Despite tremendous advances in mass spectrometry instrumentation and mass spectrometry-based methodologies, global protein profiling of organellar, cellular, tissue and body fluid proteomes in different organisms remains a challenging task due to the complexity of the samples and the wide dynamic range of protein concentrations. In addition, large amounts of produced data make result exploitation difficult. To overcome these issues, further advances in sample preparation, mass spectrometry instrumentation as well as data processing and data analysis are required. The presented study focuses as first on the improvement of the proteolytic digestion of proteins in in-gel based proteomic approach (Gel-LCMS). To this end commonly used bovine trypsin (BT) was modified with oligosaccharides in order to overcome its main disadvantages, such as weak thermostability and fast autolysis at basic pH. Glycosylated trypsin derivates maintained their cleavage specifity and showed better thermostability, autolysis resistance and less autolytic background than unmodified BT. In line with the “accelerated digestion protocol” (ADP) previously established in our laboratory modified enzymes were tested in in-gel digestion of proteins. Kinetics of in-gel digestion was studied by MALDI TOF mass spectrometry using 18O-labeled peptides as internal standards as well as by label-free quantification approach, which utilizes intensities of peptide ions detected by nanoLC-MS/MS. In the performed kinetic study the effect of temperature, enzyme concentration and digestion time on the yield of digestion products was characterized. The obtained results showed that in-gel digestion of proteins by glycosylated trypsin conjugates was less efficient compared to the conventional digestion (CD) and achieved maximal 50 to 70% of CD yield, suggesting that the attached sugar molecules limit free diffusion of the modified trypsins into the polyacrylamide gel pores. Nevertheless, these thermostable and autolysis resistant enzymes can be regarded as promising candidates for gel-free shotgun approach. To address the reliability issue of proteomic data I further focused on protein identifications with borderline statistical confidence produced by database searching. These hits are typically produced by matching a few marginal quality MS/MS spectra to database peptide sequences and represent a significant bottleneck in proteomics. A method was developed for rapid validation of borderline hits, which takes advantage of the independent interpretation of the acquired tandem mass spectra by de novo sequencing software PepNovo followed by mass-spectrometry driven BLAST (MS BLAST) sequence similarity searching that utilize all partially accurate, degenerate and redundant proposed peptide sequences. It was demonstrated that a combination of MASCOT software, de novo sequencing software PepNovo and MS BLAST, bundled by a simple scripted interface, enabled rapid and efficient validation of a large number of borderline hits, produced by matching of one or two MS/MS spectra with marginal statistical significance.

Tripsinas são enzimas comuns à maioria dos insetos e de fundamental importância para a digestão inicial de proteínas. Desta forma, tornam-se alvos importantes para orientar a construção de plantas transgênicas resistentes a insetos. As tripsinas são serina endopeptidases que clivam cadeias protéicas na porção carboxílica de resíduos de aminoácidos básicos como lisina e arginina, sendo que a hidrólise da ligação peptídica formada por um resíduo de arginina é de duas a dez vezes mais eficiente que a hidrólise da ligação peptídica formada por lisina. A purificação das tripsinas de insetos de diferentes ordens e o estudo da especificidade de seus subsítios utilizando substratos de fluorescência apagada servem de base para a seleção de um método mais eficiente de inibição da sua atividade, assim como para desvendar as tendências evolutivas da especificidade destas enzimas. O trabalho dessa dissertação levou ao desenvolvimento de processos de purificação das tripsinas de Periplaneta americana, Tenebrio molitor, Musca domestica e Diatraea saccharalis. O estudo da especificidade dos subsítios S1, S2, S3 e S1\' das tripsinas demonstraram que, diferentemente das tripsinas dos outros insetos e das tripsinas de mamíferos, a tripsina de Diatraea saccharalis hidrolisa com maior eficiência substratos que apresentem lisina em P1, demonstrando uma diferença na especificidade primária desta enzima. Além disso, é possível verificar ao longo da evolução dos grupos de insetos estudados uma tendência a tornar os subsítios cada vez mais hidrofóbicos. / Trypsins are serine endopeptidases that hydrolyze peptide bonds at the carboxyl side of positively charged residues: arginine and lysine. Mammalian trypsin preferentially cleaves the peptide bond formed by arginine. Site directed mutagenesis has shown that trypsin specificity is related to residues present at the primary specificity site and to structural determinants like two surface loops. Differences in trypsins specificity may be the cause of some insects be resistant to serine endopeptidases plant inhibitors and to Bacillus thuringiensis toxins. Trypsins are usual enzymes in insects and are very important to protein digestion. There are few studies dealing with insect trypsin specificity. They generally consist in analyses of fragments formed by the action of the enzyme on peptide chains like insulin β chain. As these studies were semi-quantitative, insect trypsin specificity requires a better characterization. This dissertation describes the purification of trypsins from Periplaneta americana, Tenebrio molitor, Musca domestica and Diatraea saccharalis and the characterization of the specificity of the subsites S1, S2, S3 e S1\' by the use of quenched fluorescence peptide substrates. The results showed that trypsins from the mentioned insects have different specificities, including the primary specificity. Thus, Diatraea saccharalis trypsin cleaves at Lys more efficiently than at Arg, whereas the eontrary is true for the other insects. The data also showed that trypsin subsites tend to beeome more hydrophobic as the insects are more evolved.

