Indiana University-Purdue University Indianapolis (IUPUI) / The proteasome is responsible for breaking down the majority of the proteins in the cell. However, a complete understanding of how this large multi-subunit protease is assembled is currently lacking. Proper and timely assembly of the proteasome is critical for the functioning of the ubiquitin-proteasome pathway, defects in which have been associated with several different cancers. A recently discovered heterodimeric proteasome assembly chaperone, Pba1p-Pba2p, has been suggested to prevent the assembly process from straying off path. Pba1p-Pba2p associates with proteasomal assembly intermediates via C-terminal HbYX motifs. The HbYX motif is a tri-peptide sequence containing a hydrophobic residue (Hb) followed by a tyrosine (Y), then any amino acid (X). This motif was originally identified in proteasomal activators, and shown to mediate the association of activators with the proteasome by inserting into intersubunit pockets on either end of the proteasome. There are seven unique intersubunit binding pockets, located between neighboring α subunits on the proteasome, to which a HbYX-containing protein can bind; which of these pockets Pba1p-Pba2p binds to remains elusive. I attempted to identify where Pba1p and Pba2p bind via a crosslinking approach. Specific residues were mutagenized to cysteines on Pba1p, Pba2p, and the individual α subunits in order to generate crosslinkable species. By exposing yeast cells expressing these crosslinkable proteins to mild oxidizing conditions, I attempted to trap the Pba1p and Pba2p α intersubunit pocket interactions. In order to optimize crosslinking conditions, the assay was modified several ways. Additionally, measures were taken to increase detection of the crosslinked species via immunoblotting. Despite the efforts to improve the crosslinking and detection, I was unable to successfully detect a crosslinked species. However, crosslinking is a reasonable method to identify the Pba1p and Pba2p proteasomal binding sites, having been successfully used to identify binding sites for other HbYX-motif-containing proteins; further assay optimization should yield Pba1p and Pba2p proteasomal crosslinks.

PEGylation can improve the pharmacokinetic properties of protein therapeutics via decreasing renal clearance and shielding the protein surface from proteases, antibody neutrailization, and aggregation. Conformational stability enhancement can provide criteria for the identification of optimal sites for PEGylation, but how PEG influence the noncovalent interactions from the surface of proteins has not been well illustrated. Macrocyclization can effectively enhance the conformational stability of small peptides and large proteins. Combination of PEG-based conformational stability enhancement and macrocyclization-based conformational constraint has not been explored. Macrocycliziation has been employed to stabilize protein tertiary structures, but there are no general guidelines for interhelical staple to stabilize coiled-coil motifs of proteins. Chapter 1 is an introduction to peptide stapling and macrocyclization of proteins. Chapter 2 describes our test of the hypothesis that PEG increases the conformational stability of proteins by desolvating nearby salt bridges. In chapter 3, we explore the combination of PEG-based conformational stability enhancement with macrocyclization on WW domain, and find that the most important criteria for PEG stapling is ensuring the side chains cross-linked by PEG are distant in primary sequence but close in tertiary structure. In chapter 4, we further apply this macrocyclization criteria to another -sheet-based protein, SH3 domain of the chicken Src protein, and to a disulfide-bonded parallel coiled-coil heterodimer derived from the yeast transcription factor GCN4. In chapter 5, we explore the determinants of PEG-staple-based stabilization by changing the distance of the staple to the terminal interhelical disulfide bond, varying the length of staple, exploring different solvent exposed positions for stapling and employing heterochiral residues for stapling. We further apply the interhelical PEG staple to a HER-2 affibody, and find that PEG-stapling increases the conformational stability and proteolytic resistance of the stapled affibody relative to its non-stapled counterpart and to the native unmodified affibody.

