Nos últimos anos tem se intensificado o uso de produtos com a finalidade de aumentar a produtividade na cultura da soja. Dentre estes estão os bioestimulantes que podem possuir em sua constituição extratos de algas, aminoácidos e hormônios. No entanto, pouco se sabe sobre o efeito isolado de cada um destes constituintes. Frente a isto, esta pesquisa teve por objetivos avaliar o efeito da aplicação de aminoácidos isolados em plantas de soja. Para isto, o trabalho foi dividido em três experimentos. No primeiro, foi realizada a aplicação via sementes de glutamato, cisteína, fenilalanina e glicina em doses variáveis. Essa etapa foi conduzida em sistema de canteiros e foi avaliada a emergência, índice de velocidade de emergência, acúmulo de massa de matéria seca, metabolismo antioxidante (enzimas superóxido dismutase - SOD, catalase - CAT, peroxidase - POD, teor de peróxido de hidrogênio - H2O2, prolina e peroxidação lipídica - PL) e produtividade. A partir da seleção das melhores doses obtidas na primeira etapa, foi realizado o segundo experimento, conduzido em casa de vegetação. As aplicações desse experimento foram realizadas no tratamento de semente, via foliar ou em ambas as épocas, além disso, foi realizada a aplicação de todos os aminoácidos em associação. Nesse experimento foram avaliados metabolismo antioxidante, enzimas de resistência (polifenoloxidase - PFO e fenilalanina amônia-liase - PAL), metabolismo do nitrogênio (enzimas nitrato redutase e urease, teor de NO3-, NH4+, N-Aa, ureídeos e N-Total), variáveis de crescimento de raíz, acúmulo de massa de matéria seca e produtividade. Já o experimento III foi realizado em campo, utilizando os mesmos tratamentos do experimento II. Foram avaliados o metabolismo antioxidante, enzimas de resistência, metabolismo do nitrogênio, massa de matéria seca e produtividade. Todos os experimentos foram conduzidos em delineamento em blocos casualizados com quatro repetições para cada tratamento. Todos os aminoácidos proporcionaram efeito positivo em diversas variáveis fisiológicas analisadas. O uso de glutamato, fenilalanina, cisteína e glicina de forma isolada repercutiram em melhores efeitos quando a aplicação é realizada somente no tratamento de sementes. A partir da aplicação desses aminoácidos ocorreu incremento da assimilação de nitrogênio e no acúmulo de massa de matéria seca, o que levou a maior produtividade dessas plantas. O maior efeito na produtividade foi observado por meio da aplicação de fenilalanina em todos os experimentos, quando comparados com os demais aminoácidos. Com relação ao metabolismo antioxidante o uso de cisteína no tratamento de sementes proporcionou aumento da atividade das enzimas SOD e PAL e redução da PL. O uso de fenilalanina no tratamento de sementes induz ao incremento da CAT e SOD e o glutamato induz o aumento de PAL e SOD. A utilização de todos os aminoácidos em associação somente foi eficiente na aplicação foliar, o que proporcionou maior desenvolvimento de raíz, maior assimilação de nitrogênio, acúmulo de massa de matéria seca e produtividade. Portanto, foi possível perceber que o glutamato, cisteína, fenilalanina e glicina apresentam importante papel de sinalização em plantas, pois pequenas doses já são suficientes para induzir ao incremento de parâmetros fisiológicos e, consequentemente aumentar a produtividade. / In recent years, the use of products to increase productivity in soybean has been intensified. Bio-stimulants can have in their constitution algae extracts, amino acids and hormones. However, little is known about the isolated effect of each of these constituents. Facing this problem, this research aimed to evaluate the effect of the application of single amino acids to soybeans. For this, the work was divided into three experiments. In the first, the application of amino acids was performed via glutamate, cysteine, phenylalanine and glycine to seeds. This stage was carried out on planting beds and the following variables were evaluated: emergency, emergency speed index, dry matter accumulation, antioxidant metabolism (superoxide dismutase - SOD, catalase - CAT, peroxidase - POD, hydrogen peroxide - H2O2 - content, proline and lipid peroxidation - PL) and productivity. From the selection of the best rates obtained in the first stage, the second experiment was carried out in a greenhouse. The applications of this experiment were performed as seed treatments, foliar application and both procedures; furthermore, the application of all amino acids in combination was also performed. In this experiment, the following variables were evaluated: antioxidant metabolism, resistance enzymes (polyphenol oxidase - PFO and phenylalanine ammonia lyase - PAL), nitrogen metabolism (nitrate reductase and urease, NO3- content, NH4+, N-Aa, ureide and N-Total), root growth, dry matter accumulation and productivity. The third experiment was carried out in the field using the same treatments of the second experiment. The following variables were evaluated: antioxidant metabolism, resistance enzymes, nitrogen metabolism, dry matter and productivity. All experiments were carried out in a randomized block design with four replications for each treatment. All amino acids provided positive effect on several physiological variables. The use of glutamate, phenylalanine, cysteine, and glycine alone lead to the best effect when the application was done only as seed treatment. From the application of these amino acids, the nitrogen assimilation was increased and the dry matter accumulation, which led to higher productivity of the plants. The greatest effect on productivity was observed by application of phenylalanine in all experiments, when compared with other amino acids. Regarding the antioxidant metabolism, cysteine use in seed treatment increased SOD and PAL activity and PL reduction. The phenylalanine use in seed treatment increased CAT and SOD activities and glutamate induced an increase of PAL and SOD activities. The use of all amino acids in association was only effective in foliar application, which provided further development of root, greater assimilation of nitrogen, dry matter accumulation and productivity. So, it was possible to conclude that glutamate, cysteine, phenylalanine and glycine have an important signaling role in plants, because small rates are enough to induce the increase of physiological parameters and consequently increase productivity.