Tripsinas e quimotripsinas são classes de serina peptidases amplamente estudadas e fortemente responsáveis pela digestão proteica, pela clivagem de ligações peptídicas no lado carboxila de L-aminoácidos de cadeia lateral básica e hidrofóbica, respectivamente. Três processos regulam finamente a ação dessas peptidases: secreção, ativação do precursor (zimogênio) e o sítio de reconhecimento do substrato. No presente trabalho é apresentada uma análise filogenética detalhada das tripsinas e quimotripsinas de três ordens de insetos holometábolos, revelando características divergentes nas enzimas de Lepidóptera em relação a Coleóptera e Díptera. Em particular, o sub-sítio S1 das tripsinas foi observado como mais hidrofílico em Lepidóptera do que em Coleóptera e Díptera, enquanto os sub-sítios S2-S4 parecem mais hidrofóbicos, sugerindo diferente preferências pelo substrato. Além disso, Lepidóptera mostrou um grupo de tripsinas bastante específico a um grupo taxonômico, compreendendo somente proteínas de espécies da família Noctuidae. Evidências de eventos de auto-ativação facilitada foram também observadas em todas as ordens de insetos estudadas, com as características do motivo de ativação do zimogênio complementárias ao sítio ativo das tripsinas. Em contraste, as quimotripsinas de insetos não parecem ter uma história evolutiva peculiar com respeito a, por exemplo, seus homólogos em mamíferos. Em geral, os presentes resultados sugerem que a necessidade de uma rápida taxa de autoativação fez os insetos holometábolos selecionarem grupos especializados de tripsinas com altas taxas de auto-ativação e também destacam que a evolução das tripsinas culminou em um grupo especializado de enzimas em Lepidóptera. / Trypsins and chymotrypsins are well-studied classes of serine peptidases largely responsible for the digestion of proteins by cleavage of the peptide bond at the carboxyl side of basic and hydrophobic L-amino acids, respectively. Three processes mainly regulate the action of these peptidases: secretion, precursor (zymogen) activation and substrate-binding site recognition. In the present work is presented a detailed phylogenetic analysis of trypsins and chymotrypsins in three orders of holometabolous insects revealing divergent characteristics in the Lepidoptera enzymes in relation to Coleoptera and Diptera. In particular, trypsin subsite S1 was observed to be more hydrophilic in Lepidoptera than in Coleoptera and Diptera, whereas subsites S2-S4 appeared more hydrophobic, suggesting different substrate preferences. Furthermore, Lepidoptera displayed a very specific taxonomic trypsin group, only encompassing proteins from the Noctuidae family. Evidences for facilitated trypsin auto-activation events were also observed in all the insect orders at hand, with the characteristic zymogen activation motif complementary to the trypsin active site. In contrast, insect chymotrypsins did not seem to have a peculiar evolutionary history with respect to e.g. their mammal counterparts. Overall, the present findings suggest that the need for fast digestion made holometabolous insects evolve specialized groups of trypsins with high autoactivation rates and highlight that the evolution of trypsins culminated in a specialized group of enzymes in Lepidoptera.

by Ricardo Wong Chi Ho. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2000. / Includes bibliographical references (leaves 128-138). / Abstracts in English and Chinese. / Acknowledgments --- p.i / Abstract --- p.ii / 論文摘要 --- p.iv / Table of Contents --- p.vi / List of Figures --- p.xi / List of Tables --- p.xiii / List of Abbreviations --- p.xiv / Chapter Chapter 1 --- Introduction --- p.1 / Chapter 1.1 --- Overview of Serine Protease Inhibitors --- p.1 / Chapter 1.2 --- Classification of Serine Protease Inhibitors --- p.2 / Chapter 1.2.1 --- Kunitz Type Serine Protease Inhibitors --- p.7 / Chapter 1.2.2 --- Bowman-Birk Type Serine Protease Inhibitors --- p.11 / Chapter 1.2.3 --- Squash Type Serine Protease Inhibitors --- p.16 / Chapter 1.3 --- Role of Serine Protease Inhibitors in Plants --- p.20 / Chapter 1.4 --- Nutritional Fact of Serine Protease Inhibitors --- p.22 / Chapter 1.5 --- Possible Applications of Serine Protease Inhibitors --- p.25 / Chapter 1.5.1 --- Medical Applications --- p.25 / Chapter 1.5.2 --- Agricultural Applications --- p.29 / Chapter 1.6 --- Rationale of the Present Study --- p.31 / Chapter Chapter 2 --- Screening of Seeds for Inhibitory Activities Against Serine Proteases --- p.33 / Chapter 2.1 --- Introduction --- p.33 / Chapter 2.2 --- Materials and Methods --- p.37 / Chapter 2.2.1 --- Materials --- p.37 / Chapter 2.2.2 --- Extraction Method --- p.37 / Chapter 2.2.3 --- Assays for Proteases Inhibitory Activities --- p.38 / Chapter 2.2.3.1 --- Assay for Chymotrypsin Activity --- p.38 / Chapter 2.2.3.2 --- Assay for Trypsin Activity --- p.38 / Chapter 2.2.3.3 --- Assay for Elastase Activity --- p.39 / Chapter 