Thesis (PhD)--Stellenbosch University, 2012. / ENGLISH ABSTRACT: Introduction: The anthracyclines (ACs), daunorubicin (DNR) and doxorubicin (DXR) are two of the most effective drugs known for the treatment of systemic neoplasms and solid tumours. However, their clinical use is often hampered by their dosedependent cumulative cardiotoxicity, which leads to irreversible and fatal druginduced congestive heart failure. The mechanism by which ACs induces heart damage is not fully understood. Recent reports have indicated that DXR activates autophagy and ubiquitin proteasome-mediated degradation of specific transcription factors, however, no reports exists on the effect of ACs on the E3 ubiquitin ligases, MuRF-1 and MAFbx. The aim of the first part of the study was therefore to investigate the effect of DNR treatment on the protein and organelle degradation systems in the heart and to elucidate the signalling mechanisms involved. Although this model was ideal in allowing the investigation of the signalling pathways which are affected by DNR, it did not allow for further exploration or manipulation of signalling pathways that may be of potential benefit in this context. The in vitro model was therefore used to validate the hypothesis that increased autophagy alleviates AC-induced cardiotoxicity and delays the onset of cardiomyocyte death. The aims for the second part of the study were (i) to characterize the effect of DXR in H9C2 cells, (ii) to determine whether the induction/inhibition of autophagy in combination with DXR alleviates cytotoxicity and (iii) to investigate the influence of increased/decreased autophagy in combination with DXR on reactive oxygen species (ROS) production, mitochondrial function, endoplasmic reticulum (ER) stress and the ubiquitin proteasome pathway. In the final part of this study, an in vivo model was used to assess the potential benefit of autophagy in a novel GFP-LC-3 tumour bearing mouse model of acute DXR-induced cardiotoxicity. Material and Methods: Adult rats were divided into two groups where one group received six intraperitoneal injections of 2 mg/kg DNR on alternate days and the other group received saline injections as control. Hearts were excised and perfused on a working heart system the day after the last injection and freeze clamped for biochemical analysis. H9C2s were cultured and treated with Bafilomycin A1 (10 nM, inhibitor of autophagy) for 6 hrs, Rapamycin (50 μM, inducer of autophagy) for 24 hrs, DXR (3 μM) for 24 hrs or a combination of these drugs. Following treatment, cells were harvested and assessed for cell death, proteolytic activity and oxidative stress using western blotting, fluorescence microscopy and flow cytometry. In the final phase of the study, twenty-four female mice were injected at 8 weeks with a mouse breast cancer cell line (EO771) and after observation of tumour growth, animals were either treated with one injection (i.p.) of Rapamycin (4 mg/kg), two injections (i.p.) of DXR (10 mg/kg) or a combination of the two drugs. After the experimental protocol, mice were terminated and their hearts were rapidly excised. The hearts were divided cross-sectionally and utilized for biochemical and histological analyses. Results and Discussion: DNR treatment significantly attenuated myocardial function and increased apoptosis in the ex vivo heart model. DNR-induced cardiac cytotoxicity was associated with the upregulation of two E3 ubiquitin ligases, MuRF-1 and MAFbx as well as a significant increase in two markers of autophagy, beclin-1 and LC-3. These changes observed in the heart were also associated with attenuation of the PI3-kinase/Akt signalling pathway. The augmentation of autophagy with rapamycin before DXR treatment significantly reduced cell death in the in vitro model. Indeed, rapamycin treatment demonstrated to be a vital survival mechanism for acute DXR-induced cardiotoxicity as it decreased cellular ROS production, improved mitochondrial function and prevented nuclear translocation of DXR. Moreover, these changes in cardiomyocytes were also associated with a reduction in the ubiquitin-proteasome pathway (UPP). In the final part of this study, a novel tumour bearing GFP-LC3 mouse model was developed to confirm the results obtained in the in vitro study. It was demonstrated that acute DXR-induced cardiotoxicity resulted in increased apoptosis, the inhibition of autophagy and increased proteolysis via the UPP. These findings were associated with a reduction in body weight and cardiomyocyte cross-sectional area. The cardiotoxic effects of DXR were substantially reduced when autophagy was induced with rapamycin. Taken together, our data strongly indicates that it is possible to attenuate the cardiotoxic effects of doxorubicin in cancer patients by carefully controlling the levels of autophagy using rapamycin as adjuvant therapy. / AFRIKAANSE OPSOMMING: Inleiding: Die antrasikliene (AC’s), daunorubisien (DNR) en doksorubisien (DKS), is twee van die mees effektiewe AC wat bekend is vir die behandeling van sistemiese neoplasmas en soliede tumore. Hulle kliniese gebruik word egter deur dosis afhanklike kumulatiewe kardiotoksisiteit benadeel, wat tot onomkeerbare en dodelike kongestiewe hartversaking kan lei. Die meganisme waardeur AC’s hartversaking kan veroorsaak, word nog nie ten volle verstaan nie. Onlangse navorsing het aangetoon dat DKS autofagie en die ubikwitienproteosoom-bemiddelde degradasie van spesifieke transkripsie faktore aktiveer. Daar is egter geen literatuur wat die effek van AC’s op die E3-ubikwitienligases, MuRF-1 en MAFbx beskryfnie. Die doel van hierdie eerste afdeling van die studie is om die effek van DNR behandeling op die proteïen- en organel degradasie sisteme in die hart te ondersoek en om van die betrokke seinmeganismes te bepaal. Alhoewel hierdie model ideaal is om sommige seinweë wat deur DNR geaffekteer word, te ondersoek, kon seinoordragpaaie wat potensieël voordelig in hierdie konteks is, nie in bg. model gemanipuleer word nie. Die in vitro model is gebruik om die hipotese dat verhoogde outofagie AC-geïnduseerde kardiotoksisiteit verlaag en sodoende seldood verminder, te bevestig. Die doel van hierdie afdeling van die studie was: (i) om die effek van DKS op H9C2 selle te karakteriseer, (ii) om te bepaal of die induksie/inhibisie van outofagie in kombinasie met DKS kardiotoksisiteit verbeter (iii) om die invloed van verhoogde/verlaagde outofagie in kombinasie met DKS op reaktiwe suurstof species (ROS), mitokondriale funksie, endoplasmiese retikulum (ER) stress en die ubikwitienproteosoompad te ondersoek. In die finale deel van hierdie studie, is ‘n in vivo model gebruik om die moontlike voordelige effek van verhoogde outofagie in ‘n GFP-LC-3 tumor-draende muismodel met akute DKSgeïnduseerde kardiotoksisiteit, ondersoek. Materiaal en Metodes: Volwasse rotte is in twee groepe verdeel waar een groep ses intraperitoneale inspuitings van 2 mg/kg DNR op afwissellende dae ontvang het en die andergroep as ‘n kontrole, ‘n soutoplossing gekry het. Die harte is verwyder en geperfuseer op ‘n werkende hartsisteem een dag na die laaste inspuiting en gevriesklamp vir biochemiese analises. H9C2 selle is vir 6 uurgekweek en behandel met Bafilomisien A1 (10 nM, ‘n autofagie inhibitor), 24 uur met Rapamisien (50 μM, ‘n autofagie induseerder), 24 uur met DKS (3 μM) of ‘n kombinasie van hierdie middels. Na behandeling is selle ge-oes vir analises in seldood, proteolitiese aktiwiteit en oksidatiewe stress deur van westelike kladtegniek, fluoresensie mikroskopie en vloeisitometrie gebruik te maak. In die finale fase van hierdie studie is vier en twintig, agt weke oue wyfie muise ingespuit met ‘n muisborskankersellyn (E0771) en is tumorgroei waargeneem; die diere is of behandel met een rapamisien inspuiting (i.p) (4 mg/kg), of twee DKS inspuitings (i.p.) (10 mg/kg) of ‘n kombinasie van die twee middels. Na die eksperimentele protokol, is die muise van kant gemaak en hulle harte vinnig verwyder. Die harte is in twee verdeel en gebruik vir biochemiese- en histologiese analises. Resultate en Bespreking: DNR behandeling het kardiale funksie betekenisvol verswak en apoptose in die hart verhoog. DNR-geïnduseerde kardiotoksisiteit is geassosieer met die opregulering van E3-ligases, MuRF-1 en MAFbx en het ook ‘n betekenisvolle toename in twee outofagie merkers, beclin-1 en LC-3 veroorsaak. Hierdie veranderinge wat in die hart waargeneem is, is ook geassosieer met ‘n onderdrukking van die PI3-kinase/Akt seinweg. Die toename in outofagie met rapamisien voor DKS behandeling het seldood in die vorm van apoptose betekenisvol verlaag. Daarmee saam het verhoogde outofagie ‘n noodsaaklike oorlewings meganisme vir akute DKS-geïnduseerde kardiotoksisiteit gedemonstreer. Die rede hiervoor is dat dit ROS produksie verlaag het, mitokondriale funksie verbeter het en DKS translokasie vanuit die sitoplasma tot binne die nukleus verhoed het. Hierdie veranderinge in kardiomiosiete is ook met ‘n afname in die ubikwitienproteosoomseinweg (EPS) geassosieer. In die finale deel van hierdie studie, is ‘n nuwe tumor-draende muismodel ontwikkel om die resultate wat in die in vitro studie gekry is, te bevestig. Daar is bewys dat akute DKS-geïnduseerde kardiomiotoksisiteit aanleiding gegee het tot verhoogde apoptose, outofagie inhibisie en verhoogde proteolise via die EPS. Hierdie bevindinge is geassosieer met ‘n verlaging in liggaamsgewig en kardiomiosiet dwarssnit area. Die kardiotoksiese effekte van DKS is insiggewend verminder as autofagiege ïnduseer is met rapamisien. Om saam te vat: Ons data bevestig dat dit moontlik is om die kardiotoksiese effekte van DKS in kanker pasiënte te verminder deur outofagie vlakke te monitor en te kontroleer deur middel van rapamisien behandeling as bykomende terapie.

