PAGE indicated that the Q1 is a monomeric protein with molecular mass of 64 KDa. and optima pH and temperature were 8,5 e 50°C, respectively. The inhibition profile indicates to be a Zn-metalloprotease and analysis of tryptic peptides sequence revealed sequence homology to the conserved active site and Zn binding site, which may characterize keratinase Q1 as a member of M14 metalloprotease family (Carboxipeptidase). The activity was stimulated by of Ca2+ and Mg2+ and inhibited by Cu2+, Zn2+, Al2+, Hg 2+ and reducing agents. Q1 presented keratinolytic activity under substrate keratin azure, but was unable to hydrolyze poultry feather, suggesting the requirement by other enzymes in the feather hydrolysis mechanism. Degenerate primers amplified a 470 bp, corresponding to a probable gene region of this metalloprotein, with DNA and cDNA. The sequence is being expressed but do not showed similarity and homology to known proteins, thus indicating a new metalloprotease.

As espécies de Candida são patógenos oportunistas e as infecções nas cavidades bucais causadas por este gênero são comuns em pacientes com fatores predisponentes, entre eles imussuprimidos, diabéticos e usuários de próteses dentais. No Brasil o índice de endentados é elevado sendo necessária a utilização de próteses bucais, que são locais favoráveis à colonização de microrganismos e o desenvolvimento de biofilme. A utilização de antissépticos como medida complementar na higiene oral é cada vez mais difundida. O objetivo deste trabalho foi detectar em amostras de C. albicans e C. não-albicans, isoladas da saliva de portadores de próteses bucais, os fatores de virulência, proteinase e biofilme e genes relacionados à proteinase (SAP1, SAP3) e à adesão (ALS1 e ALS3) e avaliar a atividade antifúngica in vitro de três formulações comerciais à base de clorexidina 0,12%, cetilpiridínio 0,07% e 0,075% frente aos isolados de Candida e biofilmes. Foram coletadas amostras de saliva de 70 pacientes usuários de próteses bucais. As leveduras foram isoladas em meio de CHROMagar® Candida e identificadas pela metodologia clássica e a confirmação de C. albicans por biologia molecular (PCR). Leveduras do gênero Candida foram isoladas de 32 (45,7%) amostras. Destas foram identificadas: C. albicans (29), C. krusei (5), C. glabrata (4), C. tropicalis (3) e C. parapsilosis (2), totalizando 43 leveduras entre monoculturas e culturas mistas. Os genes pesquisados foram detectados somente em amostras de C. albicans, os genes ALS2, ALS3 e SAP3 foram identificados em 86% dos isolados e o SAP1 em 93%. A atividade de proteinase entre os dos isolados de C. albicans foi de 72,4% e entre das espécies de C. não-albicans 35,7%. A de formação de biofilme sobre placas de 96 poços, e após coloração com XTT, demonstrou que a maioria dos isolados de Candida e todas as culturas mistas desenvolveram biofilmes em 24 horas. A atividade de três antissépticos frente as leveduras foi de <=1,25%, equivalente a uma diluição de 1:80 do antisséptico. Concluímos os três antissépticos também foram eficazes frente aos biofilmes de monoculturas e culturas mistas, as cepas de C. albicans continua sendo a espécie prevalente na cavidade bucal, os genes SAP1, SAP3, ALS2 e ALS3 estão presentes na maioria dos isolados de C. albicans, nestas amostras a maioria foram proteinase e biofilme positivos. A atividade de proteinase foi superior nas espécies de C. albicans em comparação com C. não-albicans. Os biofilmes das espécies de Candida quando formados em culturas mistas se desenvolvem mais em comparação com a formação de biofilme em monocultura. As três formulações de antissépticos foram eficazes contra todos isolados de leveduras em forma planctônica e na maioria dos biofilmes. / Candida species are opportunistic pathogens and infections in the oral cavity caused by these yeasts are common in patients with predisposing factors, such as diabetic or immunocompromised individuals with dental prosthesis. In Brazil, the number of toothless patients is high and the use of dental prosthesis is common, which represents a niche for colonization and formation of microbial biofilms in the oral cavity. The use of mouthwashes to aid in the oral hygiene has increased. The objective of this research was to isolate C. albicans and C. non-albicans from saliva of dental prosthesis users and to evaluate the isolates for the presence of virulence factors, proteinase production, biofilm formation and to search for genes encoding for proteinases (SAP1, SAP3) and adhesion factors (ALS1 and ALS3). Another objective was to evaluate in vitro the antifungal activity of three commercial mouthwashes containing 0.12% chlorhexidine and 0.07% or 0.075% cetylpyridinium, against planktonic Candida sp. cultures and in biofilms. Saliva samples of 70 patients with dental prosthesis were collected, the yeasts were isolated on CHOMagar® Candida and identified by classical biochemical tests combined with molecular test (PCR) for confirmation of C. albicans. Yeasts of Candida genus were isolated from 32 samples (45.7%) and were identified as C. albicans (29), C. krusei (5), C. glabrata (4), C. tropicalis (3) and C. parapsilosis (2), with a total of 43 yeasts, including mono and mixed cultures. The genes studied were detected only in C. albicans: ALS2, ALS3 and SAP3 genes were detected in 86% of the isolates and SAP1 in 93%. The proteinase activity among the isolates of C. albicans was 72.4% and among the species of C. non-albicans it was 35.7%. Assay done with cultivation in 96-wells microplates and staining with XTT, showed the majority of Candida isolates and all the mixed cultures were able to form biofilms within 24h. The activity of the three mouthwashes towards the yeasts was < 1.25%, equivalent to a dilution of 1:80 of the formulation. The three mouthwashes tested were also active against mono or multispecies biofilms. In conclusion, it was shown C. albicans is the most prevalent species. The genes SAP1, SAP3, ALS2 and ALS3 are present in the majority of C. albicans isolates, which were also positive for proteinase and biofilm formation. There was more proteinase activity in C. albicans in comparison with C. non-albicans. The biofilms of Candida species grew better in mixed cultures than in monoculture. The three commercial mouthwashes formulations were effective against all the yeast isolates in planktonic growth and they also inhibited the majority of yeasts in biofilm. Future work is needed to completely elucidate the role of Candida species in biofilms of oral cavity. It is also interesting to propose studies to standardize sensitivity tests for mono and multi-species biofilms.

