Thesis (MSc)--Stellenbosch University, 2014. / ENGLISH ABSTRACT: Metabolic networks of cellular systems are complex, in that there are numerous components with multiple non-linear interactions. To understand how these networks work they are often split into manageable pieces and studied individually. However, an individual part is unable to account for the complex properties of systems. In order to study these interactions the eld of systems biology has developed. Systems biology makes use of computers to construct models as a method to describe aspects of living systems. Using cellular pathways, kinetic models of metabolic pathways can be constructed and used as a tool to study the biological systems and provide a quantitative description. This thesis describes the quantitative analysis of a bacterium using a systems biology approach. Zymomonas mobilis is a rod shaped, Gram-negative, non-mobile facultative anaerobe and has one of the fastest observed fermentations, yet least energy e cient extractions found in nature. Furthermore it is the only known micro-organism to use the Entner-Doudoro (2-keto-3-deoxy-6- phosphogluconate) pathway anaerobically. The low energy yield of fermentation in Z. mobilis is a result of the usage of the Entner-Doudoro glycolytic pathway, which has half the energy yield per mol substrate compared to the well known Embden-Meyerhof-Parnas glycolytic pathway. The work presented in this thesis forms part of a larger project to compare glycolytic regulation in di erent micro-organisms Z. mobilis, Escherichia coli, Saccharomyces cerevisiae and Lactococcus lactis. These organisms were chosen based on their usage of di erent glycolytic mechanisms. Kinetic models are suitable tools to draw a comparison between these organisms. The emphasis here is on the construction of a kinetic model of the Entner-Doudoroff glycolytic pathway as it occurs in Z. mobilis. The aim of this thesis was to characterise as many of the Entner-Doudoro pathway enzymes as possible, under standard conditions. This was done using enzyme assays, to obtain the kinetic parameters of each of the enzymes. Microtitre plate assays were used to characterise most of the enzymes of the Entner-Doudoro pathway. However, not all characterisations could be done using plate assay methods, as some intermediates were not commercially available to perform coupled assays. Nuclear magnetic resonance (NMR) spectroscopy was used to characterise these enzymes. These experimentally obtained parameters were then incorporated in a mathematical framework. Time simulations on the initial model were unable to reach a steady-state, with a build up of metabolic intermediates. A secondary model was constructed (using calculated maximal activities) which allowed us to identify discrepancies in the initial model. This showed that the experimentally determined maximal activities of three enzymes in lower glycolysis were unrealistically low, which might be due to protein denaturation by sonication. A nal model was constructed which incorporated a correction factor for these three enzymes. The models' predicted output (steady-state concentrations and ux) was compared to that of either literature or experimentally determined values, as a method to validate the model. The model output compared well to literature values. The constructed and partially validated kinetic model was then used as an analytical tool to identify points of control and regulation of glycolysis in Z. mobilis. The model presented in this work was also compared to published models. Our model relies much less on literature obtained values, and uses kinetic parameters experimentally determined under the same conditions. The parameters of the published models were obtained from the literature and in many instances, the assay conditions for these parameters were set-up to yield the maximum activity under non-physiological conditions. Furthermore, the number of excluded or assumed parameters is much less in our model. However, introduction of a milder, more predictable extraction technique for preparing cell lysates, should be considered for future work, to obtain the parameters that was not determined during this study. The published models do include reactions not included in our model (e.g ATP metabolism), which should be considered for inclusion, as we strive to construct a detailed kinetic model of glycolysis in Z. mobilis in the future. / AFRIKAANSE OPSOMMING: Sellul^ere metaboliese netwerke is komplekse stelsels, omdat hulle bestaan uit talle komponente met verskeie nie-lineêre interaksies. Om die funksionering van hierdie netwerke te verstaan, word hulle dikwels in hanteerbare stukke verdeel en individueel bestudeer. 