2.2.3.4 --- Assay for Subtilisin Activity --- p.39 / Chapter 2.2.3.5 --- Assays for Protease Inhibitory Activities --- p.40 / Chapter 2.2.4 --- Determination of Protein Concentration --- p.41 / Chapter 2.3 --- Results --- p.42 / Chapter 2.3.1 --- Extraction --- p.42 / Chapter 2.3.2 --- Serine Proteases Inhibitory Activities --- p.42 / Chapter 2.4 --- Discussion --- p.47 / Chapter Chapter 3 --- Isolation of Chymotrypsin Inhibitor and Trypsin Inhibitors from Momordica cochinchinensis Seeds --- p.49 / Chapter 3.1 --- Introduction --- p.49 / Chapter 3.2 --- Materials and Methods --- p.56 / Chapter 3.2.1 --- Materials --- p.56 / Chapter 3.2.2 --- Protein Extraction --- p.57 / Chapter 3.2.3 --- SP-Sepharose Chromatography --- p.57 / Chapter 3.2.4 --- Reversed Phase High Pressure Liquid Chromatography --- p.58 / Chapter 3.2.5 --- Assays for Chymotrypsin and Trypsin Inhibitory Activities --- p.60 / Chapter 3.2.6 --- Titration of Chymotrypsin --- p.61 / Chapter 3.2.7 --- Tricine Sodium Dodecyl Sulfate Polyacrylamide Gel Electrophoresis --- p.62 / Chapter 3.2.8 --- Coupling of Trypsin-Sepharose 4B Affinity Column --- p.63 / Chapter 3.2.9 --- Affinity Chromatography on Trypsin-Sepharose 4B --- p.64 / Chapter 3.3 --- Results --- p.65 / Chapter 3.3.1 --- SP-Sepharose Chromatography --- p.65 / Chapter 3.3.2 --- Reversed Phase High Pressure Liquid Chromatography --- p.67 / Chapter 3.3.3 --- Summary of Purification --- p.71 / Chapter 3.3.4 --- Titration of Chymotrypsin --- p.74 / Chapter 3.3.5 --- Tricine Sodium Dodecyl Sulfate Polyacrylamide Gel Electrophoresis --- p.74 / Chapter 3.3.6 --- Affinity Chromatography on Trypsin-Sepharose 4B --- p.78 / Chapter 3.4 --- Discussion --- p.81 / Chapter Chapter 4 --- Characterization of Chymotrypsin Inhibitor and Trypsin Inhibitors --- p.88 / Chapter 4.1 --- Introduction --- p.88 / Chapter 4.2 --- Materials and Methods --- p.90 / Chapter 4.2.1 --- Materials --- p.90 / Chapter 4.2.2 --- Determination of Molecular Weight --- p.90 / Chapter 4.2.3 --- Amino Acid Sequence Analysis --- p.91 / Chapter 4.2.4 --- Surface Plasmon Resonance Measurement --- p.92 / Chapter 4.2.4.1 --- Immobilization of Ligands on the Surface of Optical Biosensors --- p.92 / Chapter 4.2.4.2 --- Determination of Kinetics Constants --- p.93 / Chapter 4.2.4.3 --- pH Dependence of the Inhibition by Chymotrypsin Inhibitor --- p.93 / Chapter 4.2.4.4 --- Data Analysis --- p.94 / Chapter 4.2.5 --- Effect of Chymotrypsin Inhibitor on the Estereolytic Activity and Proteolytic Activity of Chymotrypsin --- p.95 / Chapter 4.2.6 --- Specificities of the Inhibitors % --- p.96 / Chapter 4.2.7 --- Binding Ratio of CI to Different Proteases --- p.97 / Chapter 4.2.8 --- Effects of the Proteases on Their Corresponding Inhibitors --- p.97 / Chapter 4.2.8.1 --- Tricine Sodium Dodecyl Sulfate Polyacrylamide Gel Electrophoresis --- p.97 / Chapter 4.2.8.2 --- Assay for Chymotrypsin Inhibitory Activity --- p.98 / Chapter 4.3 --- Results --- p.99 / Chapter 4.3.1 --- Molecular Weight of the Inhibitors --- p.99 / Chapter 4.3.2 --- N-terminal Amino Acid Sequence --- p.99 / Chapter 4.3.3 --- Surface Plasmon Resonance Measurement --- p.102 / Chapter 4.3.3.1 --- Kinetics of Chymotrypsin Inhibitor --- p.102 / Chapter 4.3.3.2 --- Kinetics of Trypsin Inhibitors --- p.106 / Chapter 4.3.3.3 --- pH Dependence of the Inhibition by Chymotrypsin Inhibitor --- p.106 / Chapter 4.3.4 --- Effect of Chymotrypsin Inhibitor on the Estereolytic Activity and Proteolytic Activity of Chymotrypsin --- p.106 / Chapter 4.3.5 --- Specificities of the Inhibitors --- p.110 / Chapter 4.3.6 --- Binding Ratio of CI to Different Proteases --- p.112 / Chapter 4.3.7 --- Effects of the Proteases on Their Corresponding Inhibitors --- p.112 / Chapter 4.4 --- Discussion --- p.119 / Chapter Chapter 5 --- Conclusion --- p.125 / References --- p.128

Submitted by Sara Ribeiro (sara.ribeiro@ucb.br) on 2018-04-10T13:05:43Z No. of bitstreams: 1 FabioCorreiaCarneiroDissertacao2018.pdf: 2306587 bytes, checksum: ed2572dbb41a30ee1c54682a411c833d (MD5) / Approved for entry into archive by Sara Ribeiro (sara.ribeiro@ucb.br) on 2018-04-10T13:06:06Z (GMT) No. of bitstreams: 1 FabioCorreiaCarneiroDissertacao2018.pdf: 2306587 bytes, checksum: ed2572dbb41a30ee1c54682a411c833d (MD5) / Made available in DSpace on 2018-04-10T13:06:06Z (GMT). No. of bitstreams: 1 FabioCorreiaCarneiroDissertacao2018.pdf: 2306587 bytes, checksum: ed2572dbb41a30ee1c54682a411c833d (MD5) Previous issue date: 2018-02-20 / Protease inhibitors have a broad biotechnological application, which goes since the development of several drugs to your utilization as a bioinsecticide, antifungal and as an antibacterial agent. However, those are found in small quantities in their natural sources, which unfeasible it utilization in industrial scale. Therefore, the heterologous production ends up as a method that allows the increase of scale production of those proteins. The Inga laurina Trypsin Inhibitor (ILTI) previously characterized showed an inhibitory effect in proteases extracted from the midgut of insects, besides reducing its larval developments by up to 84%, therefore, boing a candidate to be used as a potential bioinsecticide. Thus, the present work aimed at the heterologous production of ILTI in Komagataella phaffii (Pichia pastoris), followed by the optimization of the culture modes in a bioreactor with the objective of maximizing the production of the recombinant protein. For this, the gene that codifies ILTI were cloned in the expression vector pPIC9K, followed by your insertion on the strain GS115 by electroporation. PCR analysis showed that the recombinant vector was integrated into the genome of the yeast, and all the clones obtained had MutS genotype. The expression was performed for 96 hours by adding 0.5% methanol. An analysis of the proteins on the supernatant of the recombinant strain culture, by SDS-PAGE, confirmed the production of a protein with a size close to 20 KDa. Data from MALDI-TOF confirmed that the obtained protein is, in fact, the recombinant ILTI. Furthermore, inhibitory assays showed that the produced protein had activity against trypsin. Thus, culture in bioreactors was performed to optimize the production of this heterologous protein. In order to increase its expression, fed-batch was performed where on the batch phase the biomass production was favored, and the feeding phase was programmed to continuously supply methanol, based on the methanol specific consumption and its specific growth velocity, using methanol as carbon source. During the fermentations, 351.27 UIT were obtained in the extract of crude fermentation broth, and a specific activity of 2.07 UIT/mg protein. Although widely used as a host for the production of heterologous proteins, studies of the production of protease inhibitors in K. phaffii are still very limited. Until the moment, there is no report in the optimization of the production of serine protease inhibitors in K. phaffii, making this study pioneering and essential for the beginning of scaling up the process of this technology. / Os inibidores de protease possuem uma ampla aplica????o biotecnol??gica que vai desde o desenvolvimento de diversos f??rmacos at?? sua utiliza????o como bioinseticidas, antif??ngicos e como agentes antibacterianos. Por??m, estes s??o encontrados em pequenas quantidades nas suas fontes naturais, o que inviabiliza sua utiliza????o em escala industrial. Sendo assim, a produ????o heter??loga acaba sendo um m??todo que permite o aumento da escala de produ????o dessas prote??nas. O inibidor de tripsina de Inga laurina (ILTI) foi caracterizado previamente e mostrou possuir efeito inibit??rio em proteases extra??das do trato digestivo de insetos, al??m de diminuir em at?? 84% seu desenvolvimento larval, sendo, portanto, um candidato a ser utilizado como um poss??vel bioinseticida. Dessa forma, o presente trabalho teve como objetivo a produ????o heter??loga do inibidor ILTI, em Komagataella phaffii (Pichia pastoris), seguido da otimiza????o dos modos de cultivo em biorreator com o objetivo de maximizar a produ????o da prote??na recombinante. Para isso, o gene que codifica o ILTI foi clonado no vetor de express??o pPIC9K seguindo de sua inser????o na cepa GS115 por eletropora????o. An??lises de PCR mostraram que o vetor recombinante foi integrado ao genoma da levedura e que todos os clones obtidos possu??am gen??tipo MutS. A indu????o da express??o foi realizada durante 96 horas por meio da adi????o de metanol ?? 0,5%. A an??lise de prote??nas presentes no sobrenadante da cultura da cepa recombinante, por meio de SDS-PAGE, confirmou a produ????o de uma prote??na com tamanho pr??ximo a 20 KDa. Dados obtidos em MALDI-TOF confirmaram que a prote??na obtida ?? de fato ILTI recombinante. Al??m disso, ensaios inibit??rios mostraram que a prote??na produzida possui atividade contra tripsina. Dessa forma, cultivo em biorreatores foram realizados com a finalidade de otimizar a produ????o dessa prote??na heter??loga. A fim de aumentar sua express??o foram realizadas bateladas alimentadas, onde durante a fase de batelada foi favorecida a produ????o de biomassa, e a fase de alimenta????o programada para fornecer metanol de forma cont??nua, com base nos dados de velocidade espec??fica de consumo de metanol e velocidade de crescimento espec??fica nesta fonte de carbono. Ao longo das fermenta????es realizadas foi obtido 351,27 UIT no extrato bruto do caldo fermentado e uma atividade espec??fica de 2,07 UIT/mg de prote??na. Apesar de ser amplamente utilizada como hospedeira para a produ????o de prote??nas heter??logas, estudos da produ????o de inibidores em K. phaffii ainda s??o muito limitados. At?? o momento n??o existem relatos de otimiza????o da produ????o de inibidores de serinoproteases em K. phaffii, sendo esse estudo pioneiro e essencial para o in??cio do processo de escalonamento dessa tecnologia.

