The pathogen Streptococcus pyogenes is a significant cause of human morbidity and mortality. Most of the work in this thesis is focused on streptococcal virulence factor IdeS, but the thesis also features work on SpeB, another streptococcal virulence factor. Both IdeS and SpeB are secreted cysteine proteases and both have previously been shown to degrade human IgG. IgG is the only known substrate for IdeS while SpeB is a more promiscuous protease with a larger number of identified substrates. A significant part of the data presented in this thesis is the result of designing and optimizing methods to detect and accurately measure the proteolytic degradation of IgG. Methods aimed at measuring the binding interactions between enzyme and substrate have also been frequently utilized. I show that IdeS is a monomeric protease, as opposed to previously published data that suggested it to be dimeric. IdeS cleaves the two heavy chains of IgG in a two-step reaction and I demonstrate that the first cleavage is magnitudes faster than the second one. This means that IdeS is a more efficient enzyme than previously thought. The difference in rate cannot completely be explained by a loss of affinity between IdeS and IgG after the cleavage of the first heavy chain. The velocity of IdeS is further increased by the presence of human Cystatin C, via an unknown mechanism. Cystatin C is normally a protease inhibitor and it having an opposite effect is puzzling.The synthesis and evaluation of novel inhibitors are also described. Peptide analogues mimicking the sequence surrounding the scissile bond on IgG - with an amino acid replaced with a more rigid motif - act as specific, but low-affinity, inhibitors of IdeS. The peptide analogues’ inhibitory capacity for SpeB and papain was also assayed.When it comes to SpeB, I show that it does not have IgG as a substrate under physiological conditions, in contrast to what was previously thought. This thesis does not only present findings on the IgG degrading capacity of IdeS and SpeB but also include data on fundamental enzymatic properties for these proteases.

Le système Tol-Pal est un complexe de l’enveloppe d’Escherichia coli composé de CINQ protéines. Les protéines ToIQ, ToIR, TolA forment un complexe dans la membrane interne; la lipoprotéine Pal interagit avec le peptidoglycane avec la protéine périplasmique TolB. Ce système est conservé chez la plupart des bactéries à Gram négatif. Il joue un rôle important dans le maintien de la stabilité de l’enveloppe et dans l’étape tardive de la division cellulaire. Une interaction entre TolA et Pal relie les membranes interne et externe, et dépend des protéines ToIQ, TolR et de la force proton motrice (PMF). Les protéines ToIQ-R-A formeraient un moteur moléculaire utilisant la PMF afin de relier membranes interne, externe et le peptidoglycane. Mon travail a consisté à étudier l’organisation des segments transmembranaires (STs) de TolQ et TolR au sein de la membrane interne d’E. coli en utilisant l’approche expérimentale du « cysteine scanning ». Ainsi, nous avons pu identifier les résidus impliqués dans les interactions entre les STs et améliorer la connaissance de l’organisation moléculaire de ce système. Nous avons aussi démontré la dimérisation du ST de TolRet l’importance de la dynamique dans le fonctionnement de ce moteur. Le système Tol est parasité par certaines toxines (comme les colicines) et par des phages filamenteux. Les colicines sont produites par des souches d’Escherichia coli et active contre les entérobactéries. Je me suis aussi intéressé à l’organisation structurale de la protéine d’immunité de la colicine A. La colicine A forme un canal ionique dans la membrane interne pour tuer la bactérie cible. Les cellules produisant la Colicine A synthétisent également une protéine d’immunité (Cai) qui les protègent de l’action de la colicine A. Par une approche combinant « cysteine scanning » classique et un « anti-cysteinescanning », nous avons pu apporter des informations nouvelles sur l’organisation des quatre STs deCai. Nous avons montré que Cai forme un dimère dans la membrane et que ce dimère se dissocie au contact de sa cible, la colicine A. / The Tol-Pal system is a protein complex of the Escherichia coli cell envelope. It consists offive proteins. The ToIQ, TolR, TolA proteins form a complex in the inner membrane, the lipoproteinPal interacts with the peptidoglycan and with the periplasmic protein TolB. This system is conservedin most Gram-negative bacteria. It plays an important role in maintaining the integrity of the outermembrane and in