M.Sc. / Proteinases are involved in many cellular reactions involving protein degradation, such as degradation of storage proteins and protein degradation during senescence processes. Their action can be inhibited by proteinase inhibitors. Information is still limited about the regulation of these inhibitors in plants and their possible interaction with proteinases under stress conditions. To obtain a better understanding of the physiological role of a proteinase inhibitor in plants under stress, the expression of a papaya cysteine proteinase inhibitor (cystatin) and its relation to proteinase expression was investigated in more detail. For this purpose, expression of the inhibitor was studied in papaya plants exposed to different physiological stress conditions, such as high/low temperature, and treatment with selected chemicals, such as glutathione, OTC (L-2- Oxothiazolidine-4-carboxylate), bestatin ([(2S, 3R)-3-amino-2-hydroxy-4-phenyl butanoylj-L-leu) and 2.4-D (2,4-dichiorophenoxyacetic acid). Using detection tools like activity gel electrophoresis, immunoblotting and enzymatic assays, the production of the cystatin under stress was monitored in different papaya explants, such as roots, leaves and embryos. Inhibitor production increased under different stress conditions when compared to untreated controls. However, this increase was not dramatic in any of the stresses applied. Exact quantification of the increase by using immunoblotting as the only specific tool to determine cystatin expression, was difficult. Neither activity gel electrophoresis nor enzymatic assays were successful to further quantify the exact cystatin levels. Higher cystatin expression was accompanied with a decrease in proteinase activity. Transgenic tobacco plants carrying the gene for a rice cystatin had a significantly lower cysteine proteinase activity when compared to non-transgenic tobacco plants after prolonged cold stress. Furthermore, protein degradation and leaf yellowing as a consequence of cold treatment were prevented in transgenic plants. An attempt to obtain a transformed papaya plant to study silencing of cystatin expression under stress was unsuccessful. In this study, the protective role of a cystatin in cold stress was described for the first time.

Rapid technological advances are providing unprecedented insights in the biologicalsciences, with massive amounts of data generated on genomic and protein sequences.These data continue to grow exponentially, and they are extremely valuable for com-putational tools where the effect of genomic variants on human health is predicted.State of the art tools in this field give varying results and only tend to agree in thecase of single variants that are strongly correlated to disease. The aim of this workis to increase the reliability of these methods, as well as our understanding of theunderlying biological mechanisms that lead to disease. We first developed machinelearning (ML) based structural bioinformatics predictors that are able to predictmolecular features of proteins from the sequence alone. We then used these tools forin silico analysis of the molecular effects of known variants on the affected proteins,and integrated these data with other sources heterogenous sources of information,such as the essentiality of a gene, that put the variants into their broader biologicalcontext. With this information we created DEOGEN, a novel predictor in this field,which is able to deal with the two most common forms of genomic variation, namelySingle Nucleotide Variants (SNVs) and short Insertions and DELetions (INDELs).DEOGEN performs at least on par with other state of the art methods in this fieldon different datasets. The method was then extended with additional contextualdata and is now available as DEOGEN2 via a web server, which visualizes the pre-dicted results for all variants in most human proteins through an interactive interfacetargeted to both bioinformaticians and clinicians. / Doctorat en Sciences / info:eu-repo/semantics/nonPublished

