Thesis (PhD)--Stellenbosch University, 2013. / ENGLISH ABSTRACT: It is widely accepted that insufficient insulin-stimulated activation of muscle glycogen synthesis is one of the major components of non-insulin-dependent (type 2) diabetes mellitus. Glycogen synthase, a key enzyme in glycogen synthesis, is extensively regulated, both allosterically (by glucose-6-phosphate, ATP, and other ligands) and covalently (by phosphorylation). Although glycogen synthase has been a topic of intense study for more than 50 years, its kinetic characterization has been confounded by its large number of phosphorylation states. Questions remain regarding the function of glycogen synthase regulation and the relative importance of allosteric and covalent modification in fulfilling this function. The regulation of glycogen synthase and glycogen phosphorylase, the enzyme that catalyses the degradation of glycogen chains, are reciprocal in many respects. In the present research, using mathematical modelling, we aim to establish the function of the allosteric and covalent regulation of glycogen synthase and glycogen phosphorylase in muscle and, in the case of glycogen synthase, the relative importance of these two mechanisms in performing this function. In order to realize these aims it is essential that a detailed kinetic model of glycogen metabolism is constructed. We begin with a thorough review of the kinetics and regulation of glycogen synthase inwhich we propose that both allosteric and covalent modification of glycogen synthase can be described by a Monod-Wyman-Changeux model in terms of apparent changes to L0, the equilibrium constant between the T and R conformers. We then proceed to develop a rate equation according to the proposed Monod-Wyman-Changeux model and determine values for its kinetic parameters from published experimental data using non-linear least-squares regression. We show that the application of the Monod-Wyman-Changeux model to glycogen synthase kinetics also has important implications for the rate equations of enzymes that catalyse the phosphorylation and dephosphorylation of glycogen synthase. We formalize these implications for a generic protein that follows Monod-Wyman-Changeux-type conformational change and then also show how the findings apply to glycogen synthase. Taking into account the kinetic model of glycogen synthase and how it also influences the covalent regulation of the enzyme, we proceed to construct a detailed mathematical model of glycogen synthesis that includes the glycogen synthase phosphorylation cascade. A variation of this model in which glycogen synthase phosphorylation is described with a single parameter is also provided. We reuse an existing model of muscle glycogenolysis and also combine these models in an overall model of glycogen metabolism. Finally, we employ the theoretical frameworks of metabolic control analysis, supply-demand analysis, and co-response analysis to investigate the function of glycogen synthase and glycogen phosphorylase regulation. We show that the function of glycogen synthase regulation is not flux control, as assumed in the textbook view, but rather the maintenance of glucose-6-phosphate within a narrow range far from equilibrium. Similarly, we show that regulation of glycogen phosphorylase functions to minimize variation in cellular energy charge in the face of highly variable energy demand. We conclude with an appeal for a renewed interest in the enzyme kinetics of muscle glycogen metabolism. / AFRIKAANSE OPSOMMING: Daar word wyd aanvaar dat onvoldoende insulien-gestimuleerde aktivering van spierglikogeensintese een van die hoofkomponente van insulien-onafhanklike (tipe 2) diabetes mellitus is. Glikogeensintase, ’n sleutelensiem in glikogeensintese is onderworpe aan breedvoerige regulering, beide allosteries (deur glukose-6-fosfaat, ATP, en ander ligande) en kovalent (deur fosforilering). Alhoewel glikogeensintase reeds vir meer as 50 jaar deeglik bestudeer word, word die kinetiese karakterisering daarvan bemoeilik deur die groot aantal fosforilasiestate waarin die ensiem voorkom. Daar is steeds vrae betreffende die funksie van die regulering van glikogeensintase en die relatiewe bydrae van allosteriese en kovalente regulering in die vervulling van hierdie funksie. Die regulering van glikogeensintase en glikogeenfosforilase, die ensiem wat die afbraak van glikogeenkettings kataliseer, is in baie opsigte resiprook. In hierdie studie beoog ons om met die hulp van wiskundige modellering vas te stel watter funksie die regulering van glikogeensintase en glikogeenfosforilase vervul en, in die geval van glikogeensintase, wat die relatiewe belang is van allosteriese en kovalente regulering in die vervulling van hierdie funksie. Om hierdie oogmerke te verwesentlik is dit nodig dat ’n kinetiese model van glikogeenmetabolisme ontwikkel word. Ons begin met ’n omvattende oorsig van die kinetika en regulering van glikogeensintase waarin ons voorstel dat beide die allosteriese en kovalente regulering van glikogeensintase beskryf kan word met die Monod-Wyman-Changeux model in terme van oënskynlike veranderings aan L0, die ekwilibriumkonstante tussen die T en R konformasies. Ons gaan dan voort om ’n snelheidsvergelyking te ontwikkel volgens die voorgestelde Monod-Wyman-Changuex-model en bepaal ook die waardes van hierdie vergelyking se parameters vanaf gepubliseerde eksperimentele data deur middel van nie-lineêre kleinste-vierkantsregressie. Ons wys dat die toepassing van die Monod-Wyman-Changuex-model op glikogeensintase-kinetika belangrike gevolge het vir die snelheidsvergelykings van die ensieme wat die fosforilering en defosforilering van glikogeensintase kataliseer. Ons formaliseer hierdie gevolge vir ’n generiese Monod-Wyman-Changeux-tipe proteïen en wys dan ook hoe die bevindings op glikogeensintase van toepassing is. Met inagneming van die kinetiese model vir glikogeensintase en hoe dit die kovalente regulering van die ensiem be¨ınvloed, gaan ons voort om ’n gedetaileerde wiskundige model van glikogeensintese, wat ook die glikogeensintase-fosforileringskaskade insluit, te ontwikkel. ’n Variasie op hierdie model waarin die fosforilering van glikogeensintase deur ’n enkele parameter beskryf word, word ook voorsien. Ons herbruik ’n bestaande model van spierglikogenolise en kombineer ook hierdie modelle in ’n oorkoepelende model van glikogeenmetabolisme. Uiteindelik span ons die teoretiese raamwerke van metaboliese kontrole-analise, vraag-aanbod-analise, en ko-responsanalise in om die funksie van die regulering van glikogeensintase en glikogeenfosforilase te ondersoek. Ons wys dat die funksie van die regulering van glikogeensintase nie fluksiekontrole, soos algemeen in handboeke aangeneem word, is nie, maar liewer dat dit glukose-6-fosfaat handhaaf binne ’n noue band ver vanaf ekwilibrium. Insgelyks wys ons dat die regulering van glikogeenfosforilase funksioneer om variasie in sellulˆere energielading te beperk ten spyte van hoogs wisselende vlakke van energie-aanvraag. Ons sluit af met ’n pleidooi vir hernieude belangstelling in die ensiemkinetika van glikogeenmetabolisme in die spier. / National Research Foundation