Hui, Pok Shun. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2009. / Includes bibliographical references (leaves 274-293). / Abstracts in English and Chinese. / Abstract --- p.i / 摘要 --- p.iv / Acknowledgements --- p.vii / Publications Based on Work in this Thesis --- p.viii / Abbreviations --- p.ix / Table of Contents --- p.xi / Chapter Chapter 1 --- Introduction --- p.1 / Chapter 1.1 --- The Mast Cell --- p.2 / Chapter 1.1.1 --- Origin and Development of Mast Cells --- p.3 / Chapter 1.1.2 --- Heterogeneity of Mast Cells --- p.5 / Chapter 1.1.2.1 --- Heterogeneity of Rodent Mast Cells --- p.5 / Chapter 1.1.2.2 --- Heterogeneity of Human Mast Cells --- p.6 / Chapter 1.1.3 --- Activation of Mast Cells --- p.8 / Chapter 1.1.3.1 --- IgE-dependent Activation of Mast Cells --- p.8 / Chapter 1.1.3.1.1 --- FceRI Aggregation and Tyrosine Residue Phosphorylation --- p.9 / Chapter 1.1.3.1.2 --- PLC Activation and Calcium Mobilization --- p.10 / Chapter 1.1.3.1.3 --- PKC and MAPK Activation --- p.11 / Chapter 1.1.3.2 --- IgE-independent Activation of Mast Cells --- p.14 / Chapter 1.1.3.2.1 --- Activation by IgG --- p.14 / Chapter 1.1.3.2.2 --- Activation by Basic Secretagogues --- p.14 / Chapter 1.1.3.2.3 --- Activation by Calcium Ionophores --- p.15 / Chapter 1.1.4 --- Mast Cell Mediators --- p.16 / Chapter 1.1.4.1 --- Preformed Mediators --- p.16 / Chapter 1.1.4.2 --- Newly Synthesized Lipid Mediators --- p.18 / Chapter 1.1.4.3 --- Cytokines and Chemokines --- p.19 / Chapter 1.1.5 --- Pathophysiological Roles of Mast Cells --- p.21 / Chapter 1.2 --- Arthritis --- p.23 / Chapter 1.2.1 --- Epidemiology of Arthritis --- p.23 / Chapter 1.2.2 --- Clinical Features of Arthritis --- p.25 / Chapter 1.2.2.1 --- Angiogenesis and Vasodilation --- p.25 / Chapter 1.2.2.2 --- Synovial Changes --- p.25 / Chapter 1.2.2.3 --- Cartilage Degradation and Bone Erosion --- p.26 / Chapter 1.2.3 --- Pathogenesis of Arthritis --- p.27 / Chapter 1.2.3.1 --- Roles of T Cells --- p.27 / Chapter 1.2.3.2 --- Roles of B Cells --- p.28 / Chapter 1.2.3.3 --- Roles of Mast Cells --- p.28 / Chapter 1.2.3.4 --- Roles of Cytokines --- p.31 / Chapter 1.2.4 --- Treatments of Arthritis --- p.32 / Chapter 1.2.4.1 --- NSAIDs --- p.33 / Chapter 1.2.4.2 --- Glucocorticoids --- p.34 / Chapter 1.2.4.3 --- DMARDs --- p.35 / Chapter 1.2.4.4 --- New Drugs --- p.36 / Chapter 1.3 --- Proteinase-Activated Receptor (PAR) --- p.38 / Chapter 1.3.1 --- Introduction to PARs --- p.38 / Chapter 1.3.2 --- Discovery of PARs --- p.39 / Chapter 1.3.2.1 --- PAR1 --- p.39 / Chapter 1.3.2.2 --- PAR2 --- p.39 / Chapter 1.3.2.3 --- PAR3 --- p.40 / Chapter 1.3.2.4 --- PAR4 --- p.41 / Chapter 1.3.3 --- Structure of PARs --- p.43 / Chapter 1.3.4 --- Activation of PARs --- p.43 / Chapter 1.3.4.1 --- Serine Proteinases --- p.44 / Chapter 1.3.4.1.1 --- Thrombin --- p.44 / Chapter 1.3.4.1.2 --- Trypsin --- p.46 / Chapter 1.3.4.1.3 --- Mast Cell Tryptase --- p.46 / Chapter 1.3.4.2 --- PAR Activating Peptides (PAR-APs) --- p.47 / Chapter 1.3.4.3 --- Proteinase Binding and the Tethered Ligand Mechanism --- p.49 / Chapter 1.3.5 --- Signaling of PARs --- p.50 / Chapter 1.3.5.1 --- Signaling of PAR1 --- p.51 / Chapter 1.3.5.2 --- Signaling of PAR2 --- p.52 / Chapter 1.3.5.3 --- Signaling of PAR 3 and PAR4 --- p.53 / Chapter 1.3.6 --- Termination of Signals and Antagonism of PARs --- p.53 / Chapter 1.3.6.1 --- Termination of Signals by Proteolysis --- p.53 / Chapter 1.3.6.2 --- Termination of Signals by Receptor Desensitization --- p.54 / Chapter 1.3.6.3 --- Antagonism of PARs --- p.55 / Chapter 1.3.7 --- Roles of PARs in Immune Responses --- p.56 / Chapter 1.3.7.1 --- PARs and Mast Cells --- p.57 / Chapter 1.3.7.2 --- PARs and A rthritis --- p.58 / Chapter 1.4 --- Aims of Study --- p.60 / Chapter Chapter 2 --- Materials and Methods --- p.62 / Chapter 2.1 --- Materials --- p.63 / Chapter 2.1.1 --- Materials for Study of PAR Gene Expression in Mast Cells by RT-PCR --- p.63 / Chapter 2.1.1.1 --- Materials for RNA Extraction --- p.63 / Chapter 2.1.1.2 --- Materials for cDNA Synthesis by Reverse Transcription --- p.63 / Chapter 2.1.1.3 --- Materials for Gene Amplification by PCR --- p.64 / Chapter 2.1.1.4 --- Materials for Agarose Gel Electrophoresis --- p.64 / Chapter 2.1.1.5 --- Miscellaneous --- p.64 / Chapter 2.1.2 --- Materials for Study of Histamine Release from RPMCs and LAD2 Cells --- p.65 / Chapter 2.1.2.1 --- Drugs --- p.65 / Chapter 2.1.2.1.1 --- Peptides --- p.65 / Chapter 2.1.2.1.2 --- Serine Proteinases --- p.65 / Chapter 2.1.2.1.3 --- Mast Cell Secretagogues --- p.66 / Chapter 2.1.2.1.4 --- Other Drugs --- p.66 / Chapter 2.1.2.2 --- Materials for Rat Sensitization --- p.66 / Chapter 2.1.2.3 --- Materials for LAD2 Cell Culture --- p.66 / Chapter 2.1.2.4 --- Materials for Buffers --- p.67 / Chapter 2.1.2.5 --- Materials for Spectrofluorometric Analysis of Histamine Contents --- p.67 / Chapter 2.1.2.6 --- Miscellaneous --- p.68 / Chapter 2.1.3 --- Materials for Histological Study of Synovial Mast Cells --- p.69 / Chapter 2.1.3.1 --- Drugs --- p.69 / Chapter 2.1.3.2 --- Chemicals --- p.69 / Chapter 2.1.3.3 --- Miscellaneous --- p.69 / Chapter 2.1.4 --- Materials for Study of Rat Knee Joint Inflammation --- p.70 / Chapter 2.1.4.1 --- Drugs --- p.70 / Chapter 2.1.4.1.1 --- Peptides --- p.70 / Chapter 2.1.4.1.2 --- Other Drugs --- p.70 / Chapter 2.1.4.2 --- Materials for Assessment of Vascular Permeability --- p.71 / Chapter 2.1.4.3 --- Miscellaneous --- p.71 / Chapter 2.2 --- Methods --- p.72 / Chapter 2.2.1 --- Study of PAR Gene Expression in Mast Cells by RT-PCR --- p.72 / Chapter 2.2.1.1 --- Animals --- p.72 / Chapter 2.2.1.2 --- LAD2 Cell Culture --- p.72 / Chapter 2.2.1.3 --- Preparation of Buffers --- p.73 / Chapter 2.2.1.4 --- RNA Extraction --- p.73 / Chapter 2.2.1.5 --- Heparinase and DNase Treatments --- p.74 / Chapter 2.2.1.6 --- cDNA Synthesis by Reverse Transcription --- p.75 / Chapter 2.2.1.7 --- Gene Amplification by PCR --- p.75 / Chapter 2.2.1.8 --- Agarose Gel Electrophoresis --- p.77 / Chapter 2.2.2 --- Study of Histamine Release from RPMCs and LAD2 Cells --- p.77 / Chapter 2.2.2.1 --- Rat Sensitization --- p.77 / Chapter 2.2.2.2 --- Preparation of Buffers --- p.75 / Chapter 2.2.2.3 --- Preparation of Stock Solutions --- p.78 / Chapter 2.2.2.3.1 --- Stock Solutions of Peptides --- p.75 / Chapter 2.2.2.3.2 --- Stock Solutions of Serine Proteinases --- p.79 / Chapter 2.2.2.3.3 --- Stock Solutions of Mast Cell Secretagogues and Other Drugs --- p.79 / Chapter 2.2.2.4 --- Preparation of Mast Cells --- p.80 / Chapter 2.2.2.4.1 --- Isolation and Purification of RPMCs --- p.80 / Chapter 2.2.2.4.2 --- Preparation of LAD2 Cells --- p.81 / Chapter 2.2.2.4.3 --- Determination of Cell Number and Viability --- p.81 / Chapter 2.2.2.5 --- General Protocol for Histamine Release Assay --- p.82 / Chapter 2.2.2.5.1 --- RPMC Experiments --- p.52 / Chapter 2.2.2.5.2 --- LAD2 Cell Experiments --- p.53 / Chapter 2.2.2.6 --- Spectrofluorometric Analysis of Histamine Contents --- p.83 / Chapter 2.2.2.6.1 --- Manual Analysis --- p.85 / Chapter 2.2.2.6.2 --- Automated Analysis --- p.85 / Chapter 2.2.2.7 --- Data Analysis --- p.86 / Chapter 2.2.2.7.1 --- Calculation of Histamine Release --- p.86 / Chapter 2.2.2.7.2 --- Data Presentation and Statistical Analysis --- p.87 / Chapter 2.2.3 --- Histological Study of Synovial Mast Cells --- p.88 / Chapter 2.2.3.1 --- Preparation of Buffers and Chemicals --- p.88 / Chapter 2.2.3.2 --- Preparation of Drugs --- p.88 / Chapter 2.2.3.3 --- Intra-peritoneal Injections of Compound 48/80 --- p.88 / Chapter 2.2.3.4 --- Fixation --- p.89 / Chapter 2.2.3.5 --- Processing --- p.89 / Chapter 2.2.3.6 --- Embedding --- p.90 / Chapter 2.2.3 --- Sectioning --- p.90 / Chapter 2.2.3.8 --- Staining --- p.90 / Chapter 2.2.4 --- Study of Rat Knee Joint Inflammation --- p.91 / Chapter 2.2.4.1 --- Animals --- p.91 / Chapter 2.2.4.2 --- Preparation of Drugs --- p.92 / Chapter 2.2.4.3 --- Induction of Anaesthesia --- p.92 / Chapter 2.2.4.4 --- Intra-articular Injection of Drugs --- p.93 / Chapter 2.2.4.5 --- Topical Administration of Drugs --- p.93 / Chapter 2.2.4.6 --- Assessment of Mechanical Allodynia --- p.93 / Chapter 2.2.4.7 --- Assessment of Joint Oedema --- p.94 / Chapter 2.2.4.8 --- Assessment of Hyperaemia --- p.95 / Chapter 2.2.4.9 --- Assessment of Vascular Permeability --- p.95 / Chapter 2.2.4.10 --- Data Analysis --- p.96 / Chapter Chapter 3 --- Studies of Roles of PAR in Mast Cells --- p.97 / Chapter 3.1 --- Introduction --- p.98 / Chapter 3.2 --- Materials and Methods --- p.103 / Chapter 3.2.1 --- Study of PAR Gene Expression in Mast Cells by RT-PCR --- p.103 / Chapter 3.2.2 --- Study of Effects of PAR Agonists on Histamine Release from Mast Cells --- p.103 / Chapter 3.2.3 --- Study of Signaling Pathways Induced by PAR Agonists in Mast Cells --- p.104 / Chapter 3.3 --- Results --- p.105 / Chapter 3.3.1 --- Study of PAR Gene Expression in Mast Cells by RT-PCR --- p.105 / Chapter 3.3.1.1 --- PAR Gene Expression in RPMCs --- p.105 / Chapter 3.3.1.2 --- PAR Gene Expression in LAD2 