<p>The aim of this study was to better understand the role of conditioned medium (CM) in Spodoptera frugiperda Sf9 insect cell proliferation and recombinant protein production using the baculovirus expression system.</p><p>CM was found to stimulate cell proliferation. Addition of CM and 10 kDa CM filtrate to an Sf9 culture decreased the lagphase and the maximum cell density was reached earlier than for cultures in fresh medium. The positive effect of 10 kDa CM filtrate showed that CM contains at least one small growth promoting factor. The effect was not eliminated by trypsin treatment. Addition of CM or 10 kDa CM filtrate to Sf9 cultures was found to have a negative effect on the recombinant protein production. The effect was thought to be indirect and most probably via the impact of CM on cell physiology. CM was also found to contain proteinase activity. The proteinase was identified as Sf9 cathepsin L. A proform with a molecular mass about 49 kDa and two active forms at about 39 and 22 kDa were found. The role of cathepsin L in Sf9 cultures is not yet clear. However, the knowledge of the presence of this proteinase in CM can be of great value for improving product quality and yield. Further, CM was found to have other properties as well: a concentrated fraction of CM exhibited strong antibacterial activity towards Bacillus megaterium and a weaker activity towards Escherichia coli. B. megaterium lysed rapidly after incubation in the CM fraction.</p><p>Repeated subculturing of Sf9 cells provoked a switch in growth kinetics. After 30-45 passages the cells started to proliferate earlier after inoculation and addition of CM had no longer a growth stimulating effect. However, CM still stimulated growth of a culture with low passage (LP) number (up to 45 passages). High passage cells (HP cells, over 100 passages) displayed a shorter lagphase than LP cells and the culture reached the maximum cell density 24-48 h earlier. Cell cycle analysis showed that the Sf9 cells were transiently synchronised in the G2/M phase 10 h after inoculation, before proliferation was initiated. This synchronisation was more pronounced for HP cells than for LP cells, which correlated to a higher recombinant protein production in baculovirus infected HP cells than in LP cells. Synchronisation of cells in G2/M by yeastolate-limitation before infection with baculoviruses suggested that the degree of synchronisation is connected to the cell density dependent decrease in recombinant protein production of Sf9 cultures.</p>

Résumé: Chaque année, les épidémies saisonnières d’influenza causent de 3 à 5 millions de cas sévères de maladie, entraînant entre 250 000 et 500 000 décès mondialement. Seulement deux classes d’antiviraux sont actuellement commercialisées pour traiter cette infection respiratoire : les inhibiteurs de la neuraminidase, tels que l’oseltamivir (Tamiflu) et les inhibiteurs du canal ionique M2 (adamantanes). Toutefois, leur utilisation est limitée par l’apparition rapide de résistance virale. Il est donc d’un grand intérêt de développer de nouvelles stratégies thérapeutiques pour le traitement de l’influenza. Le virus influenza dépend de l’activation de sa protéine de surface hémagglutinine (HA) pour être infectieux. L’activation a lieu par clivage protéolytique au sein d’une séquence d’acides aminés conservée. Ce clivage doit être effectué par une enzyme de l’hôte, étant donné que le génome du virus ne code pour aucune protéase. Pour les virus infectant l’humain, plusieurs études ont montré le potentiel de protéases à sérine transmembranaires de type II (TTSP) à promouvoir la réplication virale : TMPRSS2, TMPRSS4, HAT, MSPL, Desc1 et matriptase, identifiée récemment par notre équipe (Beaulieu, Gravel et al., 2013), activent l’HA des virus influenza A (principalement H1N1 et H3N2). Toutefois, il existe peu d’information sur le clivage de l’HA des virus influenza B, et seulement TMPRSS2 et HAT ont été identifiées comme étant capables d’activer ce type de virus. Les travaux de ce projet de maîtrise visaient à identifier d’autres TTSP pouvant activer l’HA de l’influenza B. L’efficacité de clivage par la matriptase, hepsine, HAT et Desc1 a été étudiée et comparée entre ces TTSP. Ces quatre protéases s’avèrent capables de cliver l’HA de l’influenza B in vitro. Cependant, seul le clivage par matriptase, hepsine et HAT promeut la réplication virale. De plus, ces TTSP peuvent aussi supporter la réplication de virus influenza A. Ainsi, l’utilisation d’un inhibiteur de TTSP, développé en collaboration avec notre laboratoire, permet de bloquer significativement la réplication virale dans les cellules épithéliales bronchiques humaines Calu-3. Cet inhibiteur se lie de façon covalente et lentement réversible au site actif de la TTSP par un mécanisme slow tight-binding. Puisque cet inhibiteur cible une composante de la cellule hôte, et non une protéine virale, il n’entraîne pas le développement de résistance après 15 passages des virus en présence de l’inhibiteur dans les cellules Calu-3. L’inhibition des TTSP activatrices d’HA dans le système respiratoire humain représente donc une nouvelle stratégie thérapeutique pouvant mener au développement d’antiviraux efficaces contre l’influenza. / Abstract: Seasonal influenza epidemics cause between 3 and 5 millions severe cases of disease, leading to 250 000 to 500 000 deaths worldwide. Only two