the late stage of cell division. The interaction between Pal and TolA connects innerand outer membranes and depends on ToIQ, TolR and the proton motive force (pmf). The ToIQ-R-Aproteins are suspected to form a molecular motor using pmf to connect the inner and outermembranes and the peptidoglycan. The first aim of my work was to study the organization of thetransmembrane helices (TMHs) of E. coli TolQ and TolR using the cysteine scanning approaches. Weidentified residues involved in the interactions between the TMHs and improved the knowledge ofthe molecular organization of this system. We have also demonstrated the dimerization of the TMHof TolR and the importance of its dynamic movement in the system. The second aim of my work wasto analyze the structural organization of the immunity protein to colicin A. The colicins are producedby certain strains of E. coli and are active against other Enterobacteriaceae. The colicin A forms anion channel in the bacterial inner membrane which kill the bacteria. It hijacks the Tol system to enterin the cell. Cells producing colicin A also synthesize the colicin A immunity protein (Cai) whichprotects the producing cells against the action of colicin A. The approaches combining "cysteinescanning" and "anti-cysteine-scanning”, we found that Cai form a dimer in the membrane whichdissociates upon contact with its target, the colicin A

Traumatic injuries to the spinal cord and brachial plexus induce a significant inflammatory response in the nervous tissue with progressive degeneration of neurons and glial cells, and cause considerable physical and mental suffering in affected patients. This thesis investigates the effects of the antioxidants N-acetyl-cysteine (NAC) and acetyl-L- carnitine (ALC) on the survival of motoneurons in the brainstem and spinal cord, the expression of pro-apoptotic and pro-inflammatory cell markers, axonal sprouting and glial cell reactions after spinal hemisection in adult rats. In addition, a novel MRI protocol has been developed to analyse the extent of neuronal degeneration in the spinal cord. Rubrospinal neurons and tibial motoneurons were pre-labelled with the fluorescent tracer Fast Blue one week before cervical C3 or lumbar L5 spinal cord hemisection. The intrathecal treatment with the antioxidants NAC (2.4mg/day) or ALC (0.9 mg/day) was initiated immediately after injury using Alzet2002 osmotic mini pumps. Spinal cord injury increased the expression of apoptotic cell markers BAX and caspase 3, induced significant degeneration of rubrospinal neurons and spinal motoneurons with associated decrease in immunoreactivity for microtubule-associated protein-2 (MAP2) in dendritic branches, synaptophysin in presynaptic boutons and neurofilaments in nerve fibers. Immunostaining for the astroglial marker glial fibrillary acidic protein and microglial markers OX42 and ED1 was markedly increased. Treatment with NAC and ALC attenuated levels of BAX, caspase 3, OX42 and ED1 expression after 2 weeks postoperatively. After 4-8 weeks of continuous intratheca ltreatment, NAC and ALC rescued approximately half of the rubrospinal neurons and spinal motoneurons destined to die, promoted axonal sprouting, restored the density of MAP2 and synaptophysin immunoreactivity and reduced the microglial reaction. However, antioxidant therapy did not affect the reactive astrocytes in the trauma zone. The inflammation modulating properties of ALC were also studied using cultures of human microglial cells. ALC increased the microglial production of interleukin IL-6 and BDNF, thereby possibly mediating the anti-inflammatory and pro-regenerative effects shown in vivo. To study degeneration in the spinal cord following pre-ganglionic and post-ganglionic brachial plexus injuries, adult rat models of ventral root avulsion and peripheral nerve injury were used. A novel MRI protocol was employed and the images were compared to morphological changes found in histological preparations. Ventral root avulsion caused degeneration of dendritic branches and axonal terminals in the spinal cord, followed by significant shrinkage of the ventral horn. Extensive astroglial and microglial reactions were detected in the histological preparations. Peripheral nerve injury reduced the density of dendritic branches but did not cause shrinkage of the ventral horn. Quantitative analysis of MRI images demonstrated changes in the ventral horn following ventral root avulsion only, thus validating the developed MRI technique as a possible tool for the differentiation of pre-ganglionic and post-ganglionic nerve injuries.