'n Enkele komponent is egter nie in staat om die komplekse eienskappe van sulke stelsels te verklaar nie. Die veld van sisteembiologie het ontwikkel met die doel om sulke stelsels te bestudeer. Sisteembiologie maak gebruik van rekenaarmodelle as 'n metode om aspekte van lewende sisteme te beskryf. Kinetiese modelle van metaboliese paaie word gebou en gebruik as gereedskap om die biologiese stelsels te bestudeer en 'n kwantitatiewe beskrywing te bekom. Hierdie tesis beskryf die kwantitatiewe ontleding van 'n bakterie deur middel van 'n sisteembiologiese benadering. Zymomonas Mobilis is 'n staafvormige, Gram-negatiewe, nie-mobiele fakultatiewe ana erobe, en het een van die vinnigste waargenome fermentasies, maar met die minste energie-doeltre ende ekstraksie wat in die natuur aangetref word. Verder is dit die enigste bekende mikro-organisme wat die Entner-Doudoro (2-keto-3-dioksi-6-fosfoglukonaat) pad ana erobies gebruik. Die lae-energieopbrengs van fermentasie in Z. mobilis is 'n gevolg van die gebruik van die Entner-Doudoro metaboliese pad, wat die helfte van die energie-opbrengs per mol substraat lewer, in vergelyking met die bekende Embden-Meyerhof-Parnas pad. Die werk wat in hierdie tesis aangebied word, vorm deel van 'n groter projek om glikolitiese regulering in verskillende mikro-organismes te vergelyk, naamlik Z. mobilis, Escherichia coli, Sac- charomyces en Lactococcus lactis. Hierdie organismes is gekies op grond van hul gebruik van verskillende glikolitiese meganismes. Kinetiese modellering is 'n handige metode om 'n vergelyking tussen hierdie organismes te trek. Hierdie werk fokus op die bou van 'n kinetiese model van die Entner-Doudoro glikolitiese metaboliese pad soos dit in Z. mobilis voorkom. Die doel van hierdie tesis was om so veel moontlik van die Entner-Doudoro ensieme onder standaard-toestande te karakteriseer. Die kinetiese parameters van elk van die ensieme is met behulp van ensimatiese essai's bepaal. Vir die meeste essai's is 96-put mikrotiterplate gebruik, maar nie al die karakteriserings kon met behulp van hierdie metode gedoen word nie, omdat sommige intermediate nie kommersieel beskikbaar was om gekoppelde essai's mee uit te voer nie. Kernmagnetiese resonansie (KMR) spektroskopie is gebruik om hierdie ensieme te karakteriseer. Die eksperimenteel bepaalde parameters is opgeneem in 'n wiskundige raamwerk. Tydsimulasies op die aanvanklike model was nie in staat om 'n bestendige toestand te bereik nie, omdat metaboliete opgebou het. 'n Sekond^ere model is gebou (met behulp van berekende maksimale aktiwiteite) wat ons toegelaat om teenstrydighede in die aanvanklike model te identi seer. Dit het getoon dat die eksperimenteel bepaalde maksimale aktiwiteite van drie ensieme in die laer gedeelte van glikolise te laag was, waarskynlik as gevolg van prote en denaturering tydens die ultrasoniese disintegrasieproses. 'n Finale model is gebou waarin 'n korreksiefaktor vir hierdie drie ensieme opgeneem is. Die modelle se voorspelde uitset (bestendige toestand konsentrasies en uksie) is vergelyk met waardes uit die literatuur of wat ons self bepaal het, as 'n metode om die model te valideer. Die model uitset was in goeie ooreenstemming met hierdie waardes. Die gedeeltelik gevalideerde kinetiese model is voorts gebruik as 'n analitiese instrument om beheer en regulering van glikolise in Z. mobilis te ondersoek. Die model wat in hierdie werk ontwikkel is, is ook vergelyk met die vorige gepubliseerde modelle. Ons model berus baie minder op waardes uit die wetenskaplike literatuur, en maak gebruik van parameters wat eksperimenteel bepaal is, onder identiese toestande. Die parameters van die gepubliseerde modelle is meesal verkry uit die literatuur, en in baie gevalle was die eksperimentele kondisies vir hierdie analises opgestel om die maksimale aktiwiteit te lewer onder nie- siologiese toestande. Verder bevat ons model minder parameters wat of uitgesluit is of wie se waardes aangeneem moes word. In toekomstige werk sal daar egter klem gel^e moet word op 'n minder wisselvallige ekstraksietegniek vir die verkryging van selekstrakte, om sodoende parameters te identi seer wat nie in hierdie werk bepaal kon word nie. Die gepubliseerde modelle sluit ook reaksies in wat nie ingesluit is in ons model nie (bv. ATP metabolisme). Hierdie sou in ag geneem moet word vir insluiting in 'n toekomstige uitgebreide model, om daarna te streef om 'n gedetailleerde kinetiese model van glikolise in Z. mobilis te bou.