Cells --- p.105 / Chapter 3.3.2 --- Study of Effects of PAR Agonists on Histamine Release from Mast Cells --- p.106 / Chapter 3.3.2.1 --- Effects of Serine Proteinases on Histamine Release from RPMCs --- p.106 / Chapter 3.3.2.1.1 --- Thrombin --- p.106 / Chapter 3.3.2.1.2 --- Trypsin --- p.106 / Chapter 3.3.2.1.3 --- Tryptase --- p.107 / Chapter 3.3.2.2 --- Effects of PAR-APs on Histamine Release from RPMCs --- p.107 / Chapter 3.3.2.2.1 --- TFLLR-NH2 (PAR1-AP) --- p.107 / Chapter 3.3.2.2.2 --- SLIGRL-NH2 (PAR2-AP) --- p.108 / Chapter 3.3.2.2.3 --- 2-Furoyl-LIGRLO-NH2 (PAR2-AP) --- p.108 / Chapter 3.3.2.2.4 --- SFNGGP-NH2 (PAR3-AP) --- p.109 / Chapter 3.3.2.2.5 --- AYPGKF-NH2 (PARrAP) --- p.110 / Chapter 3.3.2.3 --- Effects of PAR Control Peptides on Histamine Release from RPMCs --- p.111 / Chapter 3.3.2.4 --- Effects of PAR-APs on Histamine Release from LAD2 Cells --- p.111 / Chapter 3.3.3 --- Study of Signaling Pathways Induced by PAR Agonists in Mast Cells --- p.112 / Chapter 3.3.3.1 --- Effect of PTX on PAR-AP-induced Histamine Release from RPMCs --- p.112 / Chapter 3.3.3.2 --- Effect of BAC on PAR-AP-induced Histamine Release from RPMCs --- p.113 / Chapter 3.4 --- Discussion --- p.115 / Chapter 3.5 --- Figures and Tables --- p.132 / Chapter Chapter 4 --- Studies of Roles of PAR in Rat Knee Joint Inflammation --- p.175 / Chapter 4.1 --- Introduction --- p.176 / Chapter 4.2 --- Materials and Methods --- p.181 / Chapter 4.2.1 --- Histological Study of Synovial Mast Cells --- p.181 / Chapter 4.2.2 --- Study of Rat Knee Joint Inflammation Induced by Intra-articular Injections of PAR-APs --- p.181 / Chapter 4.2.3 --- Study of Rat Knee Joint Blood Flow Changes Induced by Topical Administration of PAR-APs --- p.182 / Chapter 4.2.4 --- Study of the Involvement of Bradykinin B2 Receptors in Rat Knee Joint Inflammation Induced by PAR-APs --- p.183 / Chapter 4.3 --- Results --- p.184 / Chapter 4.3.1 --- Histological Study of Synovial Mast Cells --- p.184 / Chapter 4.3.2 --- Study of Rat Knee Joint Inflammation Induced by Intra-articular Injections of PAR-APs --- p.185 / Chapter 4.3.2.1 --- Intra-articular Injections of Carrageenan and Ovalbumin --- p.185 / Chapter 4.3.2.2 --- Intra-articular Injections of PAR-APs --- p.187 / Chapter 4.3.2.2.1 --- TFLLR-NH2 (PARrAP) --- p.187 / Chapter 4.3.2.2.2 --- 2-Furoyl-LIGRLO-NH2 (PAR2AP) --- p.187 / Chapter 4.3.2.2.3 --- SFNGGP-NH2 (PARrAP) --- p.189 / Chapter 4.3.2.2.4 --- AYPGKF-NH2 (PAR4-AP) --- p.190 / Chapter 4.3.2.3 --- Intra-articular Injections of PAR Control Peptides --- p.191 / Chapter 4.3.3 --- Study of Rat Knee Joint Blood Flow Changes Induced by Topical Administration of PAR-APs --- p.191 / Chapter 4.3.3.1 --- Topical Administration of 2-Furoyl-LIGRLO-NH2 (PAR2-AP) --- p.191 / Chapter 4.3.3.2 --- Topical Administration of A YPGKF-NH2 (PAR4-AP) --- p.192 / Chapter 4.3.4 --- Study of the Involvement of Bradykinin B2 Receptors in Rat Knee Joint Inflammation Induced by PAR-APs --- p.193 / Chapter 4.3.4.1 --- Effect of HOE 140 on Rat Knee Joint Inflammation Induced by Bradykinin --- p.193 / Chapter 4.3.4.2 --- Effect of HOE 140 on Rat Knee Joint Inflammation Induced by 2-Furoyl-LIGRLO-NH2 (PAR2-AP) --- p.194 / Chapter 4.3.4.3 --- Effect of HOE 140 on Rat Knee Joint Inflammation Induced by AYPGKF-NH2 (PARrAP) --- p.195 / Chapter 4.4 --- Discussion --- p.196 / Chapter 4.5 --- Figures and Tables --- p.209 / Chapter Chapter 5 --- General Discussions and Concluding Remarks --- p.261 / Chapter 5.1 --- General Discussions --- p.262 / Chapter 5.2 --- Further Studies --- p.267 / Chapter 5.3 --- Conclusion --- p.271 / References --- p.274

As espécies de Candida são patógenos oportunistas e as infecções nas cavidades bucais causadas por este gênero são comuns em pacientes com fatores predisponentes, entre eles imussuprimidos, diabéticos e usuários de próteses dentais. No Brasil o índice de endentados é elevado sendo necessária a utilização de próteses bucais, que são locais favoráveis à colonização de microrganismos e o desenvolvimento de biofilme. A utilização de antissépticos como medida complementar na higiene oral é cada vez mais difundida. O objetivo deste trabalho foi detectar em amostras de C. albicans e C. não-albicans, isoladas da saliva de portadores de próteses bucais, os fatores de virulência, proteinase e biofilme e genes relacionados à proteinase (SAP1, SAP3) e à adesão (ALS1 e ALS3) e avaliar a atividade antifúngica in vitro de três formulações comerciais à base de clorexidina 0,12%, cetilpiridínio 0,07% e 0,075% frente