Serina endopeptidases de insetos, principalmente tripsinas e quimotripsinas, estão envolvidas na digestão inicial de proteínas. Genes codificadores para estas enzimas estão organizados em famílias multigênicas tendo expressão diferencial de acordo com a dieta do inseto, estando envolvidos no desenvolvimento de resistência a diferentes metabólitos secundários vegetais. Para uma melhor compreensão desta interação, fez-se necessário o isolamento destas enzimas para insetos de diferentes ordens, bem como a caracterização de suas especificidades por duas abordagens: (a) caracterização cinética dos subsítios componentes do sítio de ligação de tripsinas e quimotripsinas, utilizando diferentes substratos, modificadores químicos e inibidores e (b) estudos estruturais por modelagem molecular, clonagem, expressão e cristalização destas enzimas de insetos. Além disso, estudos evolutivos por análise de distância possibilitaram uma caracterização inicial da interação insetoplanta. Estas determinações permitiram verificar que tripsinas de insetos apresentam diferenças de especificidade tanto dentre as diferentes ordens de insetos quanto em relação às tripsinas de vertebrados, sendo que as tripsinas da ordem Lepidóptera apresentam troca de especificidade primária hidrolisando preferencialmente substratos P1 Lys. Foram também observadas diferenças de hidrofobicidade para os subsítios caracterizados sendo que estes apresentam hidrofobicidades crescentes segundo o grau de complexidade dos insetos na sua escala evolutiva. A troca de especificidade e o aumento da hidrofobicidade podem permitir a hidrólise dos inibidores vegetais protéicos. A análise das sequências de tripsinas de insetos por Neighbor Joining (NJ) compõe uma árvore de distâncias topologicamente semelhante à árvore de relações filogenéticas determinadas por morfologia. A sobreposição de estruturas pré -determinadas de tripsina complexada a diferentes inibidores permite a identificação de posições de interação enzima-inibidor que justificam a classificação em grupos distintos de enzimas sensíveis ou resistentes a presença de inibidores na dieta de insetos. Da mesma forma: a caracterização da especificidade das quimotripsinas de insetos permitiu a separação de grupos distintos de quimotripsinas. Estes grupos são sustentados pela substituição do resíduo 59 em insetos polífagos que alimentam-se de plantas que contêm cetonas naturais reativas. Estas caracterizações demonstram a importância de um estudo detalhado da especificidade de serina endopeptidases possibilitando o desenho de moléculas apropriadas para inibição destas e desenvolvimento de estratégias de controle de insetos. / Insect serine endopeptidases, mairily trypsin and chymotrypsin are involved in initial protein digestion. Genes that encode these proteins are members of complex multigene families and are differentially expressed according to insects diet , thus being involved with resistance to plant metabolites. Purification of trypsins from different insect orders and chymotrypsins, as well as, characterization of their specificity are essential to a better understanding of this interaction. Characterization relied on two approaches: (a) kinetic characterization of the binding subsities of trypsins and chymotrypsins using different substrates, chemical modification and inhibition assays and (b) study of protein structure by molecular modelling and cloning, expression and crystallization of these enzymes. Besides that, evolutionary studies performed through distance analysis, permitted the investigation of plantinsect interaction. These characterizations showed that insect trypsins, in terms of specificity, are quite different from vertebrate trypsins and among insect orders. Lepidopterans trypsins have a distinct primary specificity, since they hydrolyses preferentially P1 Lys substrates, and present a crescent subsite hydrophobicity, which is directly correlated with the evolutionary scale. Both, the specificity exchange and the crescent hydrophobicity can allow the hydrolysis of vegetal proteic inhibitors. The analysis of trypsin sequences in Neighbor-Joining (NJ) algorithm yield a distance tree that is coherent with morphological phylogenetic relationships. The superposition of predicted structures of trypsins-inhibitors complexes permits to observe amino acid residues of interaction between enzyme-inhibitor, which support the distinction of different groups between sensitive and insensitive trypsins to the presence of inhibitors on insect diet. Similarly, characterization of insect chymotrypsins according to their specificity allowed us to classify these enzymes into different groups. These groups are supported by residue 59 replacements in polyphagous insects, which feed on plants bearing natural reactive ketones. These studies show the irnportance of a detailed study of serine endopeptidases, which may help in the development of better insect control strategies.

Submitted by (edna.saturno@ufrpe.br) on 2017-02-14T14:46:32Z No. of bitstreams: 1 Janilson Felix da Silva.pdf: 986185 bytes, checksum: 050d633ae1f790751916afcd3c6fb9bb (MD5) / Made available in DSpace on 2017-02-14T14:46:32Z (GMT). No. of bitstreams: 1 Janilson Felix da Silva.pdf: 986185 bytes, checksum: 050d633ae1f790751916afcd3c6fb9bb (MD5) Previous issue date: 2009-08-03 / The silver mojarra (Diapterus rhombeus) is specie of relevant representation among the fishing community in northeastern Brazil. Also in this region, the fishing is the most representative records despite growing carapeba in extensive systems. Among the parts of the fish are not consumed are the viscera which represent 5% of the total weight of the animals. Thus, to be discarded without treatment, these wastes pose serious environmental problem. However, because they are rich in digestive enzymes, viable for use in certain biotechnological processes these viscera represent an important alternative source of industrial enzymes. Based on this information, the purpose of this study was to purify and characterize an alkaline protease from the viscera of D. rhombeus. Therefore, viscera silver mojarra were used to obtain a crude extract and thereafter used for enzyme purification. The purification process was carried out in three steps: heat treatment (45°C for 30 minutes), precipitation with ammonium