Membrane-type 5 matrix metalloproteinase (MT5-MMP) is unique among MMP family members as it is predominately expressed in the CNS. Its expression is ubiquitous during brain development and restricted to regions of neurogenesis and neuroplasticity in the adult. MT5-MMP is a mediator of pericellular proteolysis and is thought to have a functional impact on neurite outgrowth. The studies presented in this work were designed to examine MT5-MMP expression in cultured NT2 cells, a model of newogenesis and neuronal differentiation, and in adult neurogenic brain regions. We further sought to overexpress MT5-MMP and test the hypothesis that it plays a role in substrate-specific cell motility.MTS-MMP mRNA was expressed in NT2 cells and was significantly higher in differentiated neuronal hNT cells. MT5-MMP cDNA cloned from NT2 cells unexpectedly revealed a novel sequence (MTS-MMPvar) which was 92% homologous with the published MT5-MMP and was characterized by a 162 bp deletion. Both transcripts could be identified in NT2, hNT and adult human hippocampus. The newly cloned MT5-MMPvar cDNA translated into an approximately 52 kDa protein as seen in in vitro expression studies. Using an MTS-MMPvar specific antibody designed to span the 162 bp deletion, MT5-MMPvar protein could be detected in NT2 cells and these protein levels increased in their neuronal counterparts, hNT cells. MT5-MMPvar protein was also expressed in adult human hippocampal tissue. MT5-MMPvar protein was shown to be expressed in a murine region of neurogenesis and plasticity, suggesting the existence of a murine homolog of this variant.Based on bioinformatic analysis, the MT5-MMPvar transcript was predicted to lack a sufficient signal peptide and to remain a Type-I membrane protein. This computer assisted modeling suggests that the most significant functional implication of MTS-MMPvar sequence variations is to affect its direction into the ER for processing. Functional studies using COS-7 cells genetically modified to overexpress MT5- MMPvar demonstrated no difference in cellular motility compared to parental or vector control cells. Preliminary studies show MT5-MMPvar expression in COS-7 cells associated with perinuclear structures and the cell membrane. Adult human neural progenitor cells stimulated to differentiate into immature neurons demonstrated MT5-MMPvar expression associated with the cell membrane and process outgrowths. This work has identified a novel transcript variant of the human MTS-MMP gene and shown that the protein product of this gene is significantly higher in differentiated NT2 cells. This, combined with preliminary results suggesting MT5- MMPvar cellular redistribution in more mature cell types, indicates a role for MTSWvar in neural differentiation and function.

Our experimental organism Fascioloides magna is a digenetic liver fluke from Fasciolidae family which parasitizes in domestic and free-living ruminants of North America and Central Europe including Czech Republic. In Czech Republic this highly pathogenic worm causes a severe liver damage to cervids and bovids and the prevalence locally reaches up to 95%. The biology of F. magna including e.g. the characteristics of host-parasite molecular interaction and the functions of particular molecules produced by the parasite are not fully understood. According to results of our previous research the excretory-secretory products of F. magna adults contain number of molecules which play the crucial role in host tissue invasion, digestion and evasion of the host immune response. One of the most abundant is cysteine peptidase cathepsin L (FmCL). FmCL is supposed to play various key roles in biological processes of all stages during a life cycle and therefore we can suppose its different expression level in particular life stages. In order to define the expression level of FmCL we performed the pilot study with miracidia and adults where the qPCR method was applied. The results of this experiment revealed much higher expression level of FmCL1 in adults than in miracidia. The attempt to in situ localize the mRNA...