Thesis (PhD)--Stellenbosch University, 2013. / ENGLISH ABSTRACT: Exposure to food contaminates such as mycotoxins have been associated with a variety of animal and human diseases worldwide. In South Africa, maize is the most To further refine risk assessment in the socio-demographic heterogeneous population of South Africa, the development and evaluation of a sensitive and interactive model the Mycotoxin Risk Assessment Model (MYCORAM) proofed to be more sensitive compared to the classical probable daily intake (PDI). The development of the MYCORAM was based on mycotoxin distribution during dry milling of maize in milling fractions intended for human consumption which was superimposed on the maize intake profiles of the South African population. Although dry milling, including a degerming step, is an effective way to reduce mycotoxins, risk and exposure assessment are influenced by maize dietary intakes, gender and ethnicity. This became evident when considering FB dietary exposure in rural maize subsistence farming communities in the Eastern Cape Province, South Africa confirmed the vulnerability of this subpopulation to risk of fumonisin exposure. Specific maximum tolerated maximum levels (MTL) to safeguard these communities fall outside the international regulatory processes and need to be urgently addressed. With the complex nature of cancer development in mind, integration of basic science and nutritional epidemiology will be important to contribute to our understanding of the adverse effects of FB and to define relevant risk assessment parameters. important commercial grain crop not just economically but also as a local food commodity both commercially and in subsistence rural farming communities. In order to control and manage mycotoxin contamination in food, evidence-based risk assessment is needed that includes mechanistic and human exposure studies. From this perspective the current study was conducted and aimed in further unravelling fumonisin B1 (FB1) mycotoxin induced hepatocarcinogenesis via the disruption of the lipid metabolism. The study also critically evaluates aspects of human risk assessment due to its relevance and importance to food safety known to impact on food security. This entails mycotoxin distribution during maize dry milling and the assessment of mycotoxin exposure in the South African population and vulnerable rural communities at risk. Fumonisin B1 affects the integrity of biological membranes by altering key lipid and fatty acid parameter in plasma, microsomal, mitochondrial and nuclear subcellular membrane fractions in rat liver. Changes in the major lipid constituents entailing an increase in cholesterol (CHOL) and phosphatidylethanolamine (PE) whilst sphingomyelin (SM) and phosphatidylcholine (PC) tended to decrease. Isolated plasma membrane lipid rafts, from rat primary hepatocytes exposed to FB1 augments the intricate effects exerted on the lipid metabolism regarding CHOL, SM and PE. The disruption of lipid and fatty acid constituents, such as arachidonic acid and ceramide, are likely to be key determinants affecting growth regulatory signaling pathways relevant to the critical balance between cell proliferation and apoptosis during cancer promotion. These changes provide further evidence that FB1 induce cancer promotion by differential inhibition and/or stimulation process whereby a few resistant “initiated” hepatocytes proliferate in an environment where the growth of normal cells is inhibited. A specific lipogenic phenotype is effected by FB1 which is closely associated with cancer development and considered to occur via an epigenetic-type of mechanism. These effects are not adequately addressed in defining risk assessment parameters. / AFRIKAANSE OPSOMMING: Die blootstelling aan voedsel-kontaminante soos mikotoksienes word wêreldwyd met ‘n verskeidenheid van dierlike en menslike siektes geassosiseer. In Suid-Afrika word mielies as ‘n belangrike graanoes beskou, nie net vir die ekonomie nie maar ook as ‘n plaaslike voedselproduk beide kommersieel en vir bestaansboere in landelike gemeenskappe. Ten einde mikotoksien-kontaminasie van voedsel te kan beheer en bestuur, vereis bewys-gebaseerde risiko-evaluering wat insluit meganistiese en menslike blootstelling studies. Vanuit hierdie perspektief is die huidige studie uitgevoer en gemik op die verdere ontleding van die fumonisin B1 (FB1) mikotoksien geïnduseerde lewer-karsinogenese deur die ontwrigting van die lipiedmetabolisme. Die studie ondersoek terselfdetyd aspekte van menslike risiko-evaluering ingevolge die relevansie en belangrikheid hiervan in voedselveiligheid wat ook ‘n impak op voedselsekerheid sal maak. Dit sluit in die verspreiding van mikotoksiene gedurende die droëmaalproses van mielies en mikotoksien blootstelling in Suid-Afrika asook onder kwesbare landelike gemeenskappe. Fumonisin B1 beïnvloed die integriteit van biologiese membrane deur die modulasie van die belangrike lipied en vetsuur samestelling van plasma, mikrosomale, mitochondriale en kern subsellulêre membraan-fraksies in rot lewer. Veranderinge in die belangrike lipiedbestanddele, insluitende ‘n verhoging in cholesterol (CHOL) en phosphatidylethanolamine (PE), terwyl sphingomyelin (SM) en phosphatidylcholine (PC) geneig was om te verlaag. Geïsoleerde plasma membraan lipied vlotte (lipid rafts), vanaf primêre rot hepatosiete blootgestel aan FB1, versterk die ingewikkelde gevolge wat uitgeoefen word op die lipiedmetabolisme insluitende die voorgestelde veranderings in CHOL, SM en PE vlakke. Die versteuring van lipiede en vetsure soos aragidoonsuur (arachidonic acid) en ceramied kan beskou word as belangrike determinante wat inmeng in groei-regulerende seinbane verwant aan die kritiese balans tussen selgroei en seldood. Die versteurings verskaf verdere bewyse dat FB1 kanker bevorder deur ‘n seleksie proses wat onderskeidelike die onderdrukking en\of die stimulasie van ‘n paar weerstandige of geneties veranderde hepatosiete laat vermeerder in ‘n omgewing waar die groei van normale selle geïnhibeer word. Die spesifieke lipogeniese fenotipe wat FB1 versoorsaak hou ten nouste verband met kankerontwikkeling en die voorkoms van epigenetiese-soort meganismes word voorgestel. Hierdie oorsake word tans nie voldoende aangespreek tydens die bepaling van risiko-evaluerings limiete nie. Om risiko-bepaling verder te verbeter in die sosio-demografies heterogene populasie van Suid-Afrika, was die ontwikkeling en evalueering van ‘n sensitiewe en interaktiewe model, die “Mycotoxin Risk Assessment Model” (MYCORAM) meer doeltreffend vergeleke met die gewone waarskynlike daaglikse inname. Die ontwikkeling van die MYCORAM was gebaseer op die mikotoksien verspreiding tydens die droëmaalproses van mielies in fraksies wat vir menslike verbruik bedoel was tesame met mielie dieetinnames van die Suid-Afrikaanse populasie. Alhoewel, die droëmaalproses van mielies, insluitende die verwydering van die kiem doeltreffende maniere is om mikotoksienes te verminder, word risiko- en blootstellings evaluering beinvloed deur mielie dieetinnames, geslag en etnieseverbandskap. Hierdie was veral opmerklik gedurende blootstelling aan FB in die dieet van landelike mielie bestaansboer gemeenskappe in die Oos-Kaap van Suid- Afrika en bevestig hoe kwesbaar hierdie populasie is. Spesifieke maksimum toelaatbare vlakke om hierdie gemeenskappe te beskerm val buite die huidige internasionale regulatoriese prosesse en benodig dringende aandag. Met die ingewikkelde aard van kankerontwikkeling in gedagte, sal die integrasie van basiese wetenskappe en voedingsepidemiologie, ‘n belangrik bydrae lewer tot die kennis van die negatiewe eienskappe van FB om toepaslike risiko-evaluerings limiete te kan bepaal.