classes of drugs are currently available to treat influenza infections: neuraminidase inhibitors, such as oseltamivir (Tamiflu) and M2 channel inhibitors (adamantanes). However, the use of these antivirals is restricted by rapid emergence of viral resistance. It is therefore of great interest to develop new therapeutic strategies for the treatment of influenza disease. The influenza virus requires activation of its surface protein hemagglutinin (HA) to become infectious. This activation is achieved by proteolytic cleavage in a highly conserved amino acid sequence of the protein. Host cell proteases are responsible for this cleavage since the viral genome doesn’t encode any protease. For viruses that infect humans, many studies have shown the potential of type II transmembrane serine proteases (TTSP) to promote viral replication: TMPRSS2, TMPRSS4, HAT, MSPL, Desc1 and matriptase, recently identified by our team (Beaulieu, Gravel et al., 2013), activate HA of influenza A viruses (mainly H1N1 and H3N2). However, little is known about cleavage of influenza B virus HA, and only TMPRSS2 and HAT have been identified as being capable of activating this type of virus. This project aimed to identify other TTSPs able to activate influenza B HA. Cleavage efficacies of matriptase, hepsin, HAT and Desc1 were studied and compared. These four proteases were shown to be able to cleave influenza B HA using in vitro assays. However, only cleavage by matriptase, hepsin and HAT promoted viral replication. Moreover, these TTSPs also supported the replication of influenza A viruses. Thus, the use of a slow, tight-binding inhibitor (developed in collaboration with our laboratory) that binds to the TTSP active site, forming a covalent and reversible bond, significantly blocked viral replication in human bronchial epithelial Calu-3 cells. Since this inhibitor targets a host cell component, instead of a viral protein, viruses did not develop resistance after 15 passages in presence of the inhibitor in Calu-3 cells. Thus, inhibition of HA-activating TTSPs in the human respiratory tract represents a novel therapeutic strategy against influenza.

Les proprotéines convertases (PCs) sont des enzymes impliquées de nombreux processus pathologiques. Nous avons étudié deux substrats des PCs: l'apeline et la glycoprotéine B (gB) du virus d'Epstein Barr (EBV), et le rôle de cette maturation protéolytique dans la médiation de leurs fonctions. L'apeline est surexprimée dans plusieurs cancers dont le cancer colorectal (CCR), et nous avons montré que la furine, un membre des PCs, clive l’apeline. Pour déterminer le rôle de ce clivage dans le CCR métastatique, nous avons généré un mutant non clivable (apeline-DM). In vitro, ce mutant inhibe la croissance de cellules cancéreuses du côlonet ne les protège pas de l'apoptose, contrairement à l'apeline sauvage. In vivo, l'apeline-DM diminue drastiquement la croissance tumorale et la formation de métastases hépatiques chez la souris. Les mêmes résultats sont obtenus dans des modèles de souris déficientes pour l’apeline, démontrant l'intérêt d'utiliser l'apeline-DM ou des dérivés comme potentiels agents anticancéreux dans le traitement des CCR métastatiques. La gB du virus EBV, virus impliqué dans certains cancers lymphoïdes et épithéliaux chez l'homme, permet l'entrée du virus dans la cellule lors de l'infection. Nous avons montré que les PCs, et notamment la furine, clivent la gB. In vitro, l'induction de la protéine virale LMP1 augmente l'expression de la furine, qui se traduit par une augmentation de l'infection par EBV. Ces résultats suggèrent l'existence d'une boucle de régulation entre la furine et LMP1 permettant d'améliorer la propagation cellulaire du virus. L'utilisation d'inhibiteurs de l'activité des PCs permettrait donc de bloquer l'infection par EBV. / Proprotein convertases (PCs) are enzymes involved in many pathological processes. We have identified two novel substrates of the PCs: apelin and glycoprotein B (gB) of Epstein Barr Virus (EBV), and studied the role of PC-mediated proteolytic maturation in their functions. Apelin is overexpressed in some cancers including colorectal cancer (CRC), and we demonstrated that furin, one of the PCs member, cleaves apelin in two peptides. To determine the role of apelin cleavage by furin in the metastatic CRC, we generated a non-cleavable mutant (apelin-DM). This mutant inhibited the growth of colon cancer cells in vitro and could not protect against apoptosis, unlike the wild-type apelin. In vivo, apelin-DM drastically reduces tumor growth and the formation of hepatic metastases in mice. These results were confirmed in apelin deficient mouse models thus demonstrating the potential interest of using apelin-DM, or its derivatives, as anticancer agents in the treatment of metastatic CRC. The gB of EBV, a virus involved in some lymphoid and epithelial cancers in humans, is involved in the entry of the virus into the cell during infection. We have shown that PCs, especially furin, cleave gB. In vitro,induction of the LMP1 viral protein increases furin expression, which results in an increase in EBV infection. These results suggest the existence of a regulatory loop between furin and LMP1 to improve the cellular propagation of the virus. The use of inhibitors of PCs activity would thus block EBV infection, a virus against which there is no treatment nowadays.