Les thiol-disulfure oxydoréductases sont des protéines qui jouent un rôle majeur dans la cellule. Elles sont impliquées dans l'activité de nombreuses protéines cytoplasmiques, ainsi que dans la maturation et la stabilité des protéines extracytoplasmiques. Les particularités structurales conservées chez les TDORs, comme le repliement thiorédoxine et le motif CxxC, les propriétés physico-chimiques, leur environnement physiologique et leurs substrats sont autant de facteurs qui influencent la capacité de ces protéines à catalyser préférentiellement la réduction, l'oxydation, ou l'isomérisation des ponts disulfures in vivo.Je me suis intéressée aux TDORs atypiques cytoplasmiques pouvant présenter une activité thiol-oxydase ou disulfure-isomérase dans le cytoplasme des bactéries. J'ai caractérisées deux thiorédoxines atypiques, l'une provenant de l'organisme anaérobie Desulfovibrio vulgaris Hildenborough, Dtrx, et l'autre provenant de la bactérie pathogène Pseudomonas aeruginosa PAO1, PsTrx. Dtrx, possédant une séquence consensus thiol-oxydase CPHC, présente des propriétés in vitro en accord avec cette séquence. Nous avons proposé un mécanisme qui peut être appliqué de façon réversible dans le sens de la réduction et de l'oxydation des cystéines des substrats.PsTrx contient une séquence consensus CGHC dans son site actif, qui est généralement conservée chez PDI, protéine eucaryote. Les propriétés physico-chimiques, et la structure tridimensionnelle déterminées pour PsTrx par RMN, présentent des caractéristiques identiques à celles observées pour le domaine catalytique de PDI. / Thiol/disulfide oxidoreductases catalyze important redox reactions in the cell. They are implicated in the reduction of disulfide bonds in cytoplasm, and disulfide bond formation during folding of secreted proteins. All of the members of this family share the thioredoxin fold and an active site with two conserved cysteine residues that specify the biological activity of the protein in the reduction, oxidation or isomerisation of disulfide bond in vivo.In this work, I have studied atypical cytoplasmic TDORs catalyzing the oxidation or isomerisation of disulfide bond in bacteria. I have characterized two atypical thioredoxin proteins, one from the anaerobe Desulfovibrio vulgaris Hildenborough, Dtrx, and one from the pathogenic Pseudomonas aeruginosa PAO1, PsTrx.Dtrx, with the CPHC active site, presents important activities in the thiol-oxidation of proteins. We proposed a reversible mechanism for the disulfide-reduction or thiol-oxidation of substrate proteins.PsTrx presents the CGHC active site shown in the eukaryote PDI protein. Physico-chemical properties and tridimensional structure solved by NMR are the same that those of the catalytical domain of PDI.This work presents the properties of the two atypical thioredoxins, Dtrx and PsTrx. These proteins have similar functional and structural characteristics in vitro, but probably different redox functions in vivo.

Blastocystis spp. est un Straménopile parasite anaérobie fréquemment rencontré dans le tractus gastro-intestinal de l’homme et de divers animaux. Ce parasite est associé à des troubles gastro‐intestinaux aspécifiques, et semble impliqué dans des désordres fonctionnels tels que le syndrome de l’intestin irritable (IBS). Ce travail de thèse s’appuie sur le séquençage du génome de Blastocystis sp. ST7 réalisé en collaboration avec le Génoscope d’Evry, l’Université Nationale de Singapour, l’Institut Pasteur de Lille et l’Université de Provence. Ce génome est constitué d’un génome nucléaire de 18,8 Mpb pour 6020 gènes, et d’un génome mitochondrial de 29 kpb localisé dans des organites apparentés aux mitochondries. L’analyse de ce génome apporte des informations au niveau de l’évolution de ce microorganisme, de son adaptation à l’environnement intestinal et de ces facteurs de virulence potentiels. En effet, les analyses in silico de ce génome ont montré que Blastocystis sp. ST7 possède plusieurs gènes codant des protéines pouvant agir à l’interface entre l’hôte et le parasite et connues chez d’autres protozoaires pour être impliquées dans des phénomènes de pathogénie. Ce sont en particulier des PKS, des NRPS, et des hydrolases dont des protéases. D’autre part, des activités protéolytiques ont été mises en évidence expérimentalement dans les surnageants de culture du parasite. Deux protéases à cystéines (une cathepsine B et une légumaïne) pouvant être impliquées dans la physiopathologie du parasite, ont été identifiées et caractérisées dans les surnageants, confirmant ainsi nos analyses in silico. Ce travail ouvre de nombreuses pistes intéressantes à explorer pour évaluer l’impact de ce parasite en santé humaine. / Blastocystis spp. is a highly prevalent anaerobic Stramenopile parasite found in the intestinal tract of humans and various animals. This parasite