L'analyse des modifications post-traductionnelles (PTMs) est une des contributions les plus importantes de la protéomique aux sciences du vivant. Malgré les progrès importants des techniques séparatives et de la spectrométrie de masse, la quantification des PTMs reste un défi analytique. Le nombre limité de PTMs identifiées robustement dans une recherche, la nécessité d'enrichissement et l'estimation quantitative basée sur un seul peptide ne représentent que les difficultés les plus évidentes. De plus, la quantification des PTMs doit toujours être associée au profil d'expression de la protéine pour éviter les faux positifs.Nous avons développé de nouvelles stratégies analytiques de quantification des PTMs, en prenant en compte le niveau d'expression des protéines. Ces stratégies ont été appliquées à l'étude de l'oxydation des cystéines dans le cadre du stress oxydatif et de l'homéostasie redox.La stratégie OcSILAC est une adaptation de la technique biotin switch au marquage métabolique des cultures cellulaires et a été appliquée à un modèle de levure n'exprimant pas la thiorédoxine réductase. OcSILAC apporte des améliorations techniques importantes et une innovation dans le traitement des données. Les résultats obtenus sont en accord avec le système redox de ce modèle. OcSILAC a ensuite été adaptée au fractionnement subcellulaire pour étendre la couverture du redoxome.Une deuxième stratégie, OxiTMT, a été développée en se basant sur des tandem mass tags spécifiques de la cystéine. OxiTMT a été employée à l'étude de cellules E. Coli soumises à un traitement oxydatif. OxiTMT offre l'avantage d'une large gamme d'applications qui peut s'étendre aux tissus et aux biopsies. / The analysis of protein Post-Translational Modifications (PTMs) is probably the most important contribution that proteomics can give to life sciences. Although separative techniques and mass spectrometry have improved tremendously, the quantitative analysis of PTMs remains an analytical challenge. The limited number of PTMs that can be robustly computed in a single research, the necessity of enrichment steps and performing quantitative estimations using only one peptide, are just the most evident difficulties faced. Furthermore, PTMs quantification should always be associated to protein expression levels to avoid false positives. We have developed new analysis methods allowing the quantification of PTM changes while taking into account protein expression levels. These strategies were applied to the study of cysteine oxidation within the contexts of oxidative stress and redox homeostasis. The first strategy, OcSILAC, is a revision of the biotin switch adapted to Stable Isotope Labelling by Amino acids in Cell culture; it was applied to the study of a thioredoxin reductase silenced yeast model. OcSILAC leads to important technical improvements and data analysis innovations. The results obtained are in agreement with the extensive existing literature concerning the yeast redox system. OcSILAC was then adapted to a subcellular fractionation kit to extend the coverage of the cysteine redoxome. A second strategy called OxiTMT was developed based on cysteine specific tandem mass tags. OxiTMT was used to study E. Coli cells exposed to oxidative treatment. OxiTMT offers the advantage of a wide range of applications that can extended to the study of tissues and biopsies.

Malaria has consistently been rated as the worst parasitic disease in the world. This disease affects an estimated 5 billion households annually. Malaria has a high mortality rate leading to distorted socio-economic development of the world at large. The major challenge pertaining to malaria is its continuous and rapid spread together with the emergence of drug resistance in Plasmodium species (vector agent of the disease). For this reason, researchers throughout the world are following new leads for possible drug targets and therefore, investigating ways of curbing the spread of the disease. Cysteine proteases have emerged as potential antimalarial chemotherapeutic targets. These particular proteases are found in all living organisms, Plasmodium cysteine proteases are known to degrade host hemoglobin during the life cycle of the parasite within the human host. The main objective of this study was to use various in silico methods to analyze the hemoglobinase function of cysteine proteases in P. falciparum and P. vivax. Falcipain-2 (FP2) of P. falciparum is the best characterized of these enzymes, it is a validated drug target. Both the three-dimensional structures of FP2 and its close homologue falcipain-3 (FP3) have been solved by the experimental technique X-ray crystallography. However, the homologue falcipain-2 (FP2’)’ and orthologues from P.vivax vivapain-2 (VP2) and vivapain-3 (VP3) have yet to be elucidated by experimental techniques. In an effort to achieve the principal goal of the study, homology models of the protein structures not already elucidated by experimental methods (FP2’, VP2 and VP3) were calculated using the well known spatial restraint program MODELLER. The derived models, FP2 and FP3 were docked to hemoglobin (their natural substrate). The protein-protein docking was done using the unbound docking program ZDOCK. The substrate-enzyme interactions were analyzed and amino acids involved in binding were observed. It is anticipated that the results obtained from the study will help focus inhibitor design for potential drugs against malaria. The residues found in both the P. falciparum and P. vivax cysteine proteases involved in hemoglobin binding have been identified and some of these are proposed to be the main focus for the design of a peptidomimetric inhibitor.