Xylella fastidiosa é uma bactéria patogênica encontrada em várias plantas. Esta bactéria secreta proteases extracelulares detectadas em gel de eletroforese, sendo a gelatina usada como substrato co-polimerizado. Três principais bandas protéicas foram detectadas com massa molar (MM) de 122, 84 e 65 kDa produzidas pelo isolado de citros (X0) e duas bandas de aproximadamente 84 e 65 kDa de isolado de videira (9713). Estas bactérias produziram zonas de hidrólise em meio sólido contendo gelatina, caseína e hemoglobina. Os resultados usando a gelatina como substrato foram os melhores para a atividade das proteases. A atividade enzimática das proteases de X. fastidiosa de citros e videira foi completamente inibida por PMSF e parcialmente inibida por EDTA, podendo ser visualizado em gel de eletroforese nativo. A temperatura ótima de atividade protéica foi de 30oC e o pH ótimo de 7,0. Além das proteases secretadas por este fitopatógeno, quitinase e &#946;-1,3-glucanase foram também detectadas no sobrenadante das culturas. Os resultados sugeriram que estas proteases produzidas pela X. fastidiosa de citros e videira pertencem ao grupo das serina e metalo proteases. / Xylella fastidiosa is a pathogenic bacterium found in several plants. These bacteria secrete extracellular proteases into the culture broth as visualized in sodium-dodecyl-sulfate polyacrylamide activity gels containing gelatin as a co-polymerized substrate. Three major protein bands were produced by strain X0 (citrus) with molar masses (MM) of 122, 84 and 65 kDa. Grape strain 9713 produced two bands of approximately 84 and 64 kDa. These organisms produced zones of hydrolysis in agar plates amended with gelatin, casein and hemoglobin. Gelatin was the best substrate for these proteases. SDS-PAGE activity gel indicated that the protease activities of X. fastidiosa from citrus and grape were completely inhibited by PMSF and partially inhibited by EDTA. The optimal temperature for protease activity was 30oC with an optimal pH of 7.0. Among the proteolytic enzymes secreted by the phytopathogen, chitinase and &#946;-1,3-glucanase activities were also detected in cultures of X. fastidiosa (citrus). From these results, it is suggested that these proteases produced by strains of X. fastidiosa from citrus and grape, belong to the serine- and metallo-protease group.

The successful genomic era has resulted in a great demand for efficient production and purification of proteins. The main objective of the work described in this thesis was to develop methods to facilitate recovery of target proteins after recombinant production in Escherichia coli. A positively charged purification tag, Zbasic, has previously been constructed by protein design of a compact three-helix bundle domain, Z. The charged domain was investigated for general use as a fusion partner. All target proteins investigated could be selectively captured by ion-exchange chromatography under conditions excluding adsorption of the majority of Escherichia coli host proteins. A single cation-exchange chromatography step at physiological pH was sufficient to provide Zbasic fusion proteins of high purity close to homogeneity. Moreover, efficient isolation directly from unclarified Escherichia coli homogenates could also be accomplished using an expanded bed mode. Since the intended use of a recombinant protein sometimes requires removal of the purification tag, a strategy for efficient release of the Zbasic moiety using an immobilised protease was developed. The protease columns were reusable without any measurable decrease in activity. Moreover, subsequent removal of the released tag, Zbasic, was effected by adsorption to a second cation-exchanger. Using a similar strategy, a purification tag with a negatively charged surface, denoted Zacid, was constructed and thoroughly characterised. Contrary to Zbasic, the negatively charged Zacid was highly unstructured in a low conductivity environment. Despite this, all Zacid fusion proteins investigated could be efficiently purified from whole cell lysates using anion-exchange chromatography Synthesis of polypeptides occurs readily in Escherichia coli providing large amounts of protein in cells of this type, albeit often one finds the recombinant proteins sequestered in inclusion bodies. Therefore, a high throughput method for screening of protein expression was developed. Levels of both soluble and precipitated protein could simultaneously be assessed in vivo by the use of a flow cytometer. The positively charged domain, Zbasic, was shown also to be selective under denaturing conditions, providing the possibility to purify proteins solubilised from inclusion bodies. Finally, a flexible process for solid-phase refolding was developed, using Zbasic as a reversible linker to the cation-exchanger resin. / QC 20101020