sulfate and molecular exclusion chromatography (Sephadex G-75). At the end of the purification process, achieved an increase of 86.80-fold in the specific activity and a yield of 22.34%. An aliquot of purified extract was applied to gel electrophoresis (SDS-PAGE) and its molecular weight was estimated at 24.5 kDa. The optimum pH and optimum temperature for enzyme activity were 8.5 and 55°C, respectively. The enzyme was shown to be sensitive to temperatures above 45°C, after incubation for 30 min, losing 100% of its activity. The values of Km and Kcat of the protease were 0.266 mM and 0.116 mM-1 s-1, respectively, using benzoyl-DL-arginine-p-nitroanilide (BAPNA) as substrate. Its activity was increased in the presence of ions K+, Li+, Ca2+, Mn2+ and Ba2+ ions and inhibited by Fe2+, Cd2+, Cu2+, Al3+, Hg2+, Zn2+ and Pb2+. Tests with protease inhibitors showed that the enzyme was strongly inhibited by TLCK and benzamidine, classic inhibitors of trypsin. The sequence of the first 15 amino acid N-terminal protease was IVGGYECTMHSEAHE and showed high homology with trypsins of various species of fish. The data show that the purified enzyme is one trypsin-like with characteristics compatible to be used in the biotechnology industry. / A Carapeba prateada (Diapterus rhombeus) é uma espécie de relevante representatividade dentre a comunidade pesqueira da região nordeste do Brasil. Ainda nessa região, a pesca artesanal é a mais representativa apesar de registros de cultivo da carapeba em sistemas extensivos. Dentre as partes do peixe não consumidas encontramse as vísceras que correspondem a 5% do peso total dos animais. Desta forma, ao serem descartadas, sem tratamento, esses resíduos representam grave problema ambiental. Entretanto, por serem ricas em enzimas digestivas, viáveis para utilização em determinados processos biotecnológicos essas vísceras representam uma importante fonte alternativa de enzimas industriais. Visando essas informações, o objetivo do presente trabalho foi purificar e caracterizar uma protease alcalina das vísceras de D. rhombeus. Para tanto, vísceras de carapeba prateada foram utilizadas para obtenção de um extrato bruto posteriormente utilizado para purificação enzimática. O processo de purificação foi realizado em três etapas: tratamento térmico (45oC por 30min), precipitação com sulfato de amônio e cromatografia de exclusão molecular (Sephadex G-75). Ao final do processo de purificação obteve-se um incremento de 86,80 vezes na atividade específica e um rendimento de 22,34%. Uma alíquota do extrato purificado foi aplicada em gel de poliacrilamida (SDS-PAGE) e o seu peso foi estimado em 24,5 kDa. O pH ótimo e a temperatura ótima para a atividade enzimática foram 8,5 e 55 °C, respectivamente. A enzima demonstrou ser sensível a temperaturas superiores a 45 ºC, após incubação por 30 min, perdendo 100% de sua atividade. Os valores de Km e do Kcat da protease foram 0,266 mM e 0,116 s-1 μM -1, respectivamente, usando benzoil-DLarginina- p-nitroanilida (BAPNA) como substrato. Sua atividade foi aumentada na presença dos íons K+, Li+, Ca2+, Mn2+ e Ba2+ e inibidas pelos íons Fe2+, Cd2+, Cu2+, Al3+, Hg2+, Zn2+ e Pb2+. Testes com inibidores de proteases mostraram que a enzima foi fortemente inibida por TLCK e benzamidina, inibidores clássicos de tripsina. A sequência dos 15 primeiros aminoácidos do N-terminal da protease foi IVGGYECTMHSEAHE e mostrou alta homologia com tripsinas de diversas espécies de peixes. Os dados obtidos demonstram que enzima purificada é uma tripsina com características compatíveis para ser empregada na indústria biotecnológica.

CoordenaÃÃo de AperfeiÃoamento de NÃvel Superior / Cinco inibidores de tripsina da famÃlia Kunitz (JB1, JB2, JB3-1, JB3-2 e JB4) foram purificados de sementes de Pithecellobium dumosum, uma Ãrvore da subfamÃlia Mimosoideae, por precipitaÃÃo com Ãcido tricloroÃcetico (TCA), cromatografia de afinidade sobre tripsina imobilizada em Sepharose e coluna de fase reversa em sistema de CLAE. Os cinco inibidores possuem massa molecular entre 18 e 20 kDa formados por uma cadeia polipeptÃdica como determinado por SDS-PAGE na presenÃa ou ausÃncia de -mercaptoetanol. JB1, JB3-1 e JB3-2 tÃm massas moleculares de 19,70, 19,69 e 19,69 kDa, respectivamente, por MALDI-TOF. JB2 e JB4 tÃm massa molecular de 18,08 e 20,85 kDa, respectivamente. A seqÃÃncia N-terminal de JB1, JB3-1 e JB3-2 mostrou identidade com outros inibidores da famÃlia Kunitz. Os cinco inibidores foram estÃveis Ãs variaÃÃes de temperatura e pH. A inibiÃÃo da tripsina por JB1, JB2 e JB4 foi do tipo competitivo. JB1, JB2, JB3-1 e JB3-2 tiveram Kis de 3,56 x 10-8 M, 1,65 x 10-8 M, 4,20 x10-8 M, 2,88 x 10-8 M, respectivamente para a tripsina bovina. Em comparaÃÃo com os outros inibidores JB4, com Ki de 5,70 x 10-10 M, apresentou maior afinidade para tripsina. Entre os inibidores purificados apenas JB4 inibiu moderadamente a atividade da quimotripsina. A atividade da elastase e bromelaÃna nÃo foi inibida efetivamente por esses inibidores. A inibiÃÃo de JB1, JB2, JB3-1 e JB3-2 sobre a papaÃna variaram entre 32,93 a 48,82% e foi indicativo de sua bifuncionalidade, com exceÃÃo de JB4 que inibiu fracamente essa atividade (9,93% de inibiÃÃo). A inibiÃÃo da papaÃna por JB1 e JB2 foi do tipo nÃo competitiva e os valores de Ki foram de 7,6 x 10-7 e 5,1 x 10-7 M, respectivamente. Ensaios in vitro sobre as proteinases digestÃrias de Lepidoptera, Diptera e Coleoptera foram feitos. Esses inibidores foram efetivos para enzimas digestÃrias semelhantes à tripsina desses insetos em diferentes graus. As enzimas digestivas de Zabrotes subfasciatus e Ceratitis capitata foram inibidas por JB1 em 68,87 e 65,53%, respectivamente, e as enzimas de Callosobruchus maculatus, Alabama argillaceae e Plodia interpunctella foram inibidas entre 29,18 e 44,35%. Enzimas digestÃrias de Z. subfasciatus, C. maculatus e C. capitata foram inibidas por JB2 entre 70,04 e 74,54% e as enzimas de larvas de A argillaceae e P. interpunctella foram suprimidas em 13,58 e 48,67%, respectivamente. A atividade semelhante à tripsina de larvas de Z. subfasciatus foi suprimida em 67,33 e 56,93% por JB3-1 e JB3-2, respectivamente, e a atividade de C. maculatus, A argillaceae, P. interpunctella e C. capitata foram suprimidas por esses inibidores entre 5,17 e 49,00%. JB4 inibiu entre 54,53 a 