is associated with non specific intestinal disorders, and could be involved in functional disorders such as the irritable bowel syndrome (IBS). In this work, the Blastocystis sp. ST7 genome sequencing project was carried out in collaboration with the Génoscope of Evry, the National University of Singapore, the Pasteur Institute of Lille and the University of Provence. This genome consists in a nuclear genome of 18,8 Mpb encoding 6020 genes, and a mitochondria‐like genome of 29 kpb localised in the mitochondrion‐like organelles. The analysis of this genome brings information about the evolution of this micro‐organism, its adaptation to the intestinal environment and its potential virulence factors. Blastocystis sp. ST7 was predicted to harbor several genes coding proteins that could act at the parasite‐host interface, and that are known to be involved in the pathogeny of many protozoa. They are PKS, NRPS, and hydrolases among them proteases. In addition, proteolytic activities were highlighted in the parasite culture supernatants. Two cysteine proteases (a cathepsin B and a legumain) were identified and characterized from the supernatants and could play a role in the physiopathology of the parasite, that confirm our in silico analyses. This work opens new ways to evaluate the impact of this parasite in human health.

Master of Science / Department of Grain Science and Industry / Rebecca Miller / Sorghum is a vital cereal crop grown in many regions around the world. Tolerance to harsh climates and low moisture conditions are unique traits making sorghum an economical choice in an era of global water scarcity. In recent years, sorghum has gained greater recognition as a gluten-free grain and is a safe alternative for individuals suffering from gluten sensitivities or celiac disease. Still, the lack of gluten proteins does not allow sorghum to form a viscoelastic dough. In this study reducing agents were added to improve functional properties of sorghum kafirins for bread baking. Study objectives were to determine the effect of reducing agents on protein body structure of sorghum kafirins, investigate the influence on the sorghum batter consistency, and evaluate the effects on the physical characteristics of sorghum bread. Protein analysis, accomplished using RP-HPLC, showed reducing agents, L-cysteine and sodium metabisulfite, reduced protein structure; increasing RP-HPLC total peak area up to 747% and 681%, respectively. Batter consistency was obtained using a RVA. Treatments of L-cysteine (2.5% fwb) expressed increased RVA peak viscosity and decreased final viscosity. Samples treated with sodium metabisulfite (500 ppm fwb) had increased peak viscosity, holding strength and final viscosity. Yeast activity of batter treated with ≥3000 ppm (fwb) sodium metabisulfite caused volume loss of 95% yet at 500 ppm (fwb) sodium metabisulfite did not have an effect. Batter with 2.5% (fwb) L-cysteine experienced reduced yeast activity after 20 min. Sorghum bread characteristics were altered. Loaf volume and crumb grain characteristics of bread produced using sodium metabisulfite (500 ppm) were equal to that of the control, while initial texture and staling were improved. The addition of L-cysteine (2.5% fwb) to breads lowered loaf volume but produced softer initial crumb texture and improved in-vitro protein digestibility by 18.8%.

Thesis advisor: Eranthie Weerapana / Cysteine residues on proteins play important catalytic and regulatory roles in complex proteomes. These functional residues can be modified under physiological conditions by posttranslational modifications (PTMs) to regulate protein activities and modulate cysteine reactivity. Many PTMs are highly labile and dynamic, rendering it difficult to detect modified proteins within complex systems. To contribute to the chemical-proteomic methods currently available, chemical probe-Mass Spectrometry (MS) platforms were developed to study oxidative cysteine modifications. A MS platform for the assessment of S-nitrosation in vitro identified Cys329 of Cathepsin D (CTSD) as highly sensitive to S-nitrosothiol formation. To achieve a more physiological relevant representation of S-nitrosation, this platform was later adapted for study in live cells using a caged electrophile, Caged BK. Additionally, oscillation of cysteine oxidation as a function of circadian rhythm in Drosophila melanogaster and human samples was explored. As a compliment to these MS platforms, a 4-aminopiperidine-based cysteine-reactive probe library was developed. These probes have been used to target specific reactive cysteines as an alternate way to regulate protein function and can be used as tools to provide insight into the roles of these residues in protein activities. / Thesis (PhD) — Boston College, 2016. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Chemistry.