Protozoan infections such as Malaria, Leishmaniasis, Toxoplasmosis, Chaga’s disease and African trypanosomiasis caused by the Plasmodium, Leishmania, Toxoplasma and Trypanosoma genuses respectively; inflict a huge economic, health and social impact in endemic regions particularly tropical and sub-tropical regions. The combined infections are estimated at over a billion annually and approximately 1.1 million deaths annually. The global burden of the protozoan infections is worsened by the increased drug resistance, toxicity and the relatively high cost of treatment and prophylaxis. Therefore there has been a high demand for new drugs and drug targets that play a role in parasite virulence. Cysteine proteases have been validated as viable drug targets due to their role in the infectivity stage of the parasites within the human host. There is a variety of cysteine proteases hence they are subdivided into families and in this study we focus on the clan CA, papain family C1 proteases. The current inhibitors for the protozoan cysteine proteases lack selectivity and specificity which contributes to drug toxicity. Therefore there is a need to identify the differences and similarities between the host, vector and protozoan proteases. This study uses a variety of bioinformatics tools to assess these differences and similarities. The Plasmodium cysteine protease FP-2 is the most characterized protease hence it was used as a reference to all the other proteases and its homologs were retrieved, aligned and the evolutionary relationships established. The homologs were also analysed for common motifs and the physicochemical properties determined which were validated using the Kruskal-Wallis test. These analyses revealed that the host and vector cathepsins share similar properties while the parasite cathepsins differ. At sub-site level sub-site 2 showed greater variations suggesting diverse ligand specificity within the proteases, a revelation that is vital in the design of antiprotozoan inhibitors.

Novel conserved amino acid variations of papaya cystatin (PC) were investigated by amino acid substitutions using oryzacystatin-I (OCI) as a model plant cystatin for comparison. These amino acid residues in the conserved motifs are involved in binding with cysteine proteases, these include the GG (Gly-Gly) in the N-terminal region for both OCI and PC, the (Q)QVVAG (Gln-Val-Val-Ala-Gly) motif for OCI and (Q)AVVEG (Ala-Val-Val-Glu-Gly) motif for PC in the first inhibitory loop, and the PW (Pro-Trp) motif for OCI and LW (Leu-Trp) motif for PC in the second inhibitory loop. Recombinant OCI and PC mutant proteins were expressed in Escherichia coli and were tested for altered inhibitory activity against commercial cysteine proteases (papain and cathepsin L) and extracts from Colorado potato beetle (Leptinotarsa decemlineata) larvae, from banana weevil larvae (Cosmopolites sordidus) and tobacco leaf extracts (Nicotiana benthamiana). In all tests higher amounts of PC had to be used to obtain similar inhibition levels as OCI. Changing the amino acid Q at position 52 to E in OCI in the first inhibitory loop, had lowered the Ki value of the mutant against the commercial proteases. Concurrently the same amino acid string (EQ) in PC had resulted in a significantly decreased Ki value compared to PC wild-type and other mutants. All other OCI mutants were less efficient than the wild-type OCI, whereas all PC first inhibitory loop mutants had improved inhibitory activity against protease activity with the highest improvement against the protease extracts was found for the substitution of E with A at position 55. This study has shown the importance of the three conserved motifs and that it is possible to improve the binding capacity of a plant cystatins to cysteine protease activity by amino acid substitution using site-directed mutagenesis. By mutating individual amino acid residues in the first binding loop of the relatively “weak” papaya cystatin to amino acid residues found in OCI caused a significant improvement in inhibitory potency of PC. Copyright / Dissertation (MSc)--University of Pretoria, 2011. / Plant Science / unrestricted