<p>The successful genomic era has resulted in a great demand for efficient production and purification of proteins. The main objective of the work described in this thesis was to develop methods to facilitate recovery of target proteins after recombinant production in Escherichia coli.</p><p>A positively charged purification tag, Z_basic, has previously been constructed by protein design of a compact three-helix bundle domain, Z. The charged domain was investigated for general use as a fusion partner. All target proteins investigated could be selectively captured by ion-exchange chromatography under conditions excluding adsorption of the majority of Escherichia coli host proteins. A single cation-exchange chromatography step at physiological pH was sufficient to provide Z_basic fusion proteins of high purity close to homogeneity. Moreover, efficient isolation directly from unclarified <i>Escherichia coli</i> homogenates could also be accomplished using an expanded bed mode. Since the intended use of a recombinant protein sometimes requires removal of the purification tag, a strategy for efficient release of the Z_basic moiety using an immobilised protease was developed. The protease columns were reusable without any measurable decrease in activity. Moreover, subsequent removal of the released tag, Z_basic, was effected by adsorption to a second cation-exchanger. </p><p>Using a similar strategy, a purification tag with a negatively charged surface, denoted Z_acid, was constructed and thoroughly characterised. Contrary to Z_basic, the negatively charged Z_acid was highly unstructured in a low conductivity environment. Despite this, all Z_acid fusion proteins investigated could be efficiently purified from whole cell lysates using anion-exchange chromatography</p><p>Synthesis of polypeptides occurs readily in Escherichia coli providing large amounts of protein in cells of this type, albeit often one finds the recombinant proteins sequestered in inclusion bodies. Therefore, a high throughput method for screening of protein expression was developed. Levels of both soluble and precipitated protein could simultaneously be assessed <i>in vivo</i> by the use of a flow cytometer. </p><p>The positively charged domain, Z_basic, was shown also to be selective under denaturing conditions, providing the possibility to purify proteins solubilised from inclusion bodies. Finally, a flexible process for solid-phase refolding was developed, using Z_basic as a reversible linker to the cation-exchanger resin.</p>

Η σεργλυκίνη (SG) είναι η κύρια πρωτεογλυκάνη που εκφράζεται από τα αιμοποιητικά κύτταρα και συμμετέχει στη ρύθμιση διαφόρων παραγόντων που εμπλέκονται στις αντιδράσεις φλεγμονής. Επιπλέον, φαίνεται ότι διαδραματίζει σημαντικό ρόλο στη βιολογία του πολλαπλού μυελώματος αφού αναστέλλει τη δραστικότητα της κλασικής οδού και της λεκτινικής οδού του συμπληρώματος και προάγει την προσκόλληση των μυελωματικών κυττάρων στο κολλαγόνο τύπου Ι. Παράλληλα, η αυξημένη έκφρασή της σχετίζεται με τον επιθετικό φαινότυπο των κυττάρων καρκίνου του ρινοφάρυγγα. Στην παρούσα διατριβή μελετήθηκε η έκφραση της SG σε κακοήθειες. Τα αποτελέσματά μας αναδεικνύουν την έντονη παρουσία της σε συμπαγείς όγκους λόγω της αυξημένης έκφρασή της είτε από τα καρκινικά κύτταρα είτε από τα κύτταρα φλεγμονής και τα κύτταρα του στρώματος τα οποία επιστρατεύονται κατά την ανάπτυξη του όγκου. Επιπλέον, η αυξημένη έκφρασή της και η έκκρισή της σχετίσθηκαν με το μεταστατικό δυναμικό των κυτταρικών σειρών διαφόρων τύπων καρκίνου. Παράλληλα, ταυτοποιήθηκε η έκφραση του μεταγράφου της SG που προκύπτει από εναλλακτικό μάτισμα με απαλοιφή του εξωνίου 2. Επιπροσθέτως, μελετήθηκε ο βιολογικός ρόλος της SG σε επιθετικά καρκινικά κύτταρα μαστού. Βρέθηκε ότι η SG αλληλεπιδρά με πρωτεΐνες που διαδραματίζουν σημαντικό ρόλο σε κυτταρικές λειτουργίες όπως η αναδιοργάνωση του κυτταροσκελετού, η μεταφορά και ανακύκλωση μορίων από και προς την κυτταρική επιφάνεια και η γονιδιακή ρύθμιση. Η ίδια πρωτεογλυκάνη εκκρίνεται