A Xylella fastidiosa é uma bactéria gram-negativa que infecta o xilema das plantas causando muitas vezes a maturação precoce e a diminuição dos frutos. Ela é responsável por importantes perdas na economia, no Brasil é a causadora de doenças de Citrus Variegated Chlorosis (CVC) e a da doença de Pierce nos Estados Unidos. As proteases desempenham funções vitais no ciclo de vida de muitos parasitas, muitas estão envolvidas em processos infecciosos, a Xylellaína é uma cisteíno protease que é diferentemente expressa em cepas patogênicas a não patogênica. A compreensão de seu mecanismo catalítico, através do estudo da sua estrutura e função, pode ajudar no planejamento de inibidores seletivos, potenciais agentes contra as doenças fitopatológicas ocasionadas pela X. fastidiosa. Sua estrutura molecular foi elucidada no Laboratório de Cristalografia de Proteínas e Biologia Estrutural do Instituto de Física de São Carlos (USP), estudos estruturais mostraram que a proteína se apresenta na forma de uma pró-proteína, pois está inativa devido a uma pró-região que bloqueia o sítio catalítico. Também foi verificada a presença de um nucleotídeo na estrutura da Xylellaína próximo a pró-região, como hipótese foi considerada a relação entre o nucleotídeo e o mecanismo de ativação da proteína. A influência do nucleotídeo na atividade funcional da enzima foi constatada através da comparação de ensaios enzimáticos entre a enzima nativa e mutantes. As mutações foram planejadas com a intenção de ocasionar a desestabilização do nucleotídeo, por isso foram mutados os resíduos da pró-região que interagem diretamente com o ele. As mutações foram Fenilalanina 45 (F45), Arginina 43 (R43) e F45/R43, todos os resíduos foram mutados para Alaninas (A). Os resultados mostraram que os valores de Km obtidos para a proteína nativa e suas mutantes apresentaram consideráveis alterações quando comparado entre eles, esse efeito não foi percebido para a eficiência catalítica. Conclui-se que as mutações pouco alteraram a capacidade da enzima converter o subsrato em produto, mas houve significantes alterações no reconhecimento do substrato. Esse resultado corrobora com a hipótese de que a existência do nucleotídeo está relacionada com o mecanismo de ativação da proteína. / Xylella fastidiosa is a Gram-negative bacterium which infects the plant xylem system causing in many cases precocious maturation and diminution of fruits. It is responsible for economically important plant diseases, such as the Citrus Variegated Chlorosis (CVC). Proteases might be involved in the infection process by disrupting plant tissue. Xylellain is a cysteine protease which is differently expressed in strain pathogen and non-pathogen of X. fastidiosa. The 3D structure of xylellain was solved by our group and structural studies show that this protein has a proenzyme form and a ribonucleotideo close to the amine terminal region. Our hypothesis is that protein-nucleotide interactions are related to xylellains activation mechanism. To evaluate the influence of the nucleotide in the functional activity of enzyme, point mutations in aminoacids which interact directly with this ribonucleotide were carried out. The point mutations are phenylalanine 45 (F45) and arginine 43 (R43), individually mutated for alanine (A) residues. One way to quantify the changes caused by the alteration of a nucleotide is the direct comparison between the kinetic enzyme assays of native and mutant proteins. Greater variations between the values of Km than in the values of catalytic efficiency were observed. This suggests that the speed of production varied by enzyme-substrate. However the mutations caused little change on the ability of the protease to catalyze the reaction. This result is in agreement with the hypothesis that the nucleotide provides the structural support for the hinge formation on the N-terminal domain, thus directing the inhibitory peptide inside the active site of the enzyme. Therefore, the nucleotide may be exerting regulatory functions in vivo, possibly in the folding or activation of the protein and performance of catalytic function.