66,15 % as enzimas digestivas de C. maculatus, Z. subfasciatus e A argillaceae e inibiu as enzimas digestivas de larvas de P. intepunctella e C. capitata em 8,97 e 37,47%, respectivamente. A inibiÃÃo de proteinases semelhantes à tripsina e à papaÃna presentes no intestino de vÃrios insetos sugere que esses inibidores possam afetar o crescimento e sobrevivÃncia desses insetos pragas quando incorporados em sementes artificiais e esta bifuncionalidade à indicativo de que estes inibidores possam ser fortes candidatos para os programas de melhoramento de plantas via transgenia. / Five Kunitz-type trypsin inhibitors (JB1, JB2, JB3-1, JB3-2 and JB4) were purified from Pithecellobium dumosum seeds, a tree of the sub-family Mimosoideae, by TCA precipitation, affinity chromatography on immobilized trypsin-Sepharose and reverse phase HPLC using Vydac C-18 column. The five inhibitors had Mr between 18 and 20 kDa with a single polypeptide chain as determined by SDS-PAGE with and without reduction. JB1, JB3-1 and JB3-2 had Mr of 19.70, 19.69 and 19.69 kDa, respectively, by MALDI-TOF. JB2 and JB4 had Mr of 18.08 and 20.85, respectively, by SDS-PAGE. The N-terminal sequences of JB1, JB3-1 and JB3-2 showed identity with others Kunitz-type inhibitors. The five inhibitors were stable over a wide range of temperature and pH. The inhibition of trypsin by JB1, JB2 and JB4 was competitive. JB1, JB2, JB3-1 and JB3-2 showed Ki values of 3.56 x 10-8 M, 1.65 x 10-8 M, 4.20 x 10-8 M, 2.88 x 10-8 M, respectively, against bovine trypsin. In comparison with others inhibitors JB4, with Ki of 5.70 x 10-10 M, showed a high affinity toward trypsin. Among the inhibitors purified only JB4 inhibited chymotrypsin activity. The activities of elastase and bromelain were not inhibited for these inhibitors. The inhibition of JB1, JB2, JB3-1 and JB3-2 on papain varied between 32.93 to 48.82% of inhibition and was indicative of its bifunctionality with exception of JB4 that inhibited this activity in 9.9%. The papain inhibition by JB1 and JB2 were noncompetitive type and the Kivalues were 7.6 x 10-7 and 5.1 x 10-7 M, respectively. In vitro assays against digestive proteinases from Lepidoptera, Diptera and Coleoptera pests were carried out. These inhibitors were effective towards trypsin-like digestive enzymes of the insect in different degrees. The digestive enzymes from Zabrotes subfasciatus and Ceratitis capitata were inhibited by JB1 in 68.87 and 65.53% respectively, and Callosobruchus maculatus, Alabama argillaceae and Plodia intepunctella enzymes were inhibited in the range of 29.18 to 44.35%. Digestive enzymes from Z. subfasciatus, C. maculatus and C. capitata were inhibited by JB2 in the range of 70.04 to 74.54%, and the enzymes of A. argillaceae and P. intepunctella were suppressed in 13.58 and 48.67%, respectively. Trypsin-like activities of larval from Z. subfasciatus were suppressed in 67.33 and 56.93% by JB3-1 and JB3-2, respectively, and the activities of C. maculatus, A. argillaceae, P. intepunctella and C. capitata were inhibited by these inhibitors in the range of 5.17-49.00%. JB4 inhibited around 54.53 to 66.15% the digestive enzymes of C. maculatus, Z. subfasciatus and A. argillaceae and the digestive enzymes from P. intepunctella and C. capitata larvae in 8.97% and 37.47%, respectively. The inhibition of trypsin-like and papain-like proteinases of several insects suggested that these inhibitors may affect the growth and survival of these insect pests when incorporated into artificial diet and their bifunctionality are indicative that these inhibitors could be strong candidates to plant management programs cross transgenia.

Tripsinas e quimotripsinas, enzimas pertencentes à classe das serina proteinases, são as principais enzimas proteolíticas digestivas presentes no intestino médio de insetos de diversas ordens. Entretanto, enzimas de diferentes insetos possuem propriedades cinéticas distintas, sendo os motivos dessas diferenças especulados. Precipitações por sulfato de amônio das tripsinas de Tenebrio molitor, Diatraea saccharalis e Spodoptera frugiperda mostram que insetos Lepidópteros possuem serina proteinases mais hidrofóbicas, que foi confirmado através de cromatografias de interação hidrofóbica e da análise de acesso do solvente às superfícies protéicas em modelagens tridimensionais de seqüências. Tal fato está relacionado à formação de oligômeros e resistência a defesas de plantas. Inativações por TPCK mostram que quimotripsinas digestivas de S. frugiperda, inseto polífago, reagem duas ordens de grandeza mais lentamente e possui um deslocamento do pH ótimo de modificação em mais de uma unidade quando comparada com dos outros dois organismos, fato relacionado à resistência a cetonas presentes em diversas plantas. A tripsina digestiva de Periplaneta americana foi purificada e microsseqüenciada, resultando na seqüência VSPAFSYGTG e associada a um alérgeno (denominado PaTry), expresso nos cecos e na região anterior do ventrículo. O anticorpo anti-tripsina de M. domestica reconheceu apenas uma banda no intestino de P. americana e foi utilizado para imunocitolocalizar tripsinas nos tecidos epiteliais, demonstrando que esta é secretada por exocitose nos cecos e na região anterior do ventrículo, como esperado. Por último, a atividade majoritária de quimotripsina se localiza surpreendentemente na região posterior do ventrículo de M. domestica. Apesar disso, apenas 28% dessa atividade é perdida através das fezes, pois 31% da atividade enzimática se encontra firmemente aderida à membrana, e 41% na fração celular solúvel (associada ao glicocálice), sendo a atividade solúvel luminal correspondente a apenas 12%, indicando a existência de pelo menos duas espécies moleculares distintas, uma solúvel e uma aderida à membrana, comprovado inativações térmicas das duas atividades (solúvel e aderida à membrana) na presença e na ausência de Triton X-100, sendo que a atividade aderida à membrana apresentou uma maior meia vida com uma cinética de primeira ordem nos dois casos. Ensaio em gel demonstrou que o homogeneizado possui apenas uma banda de atividade quimotríptica de 30 kDa. A atividade solúvel majoritária foi purificada até a homogeneidade, apresentando uma banda de 30 kDa em SDS-PAGE, pH ótimo de 7,4 e é 90% inativada por TPCK 0,1 mM em pH 8,5 em 15 min. Ela prefere