Plant cysteine proteinase inhibitors or also called phytocystatins inhibit the action of cysteine proteinases in plants. These proteinases are involved in many developmental processes by degrading proteins. In this study possible effects of an exogenous oryzacystatin-I (OC-I) expressed in transformed tobacco has been investigated. By challenging OC-I expressing and non-expressing tobacco with drought and heat stress, OC-I transcription and translation were not affected in OC-I expressing plants and plant extracts from stressed plants containing the inhibitor inhibited papain activity in vitro. Further, plant growth and photosynthesis was not greatly different under the selected growth conditions in both plant types under stress and non-stress conditions. However, OC-I expressing plants showed slightly lower photosynthetic rate, were shorter and had a higher lower dry mass production under non-stress condition. By applying cDNA Representational Difference Analysis (cDNA-RDA) to detect differentially expressed genes in the two types of plants, a gene coding for the light harvesting chlorophyll a/b binding protein gene (lhcb1) of photosystem II (LHC II) was isolated from non-OCI expressing plants. Northern blot analysis showed lower transcript accumulation of the lhcb gene in OCI-expressing plants both under non-stress and stress conditions, which was accompanied by lower chlorophyll content in OC-I expressing plants. Furthermore, plants benefited from OC-I expression by protection of a variety of expressed proteins against degradation. Identification of possible target cysteine proteinases for OC-I in tobacco resulted in the isolation, cloning and characterization of two new papain-like cysteine proteinases from tobacco designated NtCP1 and NtCP2. NtCP1 was expressed only in senescent leaves and it was not induced in mature green leaves upon exposure to drought or heat stress. NtCP1 has therefore a possible potential as a developmental senescence marker in tobacco. In contrast, NtCP2, which was expressed in mature green leaves, has a high similarity to KDEL-tailed cysteine proteinases that are involved in programmed cell death. Both drought and heat decreased NtCP2 transcript abundance in mature green leaves. Overall, this study has provided evidence that expression of exogenous OC-I does not significantly improve plant performance in tobacco in terms of physiological traits under drought and heat stress but provides protection in terms of stability of protein expression by possibly interacting with endogenous tobacco cysteine proteinases. Further detailed studies are suggested on the interaction of endogenous cysteine proteinases and exogenous phytocystatins to elucidate in more detail the type of interaction. Copyright 2006, University of Pretoria. All rights reserved. The copyright in this work vests in the University of Pretoria. No part of this work may be reproduced or transmitted in any form or by any means, without the prior written permission of the University of Pretoria. Please cite as follows: Beyene, G 2006, Gene expression and plant performance in oryzacystatin-I expressing transformed tobacco (Nicotiana tabacum L. cv Samsun) plants under abiotic stress, PhD thesis, University of Pretoria, Pretoria, viewed yymmdd < http://upetd.up.ac.za/thesis/available/etd-12052006-144409 / > / Thesis (PhD (Botany))--University of Pretoria, 2006. / Plant Science / unrestricted

Le vieillesse conduit à une perte de masse et de fonctionnalité musculaire : la sarcopénie. Ce phénomène physiologique est reconnu comme une cause directe de fragilité et ces deux syndromes gériatriques ont été reliés à de nombreux facteurs dont le statut nutritionnel et la médication. Cependant, les interactions médication-muscle n'ont été que peu étudiées notamment au cours du vieillissement. Le médicament le plus prescrit et consommé est le paracétamol dont la détoxification hépatique nécessite un nutriment : la cystéine (Cys)[...]Sous réserve de la validité de ces résultats chez l'homme, les données obtenues indiquent qu'il serait d'intérêt de mettre en place des recommandations nutritionnelles basées sur une augmentation en Cys au cours des périodes de traitement.Ceci permettrait d'accroître le bénéfice /risque du paracétamol, qui est largement prescrit en première intention pour traiter les douleurs chroniques d'intensité faible à modérée chez les personnes âgées. / The age-related muscle mass and functionality loss, named sarcopenia is a physiological processknown as a direct cause of frailty. Both geriatrics syndromes have been correlated to various factorsas nutritional status and medication. However, the interactions between medication and muscle havenot being deeply investigated, especially in elderly. Using this model, we have highlighted a 12% loss of muscle mass in old rat under repeatedparacetamol cures. This loss was associated with paracetamol-induced sulfur amino acid disturbancesleading to altered glutathione (GSH a Cys containing tripeptide) status and circulating Cys. All together, these results emphasize that muscle mass loss induced by repeated cures withparacetamol in old rats arise from the increased protein and more specifically Cys requirements. Therelevance of these results for older persons needs to be further evaluated before considering whetherit it could be of interest to develop nutritional recommendations aimed to optimized protein intake orCys supplementation during cures with paracetamol. That could further increase the benefit/risk ratioof paracetamol which is widely prescribed for pain relief, especially in older people.

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