Thesis (PhD)--Stellenbosch University, 2013. / ENGLISH ABSTRACT: The present study employed a two-phased approach to investigate the possible mechanisms involved in the chemopreventive properties of rooibos (Aspalathus linearis) and different honeybush species (Cyclopia spp.) in vitro. In the first phase, the effect of unfermented methanol and aqueous herbal tea extracts against the growth parameters (cell viability, proliferation and apoptosis) of normal (CRL 7761); premalignant (HaCaT); and malignant (CRL 7762) skin cells was evaluated and compared to green tea extracts. The predictive potential of polyphenol content (total polyphenol and flavanol/proanthocyanidins) and antioxidant properties (ABTS; ORAC; FRAP and LPO) in the biological activity of extracts in cells was also assessed. Of the herbal teas, the methanol extract of rooibos was the most active and it inhibited the growth of skin cells presumably by inducing mitochondrial dysfunction via membrane depolarisation. At lower concentrations, this activity was associated with inhibition of cell proliferation that was selective for cancer cells whilst higher concentrations induced apoptosis that was more prominent in premalignant cells. The strong antioxidant properties of the extracts implicated the role of pro-oxidative polyphenol/iron interactions involving monomeric flavonoids and polymeric proanthocyanidins in the cytotoxic effects of rooibos. The strong relationship between total polyphenolic and flavanol/proanthocyanidins content, antioxidant properties and reduction of cell viability indicated that these parameters (polyphenols and antioxidant properties) can serve as predictive tools for the cytotoxic effects of rooibos in vitro. The aqueous extracts of honeybush species, although weaker, displayed similar effects to rooibos extracts in cells with C. genistoides being the most effective at selectively inhibiting the proliferation of cancer cells whilst the pro-apoptotic activity of C. subternata and C. intermedia was more prominent in premalignant cells. The underlying mechanisms are also likely to result from pro-oxidative mechanisms resulting from polyphenol/iron interactions that mainly involve polymeric flavanol-like proanthocyanidin compounds in honeybush. In contrast, the methanol extracts exhibited weaker cytotoxic effects and protected cancer cells from going into apoptosis. The cytoprotective effects of honeybush species are possibly mediated by the major monomeric compounds such as mangiferin and hesperidin through antioxidant mechanisms that result in reduction of oxidative stress. Due to the possible dual role of the monomeric and polymeric compounds in the honeybush extracts, the total polyphenolic content of these herbal teas may not be a good indicator of biological activity in vitro. However, as aqueous extracts displayed high flavanol/proanthocyanidins content and exceptional activity in the ABTS assay, these parameters may be considered as indicators of cytotoxicity. On the other hand, methanol extracts, particularly from the xanthone-rich species (C. genistoides and C. longifolia) which exhibited the weakest cytotoxic effects, were more active in the ORAC thus this assay may be a useful predictor for cytoprotective activity. In the second phase, an in vitro UVB/HaCaT model which used IL-1α as a biomarker for early inflammation was developed and validated with known anti-inflammatory compounds, dexamethasone and ibuprofen. It was used to determine the specific mechanisms involved in the modulatory effects of the herbal tea extracts against inflammation. Rooibos extracts and the aqueous extract of honeybush enhanced the cytotoxic effects of UVB in the model and exhibited indirect anti-inflammatory effects as they removed icIL-1α containing cells via apoptosis. In contrast, methanol extracts of honeybush exacerbated icIL-1α by protecting UVB stimulated cells from undergoing apoptosis. In conclusion, methanol extract of rooibos and aqueous extracts of honeybush species may be useful in protecting the skin after UVB exposure. These herbal tea extracts may block initiation and delay the promotion stage during skin carcinogenesis by removing premalignant cells via apoptosis and preventing onset of inflammation. In contrast, due to their cytoprotective effects, methanol extracts of honeybush may be more effective at preventing oxidative stress in skin before UVB exposure. Future studies should focus on the effects of extracts and polyphenolic fractions on the oxidative status of the cells and development of biomarkers of chemoprevention that can be utilised in vivo and in human skin. / AFRIKAANSE OPSOMMING: In hierdie studie word moontlike velkankerwerende eienskappe van rooibos (Aspalathus linearis) en ‘n aantal heuningbos (Cyclopia spp.) spesies deur twee afsonderlike benaderings bestudeer. Die eerste benadering ondersoek die effek van die kruietee op groeiparameters van velselle [lewensvatbaarheid, groei en dood van normale selle (CRL 7761), vroeë kankerselle (HaCaT) en kankerselle (CRL 7762)]. Tydens eksperimente is die moontlikheid om polifenoolinhoud (totale polifenole, en flavanol/proantosianidiene verhouding) en antioksidant-eienskappe te gebruik om die biologiese funksies van die ekstrakte in die selle te voorspel, geevalueer. Die metanolekstrak van rooibos het die groei van selle die effektiefste gestop, moontlik deur depolarisasie van die mitokondriale membraan. By lae konsentrasies van die ekstrak is die groei van kankerselle selektief gestop, terwyl vroeë kankerselle die sensitiefste by hoër konsentrasies was. Die hoë antioksidant-aktiwiteit van die rooibosekstrak kan moontlik ‘n rol speel in die indusering van sitotoksiese effekte in die selle en kan toegeskryf word aan die pro-antioksidant aktiwiteit van die polifenole weens hul interaksie met yster. ‘n Spesifieke funksie word vir die monomeriese flavonoïede en die polimeriese proantosianidiene geïmpliseer. Die sterk verwantskap tussen die totale polifenoolinhoud, flavanol/proantosianidien inhoud en antioksidant aktiwiteit met die verlaging in selgroei, maak hul relevante parameters van die voorspellingsmodel. Die waterekstrakte van heuningbos induseer ook soortgelyke maar swakker effekte met die induksie van kankersel dood, met C. genistoides die selektiefste en C. subternata en C. intermedia die aktiefste spesies wat die groei van die vroeë kanker selle inhibeer. Die onderliggende meganismes betrokke blyk ook aan ‘n pro-oksidant effek toe geskryf te wees, waartydens spesifieke polifenool/yster interaksies betrokke is. In teenstelling met rooibos, beskerm die metanolekstrak van heuningbos kankerselle teen seldood, wat moontlik verband hou met die antioksidant-eienskappe van die hoof monomeriese polifenole, mangiferien/isomangiferien en hesperidien. Vanweë die dubbele rol van die monomeriese polifenole en polimeriese verbindings in heuninghbosekstrakte is die totale polifenol inhoud nie ‘n goeie indikator van die biologiese aktiwiteit in vitro nie. Daarenteen is die flavanol/proantosianien inhoud en die hoë aktiwiteit in die ABTS antioksidanttoets goeie indikators om seldood te voorspel. In teenstelling hiermee het die metanolekstrakte van die xantoon-ryke spesies (C. genistoides en C. longifolia) ‘n baie lae effek op seldood, maar ‘n hoë aktiwitiet in die ORAC toets getoon, wat ‘n goeie rigtingwyser is om die beskermende effek in selle te voorspel. Met die tweede benadering is die anti-inflammatoriese eienskappe en die onderliggende meganismes van die kruietee ondersoek in ‘n UVB/HaCaT selmodel. Intrasellulêre interleukin 1α (IL-1α) is as merker gebruik en die model is geëvalueer deur bekende anti-inflammatoriese verbindings soos dexamethasone en ibuprofin te gebruik. Die metanolekstrak van rooibos en die waterekstrak van heuningbos het die toksiese effek van UVB in die model verhoog deur selle met verhoogde vlakke,van icIL-1α te verwyder deur middel van die induksie van seldood. Die metanolekstrak beskerm die selle teen die oksidatiewe skade wat deur UVB geïnduseer word en verwyder nie selle met hoë IL-1α vlakke nie. Ter opsomming blyk dit dat die metanolekstrak van rooibos en die waterekstrak van heuningbos moontlik gebuik kan word om die vel te beskerm teen die induksie van icIL-1α en sodoende die inisiëring van kanker te blokkeer en ook die promosie van kanker te vertraag. Die beskermende effek van die metanolekstrak kan moontlik aangewend word om die oksidatiewe skade wat deur UVB veroorsaak word teen te werk deur dit aan te wend voordat blootstelling plaasvind. Toekomstige studies behoort verdere karakterisering van die polifenoolsamestelling van die ekstrakte in te sluit en hul effek op die oksidatiewe status en anti-inflammoriese effekte van selle te bepaal ten einde sekere merkers te identifiseer vir vel studies in vivo.