aos isolados de Candida e biofilmes. Foram coletadas amostras de saliva de 70 pacientes usuários de próteses bucais. As leveduras foram isoladas em meio de CHROMagar® Candida e identificadas pela metodologia clássica e a confirmação de C. albicans por biologia molecular (PCR). Leveduras do gênero Candida foram isoladas de 32 (45,7%) amostras. Destas foram identificadas: C. albicans (29), C. krusei (5), C. glabrata (4), C. tropicalis (3) e C. parapsilosis (2), totalizando 43 leveduras entre monoculturas e culturas mistas. Os genes pesquisados foram detectados somente em amostras de C. albicans, os genes ALS2, ALS3 e SAP3 foram identificados em 86% dos isolados e o SAP1 em 93%. A atividade de proteinase entre os dos isolados de C. albicans foi de 72,4% e entre das espécies de C. não-albicans 35,7%. A de formação de biofilme sobre placas de 96 poços, e após coloração com XTT, demonstrou que a maioria dos isolados de Candida e todas as culturas mistas desenvolveram biofilmes em 24 horas. A atividade de três antissépticos frente as leveduras foi de <=1,25%, equivalente a uma diluição de 1:80 do antisséptico. Concluímos os três antissépticos também foram eficazes frente aos biofilmes de monoculturas e culturas mistas, as cepas de C. albicans continua sendo a espécie prevalente na cavidade bucal, os genes SAP1, SAP3, ALS2 e ALS3 estão presentes na maioria dos isolados de C. albicans, nestas amostras a maioria foram proteinase e biofilme positivos. A atividade de proteinase foi superior nas espécies de C. albicans em comparação com C. não-albicans. Os biofilmes das espécies de Candida quando formados em culturas mistas se desenvolvem mais em comparação com a formação de biofilme em monocultura. As três formulações de antissépticos foram eficazes contra todos isolados de leveduras em forma planctônica e na maioria dos biofilmes. / Candida species are opportunistic pathogens and infections in the oral cavity caused by these yeasts are common in patients with predisposing factors, such as diabetic or immunocompromised individuals with dental prosthesis. In Brazil, the number of toothless patients is high and the use of dental prosthesis is common, which represents a niche for colonization and formation of microbial biofilms in the oral cavity. The use of mouthwashes to aid in the oral hygiene has increased. The objective of this research was to isolate C. albicans and C. non-albicans from saliva of dental prosthesis users and to evaluate the isolates for the presence of virulence factors, proteinase production, biofilm formation and to search for genes encoding for proteinases (SAP1, SAP3) and adhesion factors (ALS1 and ALS3). Another objective was to evaluate in vitro the antifungal activity of three commercial mouthwashes containing 0.12% chlorhexidine and 0.07% or 0.075% cetylpyridinium, against planktonic Candida sp. cultures and in biofilms. Saliva samples of 70 patients with dental prosthesis were collected, the yeasts were isolated on CHOMagar® Candida and identified by classical biochemical tests combined with molecular test (PCR) for confirmation of C. albicans. Yeasts of Candida genus were isolated from 32 samples (45.7%) and were identified as C. albicans (29), C. krusei (5), C. glabrata (4), C. tropicalis (3) and C. parapsilosis (2), with a total of 43 yeasts, including mono and mixed cultures. The genes studied were detected only in C. albicans: ALS2, ALS3 and SAP3 genes were detected in 86% of the isolates and SAP1 in 93%. The proteinase activity among the isolates of C. albicans was 72.4% and among the species of C. non-albicans it was 35.7%. Assay done with cultivation in 96-wells microplates and staining with XTT, showed the majority of Candida isolates and all the mixed cultures were able to form biofilms within 24h. The activity of the three mouthwashes towards the yeasts was < 1.25%, equivalent to a dilution of 1:80 of the formulation. The three mouthwashes tested were also active against mono or multispecies biofilms. In conclusion, it was shown C. albicans is the most prevalent species. The genes SAP1, SAP3, ALS2 and ALS3 are present in the majority of C. albicans isolates, which were also positive for proteinase and biofilm formation. There was more proteinase activity in C. albicans in comparison with C. non-albicans. The biofilms of Candida species grew better in mixed cultures than in monoculture. The three commercial mouthwashes formulations were effective against all the yeast isolates in planktonic growth and they also inhibited the majority of yeasts in biofilm. Future work is needed to completely elucidate the role of Candida species in biofilms of oral cavity. It is also interesting to propose studies to standardize sensitivity tests for mono and multi-species biofilms.