substratos contendo Phe em P1, apesar clivar substratos contendo Tyr e Leu. Uma seqüência contígua similar a quimotripsina foi obtida a partir de uma biblioteca de cDNA de intestino médio de M. domestica, formada por 71 ESTs (de 826 seqüências obtidas ao acaso), indicando que esta deve corresponder à atividade majoritária. Essa seqüência, denominada MdChy1, prediz uma proteína madura de 28.639,2 Da e foi clonada e expressa de maneira recombinante em E. coli BL21 (DE-3) Star, sendo utilizada para produção de anticorpos policlonais em coelhos, que reconheceram uma banda de 30 kDa no ventrículo anterior e posterior, mas não no médio. Esses anticorpos foram utilizados para imunomarcações e reconheceram proteínas no lúmem, nas microvilosidades e em pequenas vesículas do epitélio, demonstrando que a quimotripsina é secretada ao lúmem por exocitose e indicando que o MdChy1 corresponde à atividade majoritária de quimotripsina. Análises de expressão em M. domestica indicam a existência de dois conjuntos de serina proteinases digestivas, um expresso na região anterior e um segundo na região posterior do ventrículo. O MdChy1 é expresso na região posterior, local em que se encontra a atividade majoritária de quimotripsina. Uma reconstrução filogenética dos genes similares a quimotripsinas de Drosophila melanogaster e de M. domestica demonstram que a MdChy1 se agrupa com genes expressos no intestino médio, portanto, com função digestiva. / Trypsins and chymotrypsins, serine proteinases enzymes, are the major proteolytic activities present in the midgut of insects. However, enzymes obtained from different insects present different kinetic properties, and the reason for the differences are speculated. Trypsin precipitation of Tenebrio molitor, Diatraea saccharalis and Spodoptera frugiperda with ammonium sulfate showed that Lepidopteran insects possess serine proteinases with a higher superficial hydrophobicity than insects belonging to other orders, which may be associated to oligomerization of enzymes and resistance to inhibitors present in the food. This was confirmed by hydrophobic interaction chromatography and analysis of solvent access to serine proteinases surface. Moreover, inactivations of chymotrypsins by TPCK showed that S. frugiperda chymotrypsins react one order slower and has an optimum pH of modification more than 1 unit higher than chymotrypsins of D. saccharalis and T. molitor, which was related with the resistance of the enzyme to the presence of plant ketones, since S. frugiperda is a polyphagous organism. The digestive trypsin from Periplaneta americana midgut was purified microssequenced, resulting in the sequence VSPAFSYGTG, coincident to the MPA3 allergen (named PaTry), which is expressed in the caeca and anterior ventriculus. Western blot using M. domestica trypsin antisera recognized a single band, and immunohistochemical assays using this antisera showed that the P. americana trypsin is secreted by exocitosys in caeca and anterior ventriculus, which is coincident to the expression data. Although the major M. domestica chymotrypsin activity is present in the posterior ventriculus, only 28% of the activity is lost in feces, because 31% of activity is membrane-bound, and 41% is in the cellular soluble fraction (glycocalix-associated), and only 12% of total activity is soluble in the lumen, indicating the existence of at least two molecular species of chymotrypsins. Thermal inactivations of both activities (soluble and membrane-bound) showed that they may represent two different molecular enzymes, since the membrane-bound activity has a higher half-life than the soluble both in the presence and in the absence of Triton X-100. Both activities presented a linear first-order inactivation kinetic. In gel assays showed the presence of only one activity band in the midgut of 30 kDa. The major soluble activity was purified through one affinitychromatography, and active fractions presented a single 30 kDa band, a optimum pH of 7.4 and was 90% modified by TPCK 0.1 mM at pH 8.5 during 15 min. This enzyme preferentially cleaves substrates containing Phe residues in P1, although it cleaves substrates containing Tyr and Leu. A contig of a chymotrypsin-like sequence was randomly obtained from a cDNA library of M. domestica midguts from 71 ESTs (a total of 826 sequences), indicating that this sequence corresponds to the major activity present in the lumen. This sequence, named MdChy1, predicted a protein with 28639.2 Da which was cloned, recombinantly expressed in E. coli BL21 (DE-3) Star, this recombinant MdChy1 was used to raise polyclonal antibodies in rabbit. A western blot using this antisera recognised a single band in the anterior and posterior ventriculus, but not in the middle. Imunno-gold labeling of epithelium marked proteins in the lumen, at the microvilli and inside small vesicles, demonstrating that chymotrypsin is secreted through exocytosis in M. domestica and reinforcing that MdChy1 corresponds to the major chymotryptic activity found in the midgut. A semi-quantitative RT-PCR of M. domestica serine proteinase-like genes demonstrated that there are two set of genes, one expressed in the anterior and another in the posterior ventriculus, as visualized in western blot. MdChy1 is expressed in the posterior ventriculus, where the major chymotryptic activity is found. A phylogenetic reconstruction of Drosophila melanogaster chymotrypsin-like sequences and M. domestica chymotrypsins showed that MdChy1 branched with sequences expressed in midgut, thus coding proteins involved in digestion.

We used the GENECONV program, the Hsu et al. (2010) method and phylogenetic analyses to analyze the gene conversions which occurred in the growth hormone, folate receptor and trypsin gene families of six primate species. Significant positive correlations were found between sequence similarity and conversion length in all but the trypsin gene family. Converted regions, when compared to non-converted ones, also displayed a significantly higher GC-content in the growth hormone and folate receptor gene families. Finally, all detected gene conversions were found to be less frequent in conserved gene regions and towards functionally important genes. This suggests that purifying selection is eliminating all gene conversions having a negative functional impact.