Thesis (PhD)--Stellenbosch University, 2013. / ENGLISH ABSTRACT: This dissertation explores the behaviour and regulation of central carbon metabolism in Escherichia coli K12 W3110 under fermentative microaerobic conditions. To achieve this, an integrative systems modelling approach was adopted, which is introduced in Chapter 1 along with a review of metabolism in E. coli. An open-source software suite NMRPy, developed using the Python programming language, is presented in Chapter 2. NMRPy provides a host functions for basic processing, analysis and visualisation of Nuclear Magnetic Resonance (NMR) spectroscopy data. In addition to this, NMRPy offers specialised functions for the deconvolution of arrayed reaction time series, which proved indispensable to the research presented in this dissertation. NMRPy presents an easy to use, extensible tool for both routine and advanced use. In Chapter 3, a novel methodology is presented which was developed for the effective and comprehensive determination of enzyme kinetic parameters for systems biology using NMR. In contrast to traditional enzyme kinetic assay methods, this new methodology is less labour-intensive and yields significantly more information per experiment. By fitting kinetic equations to real time NMR data, dynamic changes in substrates, products and allosteric modifiers are quantified and allowed to inform the parameter fitting procedure. These data contain information on cooperative substrate binding, reversibility, product inhibition and allosteric effects. The proposed methodology is applied to the study of the first two enzymes of the glycolytic pathway. In Chapter 4, the construction, parameterisation and validation of a number of kinetic models of glycolysis in E. coli under microaerobic conditions is detailed. To model the lower half of glycolysis, a similar technique was adopted as in Chapter 3, in which models representing the reactions from triosephosphate isomerase to pyruvate kinase were parameterised by fitting them to a collection of 31P NMR reaction time series. This approach extends the methodology to enzyme sub-networks, yielding data that encompass the full complexity of the network regulatory interactions. The verified kinetic models were subjected to scrutiny, the results of which are presented in Chapter 5. The value of the modelling approach is demonstrated by the ease with which cumbersome in vivo experiments can be performed in silico. A structural analysis of the model topology was conducted, elucidating the elementary flux modes of fermentative glycolysis in E. coli, and identifying a futile cycle around PEP carboxylase and PEP carboxykinase. Model steady-state behaviour and control properties were explored in silico under various degrees of ATP demand and oxygen availability and a number of hypotheses are presented, explaining the regulation of free energy in E. coli, and the metabolic responses of E. coli to changing redox demands. Amongst other things, the results demonstrated that the glucose importing phosphoenolpyruvate: phosphotransferase pathway controlled glycolytic flux, and that under microaerobic conditions E. coli is able to regulate redox balance not only by balancing flux between acetate and ethanol, but also by altering the balance of flux between acetate and lactate at the pyruvate formate lyase/lactate dehydrogenase branch point. This study demonstrates the value of an integrated computational and experimental systems approach to exploring biological phenomena. / AFRIKAANSE OPSOMMING: In hierdie proefskrif word die gedrag en regulering van die sentrale koolstofmetabolisme in Escherichia coli K12 W3110 onder fermenterende mikro-a¨erobiese toestande ondersoek. Dit is moontlik gemaak deur ’n ge¨ıntegreerde stelsel-modelleringsbenadering, wat in Hoofstuk 1 bekendgestel word. D´ıe hoofstuk verskaf ook ’n oorsig van die metabolisme in E. coli. ’n Oopbron-kodepakket NMRPy, wat in die programmeringstaal Python ontwikkel is, word in Hoofstuk 2 beskryf. NMRPy verskaf ’n aantal funksies vir die basiese verwerking, analise en visualisering van Kern-Magnetiese Resonansie (KMR) spektroskopiese data, sowel as gespesialiseerde funksies vir die dekonvolusie van opeenvolgende reaksie-tydreekse. Hierdie funksionaliteit was onontbeerlik vir die verdere navorsing in hierdie proefskrif. Hoofstuk 3 beskryf die ontwikkeling van ’n nuwe metodiek vir die omvangryke bepaling van ensiem-kinetiese parameters vir sisteembiologie, deur van KMR gebruik te maak. In teenstelling tot tradisionele ensiem-kinetiese essai-metodes, is hierdie nuwe metodologie minder arbeidsintensief en lewer dit beduidend meer inligting per eksperiment. Deur die kinetiese vergelykings op tydsafhanklike KMR data te pas, word dinamiese veranderinge in substrate, produkte en allosteriese effektors gekwantifiseer en hierdie inligting gebruik in die passingsprosedure. Die data bevat inligting oor ko¨operatiewe substraatbinding, omkeerbaarheid, produkinhibisie en allosteriese effekte. Die voorgestelde metodologie word toegepas op die karakterisering van die eerste twee glikolitiese ensieme. In Hoofstuk 4 word die konstruksie, parameterisering en validering van ’n aantal kinetiese modelle van glikolise in E. coli onder mikro-a¨erobiese toestande uiteengesit. Die waarde van die modelleringsbenadering lˆe in die gemak waarmee omslagtige in vivo eksperimente in silico uitgevoer kan word. Om die onderste helfte van die glikolitiese pad te modelleer word ’n soortgelyke tegniek as in Hoofstuk 3 gebruik. Modelle van die reaksies vanaf triosefosfaat-isomerase tot by pirovaat-kinase is geparameteriseer deur dit op ’n versameling 31P KMR-tydreekse te pas. Hierdie benadering brei bostaande metodologie uit tot ensiem-subnetwerke en genereer data wat die volle kompleksiteit van regulerende interaksies in die netwerk insluit. Die geverifieerde modelle word in Hoofstuk 5 noukeurig ondersoek. ’n Strukturele analise van die modeltopologie word onderneem om die elementˆere fluksie-modes van fermentatiewe glikolise in E. coli te verklaar, sowel as om ’n futiele siklus rondom fosfo¨enolpirovaat karboksilase en fosfo¨enolpirovaat karboksikinase te identifiseer. Die bestendige-toestandsgedrag en kontrole-eienskappe word in silico ondersoek onder toestande van verskeie ATP beladings en suurstofbeskikbaarheid. ’n Aantal hipoteses word voorgelˆe, wat die regulering van vry energie in E. coli, sowel as die metaboliese reaksies van E. coli onder veranderende redoks-vereistes kan verklaar. Onder andere dui die resultate daarop dat die fosfo¨enolpirovaat:fosfotransferase sisteem (wat verantwoordelik is vir glukose-opname in die sel) die glikolitiese fluksie beheer en dat E. coli onder mikro-a¨erobiese toestande die redoksbalans nie net tussen asetaat en etanol kan reguleer nie, maar ook die deur wysiging van die fluksie-balans tussen asetaat en laktaat rondom die pirovaat-formiaat-liase/laktaatdehidrogenase vertakkingspunt. Hierdie studie toon die waarde van ’n ge¨ıntegreerde rekenaarmatige en eksperimentele sisteembenadering om biologiese verskynsels te ondersoek.

Thesis (PhD)--Stellenbosch University, 2014. / ENGLISH ABSTRACT: The global rise in microbial resistance, ranging from the agricultural industry to the medical sector, has created the urgent need for novel or supplementary antibiotics. Antimicrobial peptides or “nature’s antibiotics” may be the answer to this major problem. In this study a group of antimicrobial peptides, cyclic decapeptides named tyrocidines, produced by the soil bacterium Bacillus aneurinolyticus, was investigated for their antifungal activity, possible mode of antifungal action and potential applications. The study illustrated that the tyrocidines have significant antifungal activity against a range of phytopathogens, including Fusarium solani and Botrytis cinerea, as well as the human pathogen Candida albicans. The activity of the tyrocidines is influenced by the identity of both the target organism and the media environment. Further evidence was obtained in support of the hypothesis that the tyrocidines are extremely sensitive to their environmental conditions and that they tend to self-assemble to form oligomers. The assessment of a small tyrocidine library and analogues, comprised of eight peptides, revealed no overt structure-activity relationships against fungal pathogens, except for the importance of a tyrosine residue. This indicated an important role for the conserved sequence of the tyrocidines, NQYVOLfP, together with the tendency of the tyrocidines to oligomerise into higher-order active structures in their antifungal activity. The tyrocidines were found to be membrane active toward the fungal pathogens. However, supporting evidence was also obtained for additional mode(s) of antifungal action for the tyrocidines which inter alia induces morphological abnormalities in filamentous fungal target cells. Furthermore, the results also indicated that the membrane activity of the tyrocidines may be influenced by additional factors to that of the composition of the target cell membrane, for instance components of the fungal cell wall. This investigation also indicated the significant potential of the tyrocidines to be developed for the commercial sector. The potent activity of the tyrocidines against agronomically important phytopathogens (significantly higher than the commercial fungicide bifonazole) together with their relative salt stability bodes well