La maturation des collagènes fibrillaires est régulée par la libération protéolytique des propeptides qui conduit à la formation spontanée de fibres, à partir des molécules de collagène mature. Les fibres de collagène ainsi formées confèrent résistance et solidité aux tissus. Les métalloprotéases Tolloïdes sont les principales enzymes responsables de la maturation C-terminale des procollagènes. Ces protéases possèdent de nombreux autres substrats et se distinguent par un mode de régulation original, l’utilisation de régulateurs « substrats-spécifiques », qui leur permet de moduler leur activité vis-à-vis de ces différents substrats. Parmi ces régulateurs, les Procollagen C-Proteinase Enhancers (PCPE-1 et 2) semblent jouer un rôle important car ils augmentent l’activité de clivage du C-propeptide des procollagènes jusqu’à 20 fois. Même si PCPE-1 a été découvert en 1985, son mode d’action n’est toujours pas compris. Le principal objectif de cette thèse était donc de mieux comprendre le mécanisme de l’activation. Nous avons commencé par identifier la région minimale de PCPE-1 capable d’activer les Tolloïdes et démontré une très forte coopérativité entre les domaines de cette région. Par ailleurs, nous avons mis en évidence, pour la première fois, un nouveau rôle physiologique pour le domaine C-terminal de PCPE-1 (NTR). Concernant les autres partenaires du complexe de maturation, nous avons observé une interaction d’affinité modérée entre PCPE-1 et la protéase Tolloïde appelée BMP-1 et montré que PCPE-1 se fixe uniquement sur la partie C-terminale du procollagène. Enfin, nous avons mis en évidence que d’autres métalloprotéases, les Méprines, pourraient également jouer un rôle dans la maturation de collagènes fibrillaires en étant régulées négativement par les PCPEs. L’ensemble de ces résultats nous a permis de proposer un nouveau schéma d’interaction pour les PCPEs et de faire de nouvelles hypothèses concernant leur mécanisme d’action / The maturation of fibrillar collagens is a tightly regulated process controlled by two proteolytic cleavages that remove the propeptide regions from procollagen precursors leading to spontaneous assembly of mature collagen molecules into fibrils. These fibrils provide tensile strength and toughness to connective tissues and consequently to the organism itself. The group of extracellular metalloproteinases mostly responsible for procollagen processing are the tolloids. As these enzymes have several functions other than procollagen processing, their activities on different substrates are controlled by a growing number of substrate-specific regulators. The most prominent of these regulators are the procollagen C-proteinase enhancers (PCPEs), of which PCPE-1 is a 55 kDa glycoprotein composed of two CUB and a C-terminal NTR domain, which is capable of enhancing the proteolytic activity of tolloids up to 20-fold. Even though PCPE-1 has been known since 1985 the molecular mechanism of enhancement is still unclear. The aim of this thesis was to understand and characterize this mechanism with the aid of biochemical and biophysical methods. We have identified the minimal unit responsible for enhancing activity. In addition, we propose a mechanism for how the subdomains responsible for enhancement cooperatively bind to procollagen substrates. Furthermore, we have for the first time been able to identify a possible physiological function of the NTR domain. Also, we have identified meprins as new players involved in procollagen processing and this has given valuable insights in the mechanism of action of PCPEs. Finally, we have been able to demonstrate that the interaction of PCPE-1 with procollagen is mostly limited to the C-propeptide region. Based on these findings we propose a new hypothetical interaction mechanism for PCPE-1