ιδιοσυστατικά από αυτά τα κύτταρα. Τόσο η γλυκοζαμινογλυκανική της σύσταση όσο και η ανασταλτική της δράση έναντι της ενεργοποίησης του συστήματος του συμπληρώματος είναι παρόμοιες με τη SG που εκκρίνεται από τα μυελωματικά κύτταρα. Η συμβολή της SG στον επιθετικό φαινότυπο των καρκινικών κυττάρων επιβεβαιώθηκε με την υπερέκφρασή της σε χαμηλής επιθετικότητας κύτταρα καρκίνου του μαστού. Λειτουργίες όπως ο κυτταρικός πολλαπλασιασμός, η μετανάστευση και η διήθηση των καρκινικών κυττάρων σχετίσθηκαν θετικά με την αυξημένη έκφραση και έκκριση της SG από αυτά τα κύτταρα. Οι επαγωγικές της ιδιότητες καταργήθηκαν με την απαλοιφή των θέσεων πρόσδεσης των γλυκοζαμινογλυκανών από τον πρωτεϊνικό της κορμό. Επιπλέον, διερευνήθηκε το πρωτεολυτικό δυναμικό αυτών των κυττάρων με τη μελέτη της έκφρασης πρωτεολυτικών ενζύμων του εξωκυττάριου χώρου, όπως οι tPA, uPA, MMP-1, MMP-2, MMP-3, MMP-9, MT1-MMP και του αναστολέα των μεταλλοπρωτεϊνασών TIMP-1. Παρουσιάσθηκε ότι η υπερέκφραση του πλήρους μορίου της SG αλλά και της μη γλυκοζυλιωμένης της μορφής οδηγούν στη διαφοροποίηση της έκφρασης και της ενεργότητας των μορίων αυτών με τρόπο που ποικίλει ανάλογα με την κυτταρική πυκνότητα. Παρόλα αυτά, τα δεδομένα που προέκυψαν από τη μελέτη της έκφρασης του uPA και της MT1-MMP συσχέτισαν την αυξημένη τους ενεργότητα με την υπερέκφραση της γλυκοζυλιωμένης μορφής της SG και ανέδειξαν την πιθανή συμβολή τους στην επιθετικότητα των καρκινικών κυττάρων μαστού. Συμπερασματικά, η παρουσία της SG είναι έντονη σε πληθώρα συμπαγών όγκων και καρκινικών κυτταρικών σειρών και φαίνεται να σχετίζεται με το μεταστατικό δυναμικό των κυττάρων. Η συμβολή της στον επιθετικό φαινότυπο των καρκινικών κυττάρων περιλαμβάνει τόσο ενδοκυττάριες όσο και εξωκυττάριες δράσεις που μεσολαβούνται από τη γλυκοζυλιωμένη της μορφή. / Serglycin (SG) is the major proteoglycan of hematopoietic origin cells and contributes to the regulation of several inflammatory proteins. Moreover, SG has a significant role in the biology of Multiple Myeloma; It inhibits the activation of the classical and the lectin pathway of complement system. Enhanced SG expression is correlated with the aggressive phenotype of nasopharyngeal cancer cells. In the present study, the expression of SG in several malignancies was investigated. The strong presence of SG in solid tumors due to its elevated expression either by cancer cells or by inflammatory and stomal cells was revealed. Furthermore, SG elevated expression and secretion was correlated with the high metastatic potential of several cancer cell lines. The expression of the alternatively spliced SG mRNA (variant 2) was identified. This variant lacks exon 2. The role of SG in the biology of aggressive breast cancer cells was studied. SG interacts with significant mediators of actin cytoskeleton reorganization, protein transport and regulation of gene expression. This proteoglycan is constitutively secreted by aggressive breast cancer cells and shares the same glycosaminoglycan (GAG) moieties and inhibitory effects torward complement system activation as the secreted SG by myeloma cells. SG contribution in the aggressive phenotype of cancer cells was studied via the overexpression of the moleclule in the low aggressive breast cancer cells. Cellular functions such as proliferation, migration and invasion of cancer cells were positively correlated with the elevated expression and secretion of SG. These properties were abolished by the deletion of GAG binding sites from SG core protein. Moreover, the proteolytic potential of the overexpressing cells was examined via the expression of ECM degrading molecules, such as tPA, uPA, MMP-1, MMP-2, MMP-3, MMP-9, MT1-MMP, and TIMP-1 MMP inhibitor. Altered expression and activity rates of these enzymes correlated with the overexpression of either the full length or the truncated form of SG in a manner which depends on the cellular density. Interestingly, enhanced MT1-MMP activity followed only the overexpression of the full length molecule indicating the contribution of this MMP in breast cancer cell aggressiveness. The data above revealed the intense presence of SG in several solid tumors and cancer cell lines and the correlation of SG expression with the metastatic potential of cancer cells. Its contribution to cancer cells aggressive phenotype includes both intracellular and extracellular functions which are mediated by the glycanated form of SG.