for their development as bio-fungicides for the agricultural sector. The tyrocidines also exhibited an overt sinergistic effect on the in vitro candidacidal activity of two key antifungal drugs, caspofungin and amphotericin B. Furthermore, tyrocidine A and caspofungin exhibited synergistic activity in vivo which had a significant positive effect on the survival of C. albicans infected Caenorhabditis elegans. Latter results highlighted their potential to serve as candidates for combinatorial treatment in the medical industry. / AFRIKAANSE OPSOMMING: Die globale verskynsel van mikrobiese weerstand, wat strek vanaf die landbou sektor tot in die mediese bedryf, het ’n dringende behoefte vir die ontwikkeling van nuwe antmikrobiese middels geskep. Antimikrobiese peptiede of “die natuur se antibiotika”, kan moontlik die antwoord op hierdie ernstige problem wees. Tydens hierdie studie is ‘n groep sikliese antimikrobiese peptiede, naamlik die tirosidiene wat deur die grondbakterium Bacillus aneurinolyticus geproduseer word, vir hulle antifungiese aktiwiteit, hulle moontlike meganisme(s) van antifungiese werking en hulle potensiёle aanwendings bestudeer. Hierdie studie het getoon dat die tirosidiene uitsonderlike antifungiese aktiwiteit teen ‘n reeks fitopatogene, insluitend Fusarium solani en Botrytis cinerea, asook teen die mens patogeen Candida albicans het. Die aktiwiteit van die tirosidiene is deur beide die identiteit van die teikenorganisme sowel as die mediumomgewing beїnvloed. Daar is ook verdere bewyse verkry wat die hipotese dat tirosidiene uiters sensitief is tot hulle omgewing en dat hulle neig om te oligomeriseer, ondersteun. Die studie van die klein tirosidien-biblioteek, saamgestel uit agt tirosidiene en analoё, het geen ooglopende struktuur-aktiwiteit verwantskappe opgelewer nie, behalwe vir die oёnskynlike invloed van die tirosien-residu. Laasgenoemde het die belangrikheid van die gekonserveerde aminosuurvolgorde van die tirosidiene, NQYVOLfP, asook die neiging van tirosidiene om hoё-orde aktiewe strukture te vorm deur self-verpakking, beklemtoon. Tydens die studie is daar gevind dat die tirosidiene membraan-aktiewiteit toon teenoor fungiese patogene. Daar is egter ook goeie bewyse vir alternatiewe meganisme(s) van antifungiese werking, wat ondermeer tot morfologiese abnormaliteite in filamentagtige fungi-teikenselle lei, vir die tirosidiene verkry. Die resultate het verder ook daarop gewys dat die membraan-aktiwiteit van die tirosidiene ook deur ander faktore, soos deur komponente van die fungiese selwand, en nie net deur die samestelling van die fungiese membraan beїnvloed word nie. Hierdie ondersoek het ook die aansienlike potensiaal van die tirosidiene vir kommersiёle ontwikkeling en gebruik uitgelig. Die merkwaardige aktiwiteit van die tirosidiene teen fitopatogene van agronomiese belang (wat selfs beter as diè van die kommersiёle swamdoder bifonazole was) tesame met die relatiewe sout stabiliteit van die tirosidiene, is belowende tekens om die tirosidiene as bio-swamdoders vir die landbou sektor te ontwikkel. Die tirosidiene het ook ‘n uitgesproke sinergistiese effek op die in vitro candidasidiese aktiwiteit van twee sleutel antifungiese middels, caspofungin en amphotericin B, getoon. Verder is daar in vivo sinergistiese aktiwiteit gewys deur die kombinasie van tirosidien A en caspofungin wat ’n beduidende positiewe effek op die oorlewing van C. albicans geïnfekteerde Caenorhabditis elegans gehad het. Laasgenoemde dui op die potensiaal van die tirosidiene om in die mediese bedryf as kandidate vir kombinasie-behandeling te dien.

Thesis (PhD)--University of Stellenbosch, 2004. / 426 Leaves printed single pages, preliminary pages i-xxiv and i-xxvii and 399 numberd pages. Includes bibliography. List of figures, List of tables, List of abbreviations. / ENGLISH ABSTRACT: Hypertrophic cardiomyopathy (HCM) is an autosomal dominantly inherited primary cardiac disease. The primary features of HCM are left ventricular hypertrophy, myocardial disarray, fibrosis and an increased risk of sudden cardiac death. To date, more than 264 HCM-causing mutations, occurring in thirteen genes, have been identified. As the vast majority of HCM-causing mutations occur in components of the cardiac sarcomere, HCM has been considered a disease of the cardiac sarcomere. Functional analyses of HCM-causing mutations in sarcomeric protein-encoding genes revealed that HCM-causing mutations have a vast array of effects on contractile function. The discovery of HCMcausing mutations in the gamma two subunit of adenosine monophosphate activated protein kinase highlighted the fact that mutations in non-sarcomeric proteins can also cause HCM and supports a hypothesis that HCM-causing mutations may result in energy wastage leading to energy depletion. Mutations in the cardiac myosin binding protein C (cMyBPC) gene (MYBPC3) are the second most prevalent cause of HCM. cMyBPC is a modular protein that forms an integral part of the sarcomeric thick filament, where it acts as a regulator of thick filament structure and cardiac contractility. Although cMyBPC has been studied extensively, the mechanisms through which it fulfill these functions have remained elusive, largely due to a lack of a comprehensive understanding of its interactions with other sarcomeric components and its quaternary structure. The aims of the present study were, firstly, to screen MYBPC3 for HCM-causing mutations in a panel of HCM-affected individuals and, secondly, to identify the ligands of domains of cMyBPC in which HCM-causing mutations were found.A panel of deoxyribonucleic acid (DNA) samples obtained from unrelated HCM-affected individuals was screened for HCM-causing mutations in MYBPC3, using polymerase chain reaction (PCR)- based single-strand conformation polymorphism method, as well as restriction enzyme digestion, DNA sequencing and reverse transcription PCR techniques. In order to identify the ligands of domains in which HCM-causing mutations were found, yeast two-hybrid (Y2H) candidate-ligandand library-assays were performed. Three novel and two previously described putative HCM-causing mutations were identified in MYBPC3. Data generated in this and other studies, however, suggest that two of these “mutations” are likely to be either polymorphisms, or disease-modifying factors, rather than main-locus HCMcausing mutations. Recent findings showed a specific interaction between domains C5 and C8 of cMyBPC. This finding identified domains C6 or C10 as candidate ligands of domain C7. Y2H-assays revealed a specific C7:C10 interaction. Additional Y2H assays also identified C-zone titin as a ligand of domain C7 and domain C10 as a ligand of domain C3. Several other Y2H assays, however, yielded no known sarcomeric ligands of the N-terminal region of cMyBPC. Identification of the ligands of specific domains of cMyBPC led to the development of detailed models of cMyBPC quaternary structure when cMyBPC is both unphosphorylated and fully phosphorylated. The integration of these models into an existing model of thick filament quaternary structure allows new insights into the functioning of cMyBPC as a regulator of both thick filament structure and cardiac contractility, as well as the pathophysiology of cMyBPC-associated HCM. / AFRIKAANSE OPSOMMING: Hipertrofiese kardiomiopatie (HKM) is ‘n outsosomaal dominante primêre hartsiekte. Die primêre kenmerke van HKM is linker ventrikulêre hipertrofie, miokardiale wanorde, fibrose en ‘n verhoogde risiko van skielike dood. Tot dusver is 260 HKM-veroorsakende mutasies in 13 gene geïdentifiseer. Aangesien die oorgrote meerderheid van HKM-veroorsakende mutasies in komponente van die kardiale sarkomeer voorkom, is HKM as ‘n siekte van die kardiale sarkomeer beskryf. Funksionele analise van HKM-veroorsakende mutasies in sarkomeriese protein-koderende gene het aan die lig gebring dat hierdie mutasies ‘n wye spektrum van gevolge op kontraktiele funksie het. Die ontdekking van HKM-veroorsakende mutasies in die gamma-twee subeenheid van adenosien monofosfaat-geaktiveerde proteïen kinase het die feit dat mutasies nie-sarkomeriese proteïene ook HKM kan veroorsaak onderstreep en ondersteun ‘n hipotese dat HKM-veroorsakende mutasies energievermorsing en energie uitputting tot gevolg het. Mutasies in die kardiale miosien-bindingsproteïen C (kMiBPC) geen (MYBPC3) is die tweede mees algemene oorsaak van HKM. kMiBPC is ‘n modulêre protein wat ‘n integrale deel van die sarkomeriese dik filament vorm, waar dit die struktuur van die dik filament en kardiale kontraktiliteit reguleer. Nieteenstaande die feit dat kMiBPC intensief bestudeer is, word die meganismes hoe hierdie funksies vervul word swak verstaan, grotendeels weens die afwesigheid van ‘n in diepte begrip van sy interaksies met ander komponente van die sarkomeer asook sy kwaternêre struktuur. Die doelstellings van hierdie studie was, eerstens, om MYBPC3 vir HKM-veroorsakende mutasies in ‘n paneel van HKM-geaffekteerde individue te deursoek en tweedens, om die ligande van domeine van kMiBPC waarin HKM-veroorsakende mutasies gevind is te identifiseer.