A catepsina L, uma cisteína proteinase da família da papaína, é a principal proteinase digestiva do besouro Tenebrio molitor. Estudos anteriores do nosso grupo mostraram que existem três catepsinas L no intestino médio do T. molitor, uma delas é lisossômica (CAL 1) e as outras duas são digestivas (CAL 2 e CAL 3). As estruturas 3D das enzimas digestivas foram recentemente elucidadas. Com o objetivo de estudar em detalhes as propriedades das enzimas digestivas, CAL 3 foi expressa como um zimógeno em E. coli, purificada por cromatografia de afinidade e autoativada em meio ácido. Foram realizados ensaios de atividade com 63 peptídeos FRET derivados da sequência Abz-KLRSSKQ-EDDnp em um espectrofluorímetro termostatizado a 30 ºC, monitorando-se continuamente a variação de fluorescência em 320 nm (&#955;ex) e 420 nm (&#955;em). Os parâmetros kcat e KM obtidos foram utilizados na determinação da hidrofobicidade dos subsítios (H) e da função de cada subsítio através da razão das energias livres de ativação do complexo enzima-substrato (&#916;G&#8225;T) e de ligação da enzima com o substrato (&#916;Gs). Os resultados mostram que o subsítio S2 está envolvido prioritariamente em catálise e é bastante seletivo para substratos com resíduos hidrofóbicos em P2. Esse subsítio é o mais hidrofóbico dentre os analisados, encontrando-se num bolsão localizado no interior da enzima. O subsítio S\'2, por outro lado, é o que apresentou a menor especificidade dentre os analisados. Este subsítio está envolvido prioritariamente na ligação com o substrato e se localiza na superfície da enzima, o que pode facilitar a acomodação de diferentes cadeias laterais em P\'2 do substrato, não oferecendo muitas restrições espaciais. O subsítio S1, hidrofílico, não é muito seletivo, o que pode ser consequência de sua localização na superfície da enzima. Esse subsítio está prioritariamente envolvido na ligação com o substrato. O subsítio S\'1, assim como S1, está localizado na superfície da enzima, é hidrofílico e não muito seletivo. No entanto, esse subsítio tem papel na catálise além de atuar na ligação do substrato. Numa análise inicial da estrutura 3D deste subsítio, sua função catalítica foi atribuída à presença de parte da cavidade oxiânica. Uma enzima com mutação no resíduo W187, pertencente à cavidade oxiânica e a S\'1, foi produzida e purificada, no entanto essa enzima não apresentou atividade. Uma análise mais aprofundada mostrou que a falta de atividade pode ser atribuída ao fato do resíduo de aminoácido mutado fazer parte de um cluster aromático essencial à estabilização da tríade catalítica. Os dados obtidos na caracterização de S\'1 e S\'2 permitem inferir que a acilação é o passo limitante da reação da CAL 3. Além disso, os resultados deste trabalho mostram que o conceito de hidrofobicidade de subsítios proposto anteriormente pelo grupo parece ser aplicável a subsítios que apresentem especificidades mais restritas. / Cathepsin L, a cysteine proteinase of the papain family, is the major digestive proteinase in the beetle Tenebrio molitor. Previous studies of our group showed that there are three cathepsins L in T. molitor midgut, one is lysosomal (CAL1) and two are digestive (CAL2 and CAL3). The 3D structures of the digestive enzymes were recently elucidated. With the aim to study in details the digestive enzymes specificities, CAL3 was expressed in E. coli as a zymogen, purified by affinity chromatography and autoactivated in acid conditions. Activity assays were performed in a thermostated spectrofluorometer at 30 ºC with 63 FRET peptides derived from the lead sequence Abz-KLRSSKQ-EDDnp, continuously monitoring the fluorescence changes at 320 nm (&#955;ex) and 420 nm (&#955;em). The parameters kcat and KM were used in the determination of subsite hydrophobicity (H) and subsite role based on the ratio of complex enzyme-substrate activation energy (&#916;G&#8225;T) and free energy of substrate binding (&#916;Gs). The data obtained suggest that the S2 is mainly involved in catalysis and is very selective to substrates with hydrophobic residues in P2. This subsite is the most hydrophobic among the analyzed and is located in a pocket in the enzyme interior. S\'2, on the other hand, is the less selective subsite and is mainly involved in substrate binding and is located on the enzyme surface, what can ease the accommodation of different side chains located in P\'2 by not imposing many spatial restrictions. S1, is hydrophilic and not very selective, what may be a consequence of its location on the enzyme surface. This subsite is mainly involved in substrate binding. S\'1, just like S1, is located on the enzyme surface, is hydrophilic and not very selective. However this subsite has a role in catalysis besides the role in substrate binding. In an initial 3D structure analysis its catalytic function was attributed to the presence of a part of the oxyanion hole. An enzyme with mutation in the residue W187, which apparently belonged both to the oxyanion hole and S\'1, was produced and purified, but this enzyme was inactive. A better analysis showed that the lack of activity can be attributed to the fact that the mutated residue belongs to an aromatic cluster that is essential to the catalytic triad stabilization. The data obtained in S\'1 and S\'2 characterization suggest that acylation is the limiting step in CAL 3 reaction. The results presented in this work support the concept of subsite hydrophobicity previously proposed by our group, which seems to be true to subsites with more restrict specificities