‘n Paneel van deoksiribonukleïensuur (DNS) monsters verkry van onverwante HKM-geaffekteerde individue is deursoek vir HKM-veroorsakende mutasies in MYBPC3, deur middel van die polimerase ketting-reaksie (PKR)-gebasseerde enkelstrand konformasie polimorfisme metode, sowel as restriksie ensiem vertering, DNS volgordebepaling en terugtranskripsie PKR tegnieke. Die ligande van domeine van kMiBPC waarin HKM-veroorsakende mutasies gevind is, is geïdentifiseer deur middel van gis twee-hibried (G2H) kandidaat-ligand en biblioteek-siftings eksperimente. Drie onbeskryfde en twee voorheen beskryfde vermeende HKM-veroorsakende mutasies in MYPBC3 is geïdentifiseer. Data gegenereer in hierdie en ander studies dui daarop dat twee van hierdie “mutasies” eerder polimorfismes, of siekte-modifiserende faktore, as hoof-lokus HKMveroorsakende mutasies is. Onlangse bevindings het ‘n spesifieke interaksie tussend die C5 en C8 domeine van kMiBPC getoon. Hierdie bevindings het óf domein C6, óf C10, as kandidaat-ligande van domein C7 geïdentifiseer. G2H eksperimente het ‘n spesifieke interaksie tussen domains C7 en C10 getoon. Addisionele G2H eksperimente het ook C-zone titin as ‘n ligand van domein C7 sowel as domein C10 as ‘n ligand van domein C3 geïdentifiseer. Verdere G2H eksperimente het egter geen sarkomeriese ligande van die N-terminale gedeelte van kMiBPC geïdentifiseer nie. Die identifikasie van ligande van spesifieke domeins van kMiBPC het gelei tot die ontwikkelling van ‘n gedetaileerde model van kMiBPC kwaternêre struktuur wanneer kMiBPC beide ongefosforileerd en ten volle gefosforileerd is. Die intergrasie van hierdie modelle in bestaande modelle van dik filament kwaternêre struktuur werp nuwe lig op die funksionering van kMiBPC as ‘n reguleerder van beide dik filament struktuur en kardiale kontraktiliteit, sowel as die patofisiologie van kMiBPCgeassosieerde HKM.

Thesis (PhD (Biochemistry))--Stellenbosch University, 2008. / This study describes: • the cloning and sequencing of cytochrome P450 17 -hydroxylase/17,20 lyase (CYP17), 3 -hydroxysteroid dehydrogenase (3 HSD) and cytochrome b5 from the South African Angora goat; • the identification of two CYP17 genes encoding two unique CYP17 isoforms in the Angora goat; • the development of a UPLC-APCI-LC method for the separation and quantification of seven adrenal steroids; • the characterisation of the enzymatic activity of the two Angora CYP17 isoforms expressed in non-steroidogenic COS-1 cells. The Km and Vvalues for the metabolism of pregnenolone and progesterone were determined; • the development of a rapid and accurate real-time PCR genotyping test for CYP17 in Angora goats. Three unique genotypes were identified; • the determination of blood cortisol levels upon the stimulation of the HPAaxis by intravenous insulin injection in the three Angora goat genotypes.

Thesis (PhD (Biochemistry))--University of Stellenbosch, 2009. / ENGLISH ABSTRACT: The sugarcane stalk, besides being the main structural component of the plant, is also the major storage organ for carbohydrates. Sucrose forms the bulk of stored carbohydrates. Previous studies have modelled the sucrose accumulation pathway in the internodal storage parenchyma of sugarcane using kinetic models cast as systems of ordinary differential equations. Typically, results were analysed with methods such as metabolic control analysis. The present study extends those original models within an advection-diffusion-reaction framework, requiring the use of partial differential equations to model sucrose metabolism coupled to phloem translocation. Let N be a stoichiometric matrix, v a vector of reaction rates, s a vector of species concentrations and r the gradient operator. Consider a coupled network of chemical reactions where the species may be advected with velocities, U, or diffuse with coefficients, D, or both. We propose the use of the dynamic system, s + r (Us) + r (Drs) = Nv; for a kinetic model where species can exist in different compartments and can be transported over long distances in a fluid medium, or involved in chemical reactions, or both. Darcy’s law is used to model fluid flow and allows a simplified, phenomenological approach to be applied to translocation in the phloem. Similarly, generic reversible Hill equations are used to model biochemical reaction rates. These are also phenomenological equations, where all the parameters have operationally defined interpretations. Numerical solutions to this formulation are demonstrated with time-courses of two toy models. The first model uses a simple “linear” pathway definition to study the impact of the system geometry on the solutions. Although this is an elementary model, it is able to demonstrate the up-regulation of photosynthesis in response to a change in sink demand. The second model elaborates on the reaction pathway while keeping the same geometry definition as the first. This pathway is designed to be an abstracted model of sucrose metabolism. Finally, a realistic model of sucrose translocation, metabolism and accumulation is presented, spanning eight internodes and four compartments. Most of the parameters and species concentrations used as initial values were obtained from experimental measurements. To analyse the models, a method of sensitivity analysis called the Fourier Amplitude Sensitivity Test (FAST) is employed. FAST calculates the contribution of the possible variation in a parameter to the total variation in the output from the model, i.e. the species concentrations and reaction rates. The model predicted that the most important factors affecting sucrose accumulation are the synthesis and breakdown of sucrose in futile cycles and the rate of cross-membrane transport of sucrose. The models also showed that sucrose moves down a concentration gradient from the leaves to the symplast, where it is transported against a concentration gradient into the vacuole. There was a net gain in carbohydrate accumulation in the realistic model, despite an increase in futile cycling with internode maturity. The model presented provides a very comprehensive description of sucrose accumulation and is a rigorous, quantitative framework for future modelling and experimental design. / AFRIKAANSE OPSOMMING: Benewens sy strukturele belang, is die suikerrietstingel ook die primêre bergingsorgaan vir koolhidrate. Die oorgrote meerderheid van hierdie koolhidrate word as sukrose opgeberg. Studies tot dusver het die metabolisme rondom sukroseberging in die parenchiem van die onderskeie stingellitte as stelsels gewone differensiaalvergelykings gemodelleer. Die resultate is ondermeer met metaboliese kontrole-analise geanaliseer. Hierdie studie brei uit op die oorspronklike modelle, deur gebruik te maak van ’n stromings-diffusie-reaksie-raamwerk. Parsiële differensiaalvergelykings is geformuleer om die metabolisme van sukrose te koppel aan die vloei in die floëem. Gestel N is ’n stoichiometriese matriks, v ’n vektor van reaksiesnelhede, s ’n vektor van spesie-konsentrasies en r die differensiaalvektoroperator. Beskou ’n netwerk van gekoppelde reaksies waar die onderskeie spesies stroom met snelhede U, of diffundeer met koëffisiënte D, of onderhewig is aan beide prosesse. Dit word voorgestel dat die dinamiese stelsel, _s + r (Us) + r (Drs) = Nv; gebruik kan word vir ’n kinetiese model waar spesies in verskeie kompartemente kan voorkom en vervoer kan word oor lang afstande saam met ’n vloeier, of kan deelneem aan chemiese reaksies, of albei. Darcy se wet word gebruik om die vloeier te modeller en maak dit moontlik om ’n eenvoudige, fenomenologiese benadering toe te pas op floëem-vervoer. Eweneens word generiese, omkeerbare Hill-vergelykings gebruik om biochemiese reaksiesnelhede te modelleer. Hierdie vergelykings is ook fenomenologies van aard en beskik oor parameters met ’n duidelike fisiese betekenis. Hierdie omvattende raamwerk is ondermeer gedemonstreer met behulp van numeriese oplossings van twee vereenvoudigde modelle as voorbeelde. Die eerste model het bestaan uit ’n lineêre reaksienetwerk en is gebruik om die geometrie van die stelsel te bestudeer. Alhoewel hierdie ’n eenvoudige model is, kon dit die toename in fotosintese as gevolg van ’n verandering in metaboliese aanvraag verklaar. Die tweede model het uitgebrei op die reaksieskema van die eerste, terwyl dieselfde stelselgeometrie behou is. Hierdie skema is ontwerp as ’n abstrakte weergawe van sukrosemetabolisme. Ten slotte is ’n realistiese model van sukrosevervoer, metabolisme en berging ontwikkel wat agt stingellitte en vier kompartemente omvat. Die meeste parameters en konsentrasies van biochemiese spesies wat as aanvanklike waardes in die model gebruik is, is direk vanaf eksperimentele metings verkry. Die Fourier Amplitude Sensitiwiteits-Toets (FAST) is gebruik om die modelle te analiseer. FAST maak dit moontlik om die bydrae van parameters tot variasie in modeluitsette soos reaksiesnelhede en die konsentrasies van chemiese spesies te bepaal. Die model het voorspel dat sintese en afbraak van sukrose in ’n futiele siklus, asook transmembraan sukrosevervoer, die belangrikste faktore is wat sukrose-berging beïnvloed. Die model het ook getoon dat sukrose saam met ’n konsentrasiegradiënt beweeg vanaf die blare tot by die stingelparenchiem-sitoplasma, van waar dit teen ’n konsentrasiegradiënt na die vogselholte (vakuool) vervoer word. Volgens die realistiese model was daar ’n netto toename in die totale hoeveelheid koolhidrate, ten spyte van ’n toename in die futile siklus van sukrose in die ouer stingellitte. Die model wat in hierdie proefskrif voorgestel word verskaf ’n uitgebreide, omvattende beskrywing van sukroseberging. Voorts stel dit ’n rigiede kwantitatiewe raamwerk daar vir toekomstige modellering en eksperimentele ontwerp.

Thesis (PhD (Biochemistry))--University of Stellenbosch, 2006. / Gonadotropin-releasing hormone (GnRH), acting via its cognate receptor (GnRHR) is the primary regulator of mammalian reproductive function. Pituitary sensitivity to GnRH can be directly correlated with GnRHR levels on the surface of the pituitary gonadotrope cells, which can be regulated at transcriptional, post-transcriptional and post-translational levels. This study investigated mechanisms of transcriptional regulation of mouse GnRHR expression in two mouse gonadotrope cell lines, αT3-1 and LβT2, using a combination of endogenous mRNA expression studies, promoter-reporter studies, a two-hybrid protein-protein interaction assay, Western blotting, and in vitro protein-DNA binding studies. In the first part of the study, the role of two GnRHR promoter nuclear receptor binding sites (NRSs) and their cognate transcription factors in basal and Protein Kinase A (PKA)-stimulated regulation of GnRHR promoter activity was investigated in αT3-1 cells. The distal NRS was found to be crucial for basal promoter activity in these cells. While the NRSs were not required for the PKA response in these cells, results indicate a modulatory role for the transcription factors Steroidogenic Factor-1 (SF-1) and Nur77 via these promoter elements. The second part of the study focused on elucidating the mechanism of homologous regulation of GnRHR transcription in LβT2 cells, with a view to defining the respective roles of PKA and Protein Kinase C (PKC) in the transcriptional response to GnRH. In addition, the respective roles of the NRSs, the cyclic AMP response element (CRE) and the Activator Protein-1 (AP-1) promoter cis elements, together with their cognate transcription factors, in basal and GnRH-stimulated GnRHR promoter activity, were investigated. Homologous upregulation of transcription of the endogenous gene was confirmed, and was quantified by means of real-time RTPCR. The GnRH response of the endogenous gene and of the transfected promoter-reporter construct required PKA and PKC activity, and the GnRH response of the promoter-reporter construct was found to be dependent on a functional AP-1 site. Furthermore, GnRH treatment resulted in increased binding of phosphorylated cAMP-response element binding protein (phospho-CREB) and decreased expression and binding of SF-1 to their cognate cis elements in vitro, and stimulated a direct interaction between SF-1 and CREB, suggesting that these events are also required for the full transcriptional response to GnRH. This study is the first providing detail regarding the mechanism of transcriptional regulation of GnRHR expression in LβT2 cells by GnRH. Based on results from this study, a model has been proposed which outlines for the first time the kinase pathways, the promoter cis elements and the cognate transcription factors involved in homologous regulation of GnRHR transcription in the LβT2 cell line. As certain aspects of this model have been confirmed for the endogenous GnRHR gene, the model is likely to be physiologically relevant, and provides new ideas and hypotheses to be tested in future studies.

Dissertation (PhD)--University of Stellenbosch, 2006. / ENGLISH ABSTRACT: Gonadotropin-releasing hormone (GnRH) is well known as the central regulator of the reproductive system through its stimulation of gonadotropin synthesis and release from the pituitary via binding to its specific receptor, known as the gonadotropin-releasing hormone receptor type I (GnRHR-I). The gonadotropins, luteinising hormone (LH) and follicle-stimulating hormone (FSH), bind to receptors in the gonads, leading to effects on steroidogenesis and gametogenesis. The recent finding of a second form of the GnRH receptor, known as the type II GnRHR or GnRHR-II, in non-mammalian vertebrates triggered the interest into the possible existence and function of a GnRHR-II in humans. The current study addressed this issue by investigating the presence of transcripts for a GnRHR-II in various human tissues and cells. While it was demonstrated that antisense transcripts for this receptor, containing sequence of only two of the three coding exons, are ubiquitously and abundantly expressed in all tissues examined, potentially full-length (containing all three exons), sense transcripts for a GnRHR-II were detected only in human ejaculate. Further analysis revealed that the subset of cells in the ejaculate expressing these transcripts is mature sperm. These findings, together with the reported role for GnRH in spermatogenesis and reproduction led to the further analysis of the presence of a local GnRH/GnRHR network in human and vervet monkey ejaculate or sperm. Indeed, such a network seems to be present in humans since transcripts for both forms of GnRH present in mammals, as well as transcripts for the GnRHR-I, are expressed in human ejaculate. Furthermore, transcripts for the GnRHR-II are expressed in both human and vervet monkey ejaculate. Thus, it would appear that locally produced GnRH-1 and/or GnRH-2 in the human male reproductive tract might mediate their effects on fertility via a local GnRHR-I, and possibly via GnRHR-II. Remarkably, in the pituitary, LH and FSH are present in the same gonadotropes, yet they are differentially regulated by GnRH under various physiological conditions. While it is well established that post-transcriptional regulatory mechanisms occur, the contribution of transcriptional regulation to the differential expression of the LHβ- and FSHβ-subunit genes is unclear. In this study, the role of GnRH-1 and GnRH-2 via the GnRHR-I and the GnRHR-II in transcriptional regulation of mammalian LHβ- and FSHβ genes was determined in the LβT2 mouse pituitary gonadotrope cell-line. It is demonstrated for the first time that GnRH-1 may affect gonadotropin subunit gene expression via GnRHR-II in addition to GnRHR-I, and that GnRH-2 also has the ability to regulate gonadotropin subunit gene expression via both receptors. Similar to other reports, it is shown that the transcriptional response to GnRH-1 of LHβ and FSHβ is low (about 1.4-fold for bLHβLuc and 1.2-fold for oFSHβLuc). In addition, evidence is supplied for the first time that GnRH-2 transcriptional regulation of the gonadotropin β subunits is also low (about 1.5-fold for bLHβLuc and 1.1-fold for oFSHβLuc). It is demonstrated that GnRH-1 is a more potent stimulator of bLHβ promoter activity as compared to GnRH-2 via the GnRHR-I, yet both hormones result in a similar