Os inibidores inibidores de serino proteinases do tipo Bowman-Birk (BBI) possuem dois sítios ativos e são encontrados em plantas das famílias Fabaceae e Poaceae. Neste trabalho foi apresentada a estrutura primária e o padrão de expressão de 14 seqüências expressas (EST, expressed sequence tags) de BBI putativos encontradas no banco de dados do "Projeto Transcriptoma da Cana-de-açúcar" (SUCEST). Estas quatorze seqüências foram utilizadas em conjunto com outras 87 seqüências de BBI previamente descritas e depositadas no banco de dados "GenBank" para a construção de árvores filogenéticas da família BBI. A análise filogenética mostrou que os BBI de monocotiledôneas e dicotiledôneas podem ser claramente separados em diferentes grupos e a topologia das árvores filogenéticas sugere um padrão evolutivo diferente das famílias de BBI em plantas. Os inibidores de dicotiledôneas são bem conservados e acumularam diferenças sutis durante a evolução. Em contrapartida, os inibidores de monocotiledôneas são altamente variáveis, indicando a ocorrência de um processo evolutivo interessante, baseado em eventos de duplicação intragênica e mutação. Dois inibidores de serino proteinases, um de tripsina e outro de quimotripsina, derivados do gene que codifica o inibidor Bowman-Birk de soja, foram expressos na superfície do fago filamentoso M13 e utilizados para a construção de bibliotecas de variantes. Para tal foram feitas mutações em quatro aminoácidos do sítio ativo destes inibidores e duas bibliotecas de expressão na superfície de fagos filamentosos foram construídas. Posteriormente, estas bibliotecas foram utilizadas para a seleção de variantes que melhor interagiam com a tripsina bovina e de Diatraea saccharalis e com as enzimas digestivas presentes no extrato intestinal desta praga. Os variantes selecionados foram seqüenciados, analisados e caracterizados. Os resultados mostraram que a técnica de expressão na superfície de fagos filamentosos foi eficiente para selecionar novos inibidores. Além disto, com as mutações realizadas, foi possível transformar a alça de inibição de quimotripsina em uma alça de inibição de tripsina. / The Bowman-Birk inhibitors (BBIs) are double headed inhibitors of serine proteinase found in plants from Fabaceae and Poaceae families. We describe the primary structure and the gene expression profile of 14 putative BBIs from the sugarcane expressed sequence tag (SUCEST) database and show how we used these newly discovered sequences together with 87 previously described BBI sequences from the "GenBank" database to construct phylogenetic trees for the BBI family. Phylogenetic analysis revealed that BBI-type inhibitors from monocotyledonous and dicotyledonous plants could be clearly separated into different groups, while the overall topology of the BBI tree suggests a different pattern of evolution for BBI families in flowering plants. We also found that BBI proteinase inhibitors from dicotyledonous plants were well conserved, accumulating only slight differences during their evolution. In addition, we found that BBIs from monocotyledonous plants were highly variable, indicating an interesting process of evolution based on internal gene duplications and mutation events. Two serine-type proteinase inhibitors, a trypsin and a chymotrypsin, both derived from the soybean Bowman-Birk inhibitor, were expressed on the surface of a filamentous phage. Site mutations were made in four positions of the reactive sites of these inhibitors and two phage-display libraries were constructed. Later, these libraries were used to select better ligands to the bovine and Diatraea saccharalis trypsin and to the midgut enzymes of this insect pest. The selected variants were sequenced, analyzed and characterized. The results showed that the phage-display technique is efficient to select new proteinase inhibitors. Furthermore, it was possible to modify the chymotrypsin loop into a trypsin loop using the library constructed by the insertion of a degenerated primer.