maximum induction of bLHβ. However, GnRH-2 is a more efficacious stimulator of bLHβ transcription via the GnRHR-II than GnRH-1. No discriminatory effect of GnRH-1 vs. GnRH-2 was observed for oFSHβ promoter activity via GnRHR-I or GnRHR-II. By comparison of the ratio of expression of transfected oFSHβ- and bLHβ promoterreporters via GnRH-1 with that of GnRH-2, it is shown that GnRH-2 is a selective regulator of FSHβ gene transcription. This discriminatory effect of GnRH-2 is specific for GnRHR-I, as it is not observed for GnRHR-II, where GnRH-1 results in a greater oFSHβ- to-bLHβ ratio. These opposite selectivities for GnRHR-I and GnRHR-II on the ratios of oFSHβ:bLHβ promoter activity for GnRH-1 vs. GnRH-2 suggest a mechanism for fine control of gonadotropin regulation in the pituitary by variation of relative GnRHR-I vs. GnRHR-II levels. In addition, a concentration-dependent modulatory role for PACAP on GnRH-1- and GnRH-2-mediated regulation of bLHβ promoter activity, via both GnRHR-I and GnRHR-II, and of oFSHβ promoter activity, via GnRHR-I, is indicated. The concentration-dependent effects suggest the involvement of two different signalling pathways for the PACAP response. Together these findings suggest that transcription of the gonadotropin genes in vivo is under extensive hormonal control that can be finetuned in response to varying physiological conditions, which include changing levels of GnRH-1, GnRH-2, GnRHR-I and GnRHR-II as well as PACAP. / AFRIKAANSE OPSOMMING: Gonadotropien-vrystellingshormoon (GnRH) is bekend as die sentrale reguleerder van die voorplantingsisteem deur die stimulasie van gonadotropiensintese en - vrystelling vanaf die pituïtêre klier via binding aan ‘n spesifieke reseptor, die sogenaamde tipe I gonadotropien-vrystellingshormoonreseptor (GnRHR-I). Die gonadotropiene, lutineringshormoon (LH) en follikel-stimuleringshormoon (FSH), bind aan reseptore in die gonades waar dit steroïedogenese en gametogenese beïnvloed. Die onlangse ontdekking van ‘n tweede vorm van die GnRH-reseptor, bekend as die tipe II GnRHR of GnRHR-II, in nie-soogdier vertebrate het belangstelling in die moontlike bestaan en funksie van ‘n GnRHR-II in die mens gewek. Hierdie kwessie is aangeraak deur die teenwoordigheid van transkripte vir ‘n GnRHR-II in verskeie weefsel- en seltipes van die mens te ondersoek. Daar is aangetoon dat nie-sin transkripte vir hierdie reseptor, wat die DNA-opeenvolgings van slegs twee van die drie koderende eksons bevat het, oormatig uitgedruk word in al die weefseltipes wat ondersoek is. Daarteenoor is potensieel vollengte (bevattende al drie eksons) sin transkripte vir ‘n GnRHR-II in die mens slegs in semen gevind. Verdere analise het getoon dat dit volwasse sperma binne die semen is wat laasgenoemde transkripte uitdruk. Hierdie bevindinge, tesame met die aangetoonde rol vir GnRH in spermatogenese en reproduksie het gelei tot die verdere analise van die teenwoordigheid van ‘n lokale GnRH/GnRHR-netwerk in mens- en blouaapsemen of -sperm. So ‘n netwerk blyk om teenwoordig te wees in die mens, aangesien transkripte vir beide vorme van GnRH wat in soogdiere gevind word, asook transkripte vir die GnRHR-I, in menssemen uitgedruk word. Daarbenewens word transkripte vir die GnRHR-II uitgedruk in beide mens- en blouaapsemen. Dit wil dus voorkom asof lokaalgeproduseerde GnRH-1 en/of GnRH-2 in die manlike voortplantingstelsel van die mens hul effek op vrugbaarheid bemiddel via ‘n lokale GnRHR-I, en moontlik ook via GnRHR-II. Dit is opmerklik dat LH en FSH teenwoordig is in dieselfde gonadotroopselle van die pituïtêre klier en tog verskillend gereguleer word deur GnRH tydens verskeie fisiologiese kondisies. Terwyl dit bekend is dat post-transkripsionele reguleringsmeganismes teenwoordig is, is die bydrae van transkripsionele regulering tot die differensiële uitdrukking van die LHβ- en FSHβ-subeenheidgene minder duidelik. In hierdie studie is die rol van GnRH-1 en GnRH-2 via die GnRHR-I en die GnRHR-II in transkripsionele regulering van soogdier-LHβ- en -FSHβ-gene in die LβT2 muis pituïtêre gonadotroopsellyn bepaal. Dit is vir die eerste keer aangetoon dat GnRH-1 ‘n effek mag hê op gonadotropiensubeenheid-geenuitdrukking via GnRHR-II bykomend tot GnRHR-I, en dat GnRH-2 ook die vermoë besit om gonadotropiensubeenheid-geenuitdrukking via beide reseptore te reguleer. Soos deur ander studies aangetoon is die transkripsionele respons van LHβ en FSHβ tot GnRH-1 klein (ongeveer 1.4-voudig vir bLHβLuc en 1.2- voudig vir oFSHβLuc). Verder is daar vir die eerste keer bewys gelewer dat transkripsionele regulering van die gonadotropien β-subeenhede deur GnRH-2 ook gering is (ongeveer 1.5-voudig vir bLHβLuc en 1.1-voudig vir oFSHβLuc). Daar is aangetoon dat GnRH-1 ‘n sterker stimuleerder van bLHβ-promotoraktiwiteit is in vergelyking met GnRH-2 via die GnRHR-I, hoewel beide hormone tot ‘n soortgelyke maksimum induksie van bLHβ lei. GnRH-2 is egter ‘n meer effektiewe stimuleerder van bLHβ-transkripsie as GnRH-1 via die GnRHR-II. Geen verskille is gevind tussen die effekte van GnRH-1 en GnRH-2 op oFSHβ-promotoraktiwiteit via GnRHR-I of GnRHR-II nie. Wanneer die verhouding van uitdrukking van getransfekteerde oFSHβ- en bLHβ- promotor-verslaggewers via GnRH-1 met dié van GnRH-2 vergelyk is, is aangetoon dat GnRH-2 ‘n selektiewe reguleerder van FSHβ-geentranskripsie is. Hierdie diskriminasieeffek van GnRH-2 is spesifiek vir GnRHR-I aangesien dit nie vir GnRHR-II waargeneem word nie. GnRH-1 lei tot ‘n groter oFSHβ tot bLHβ-verhouding via GnRHR-II. Hierdie teenoorgestelde selektiwiteite van GnRHR-I en GnRHR-II op die verhoudings van oFSHβ tot bLHβ-promotoraktiwiteit vir GnRH-1 teenoor GnRH-2 suggereer dat daar ‘n meganisme bestaan vir die fyn regulering van gonadotropiene in die pituïtêre klier, deurdat die relatiewe vlakke van GnRHR-I teenoor GnRHR-II gevarieer word. Daarbenewens is ‘n konsentrasie-afhanklike moduleringsrol vir PACAP op GnRH-1- en GnRH-2-bemiddelde regulering van bLHβ-promotoraktiwiteit aangetoon, via beide GnRHR-I en GnRHR-II, asook op oFSHβ-promotoraktiwiteit via GnRHR-I. Hierdie konsentrasie-afhanklike effekte dui op die betrokkenheid van twee verskillende seinpadweë vir die PACAP-respons. Tesame suggereer hierdie bevindinge dat transkripsie van die gonadotropiengene in vivo onder ekstensiewe hormonale kontrole is wat verfyn kan word in respons to veranderlike fisiologiese kondisies. Laasgenoemde sluit veranderende vlakke van GnRH-1, GnRH-2, GnRHR-I en GnRHR-II asook PACAP in.