Thesis (MSc)--Stellenbosch University, 2014. / ENGLISH ABSTRACT: This thesis gives a broad overview of what artificial chemistries (ACs) are, a brief review of several ACs and their applications, and an in depth analysis of one speci c AC: the four-bit binary string system. The model designed by Banzhaf [1] for in silico examination was recreated using the Python programming language. The initial motivation was to identify an existing AC that could be used to elucidate the sequence-function relationship, which led to the simultaneous investigation of self-organization in AC systems [7]. The interest in sequence-function relationships stems from their importance for self-production of objects [35]. For self-replication to be possible in larger organizations, the components of the organization must be able to continuously produce themselves [3, 7]. We chose the four-bit binary string system for investigation because of its simple design and implementation, its ability to yield complex results from interactions between a small population of objects, and its analogy to the DNA{RNA{protein organisation. When a population of objects are allowed to continuously interact, self-production and self-organization occur, even in simple arti cial systems [7, 8]. The stability of the emergent organizations depends on the interactions of its components, which must be capable of self-production if they are to maintain the organization [27]. Self-production of objects depends on their sequence-function relationship, which determines their rate of replication when interacting with other objects. / AFRIKAANSE OPSOMMING: Hierdie tesis verskaf `n bree oorsig van die algemene aard van artifisiele chemies (ACs), `n kort opsomming van `n paar ACs en hul toepassings, en `n diepgaande analise van een spesifieke AC: die 4-bis binere stringstelsel. Die model wat Banzhaf [1] ontwerp het vir in silico eksperimentering is hier herskep in die Python programmeringstaal. Die aanvanklike motivering was om `n bestaande AC te identifiseer wat gebruik kon word om die sekwens-funksie verwantskap te ontrafel, en dit het gelei tot die gelyktydige ondersoek van self-organisasie in AC stelsels [7]. Ons belangstelling in sekwens-funksie verwantskappe spruit uit hul belang vir die selfproduksie van objekte [35]. Om selfreplisering in meer omvangryke organisasies moontlik te maak moet die komponente in staat wees om hulself eenstryk te produseer [3, 7]. Ons het `n 4-bis stelsel vir hierdie studie gekies omdat die ontwerp en implementering eenvoudig is, omdat interaksies binne `n klein populasie van objekte komplekse resultate gee, en omdat die stelsel se organisasie analoog aan die DNA-RNA-proteien organisasie is. Wanneer `n populasie van objekte toegelaat word om eenstryk op mekaar te reageer vind self-produksie en self-organisasie vanself plaas, selfs in eenvoudige artifsiele stelsels [7, 8]. Die stabiliteit van die emergente organisasies hang af van die interaksies tussen die komponente, wat self die vermoe tot selfproduksie moet he indien hulle die organisasie in stand wil hou [27]. Selfproduksie van objekte hang af van hul sekwens-funsieverwantskap, wat op hul beurt bepaal hoe vinnig hulle repliseer wanneer in interaksie met ander objekte.

Thesis (PhD)--University of Stellenbosch, 2005. / ENGLISH ABSTRACT: Several genera of cyanobacteria produce a range of toxins. The increased rate of eutrophication of surface fresh waters due to anthropogenic inputs has resulted in more frequent and severe cyanobacterial bloom events. Such bloom events make impoundments unsuitable for recreational use and increase the cost of production of potable water due to the necessity for removal of toxins released from cells during the purification process. Microcystis aeruginosa is the major freshwater bloom-forming toxic cyanobacterium. Concentrations of the hepatotoxin, microcystin, are highly variable in blooms. Published literature on environmental conditions leading to increased microcystin production was often contradictory and in many cases did not consider all relevant parameters. However, environmental nitrogen and phosphorus, temperature and light, and growth rate were implicated in regulation of toxin content. The purpose of this work was therefore to investigate environmental factors (specifically nitrogen and phosphorus) and cellular activities (specifically carbon fixation and nitrogen uptake rates and growth rate) involved in the modulation of microcystin production in M. aeruginosa in order to clarify the role of these parameters, and in an attempt to identify regulatory mechanisms for microcystin production. Environmental nitrogen, phosphorus and growth rate were shown to co-modulate microcystin production in M. aeruginosa. Adequate phosphorus is required for photosynthetic carbon fixation. Phosphorus uptake by M. aeruginosa is strongly correlated with carbon fixation rate. Although microcystin content increased with increasing nitrogen:phosphorus ratios in culture medium, under phosphorus limitation microcystin content was lower irrespective of nitrogen concentrations. This observation and the requirements for fixed carbon for nitrogen assimilation therefore prompted investigation of the effects of cellular carbon fixation and nitrogen uptake in the modulation of microcystin production. Microcystin production was found to be enhanced when nitrogen uptake rate relative to carbon fixation rate was higher than that required for balanced growth. The cellular nitrogen:carbon ratio above which microcystin concentrations increased substantially, corresponded to the Redfield ratio for balanced growth. Investigation of potential regulatory mechanisms involving the cyanobacterial nitrogen regulator, NtcA, yielded putative NtcA binding sites indicative of repression in the microcystin synthetase gene cluster. In culture, the polypeptide synthetase module gene, mcyA, and ntcA were inversely expressed as a function of carbon-fixation:nitrogen-uptake potential. However, no increase or decrease in microcystin production could be linked to either glutamine, glutamate or a-ketoglutarate, metabolites that are involved in regulation of ntcA. The role of NtcA in regulation of microcystin production could therefore not be confirmed. In conclusion, these data suggest that microcystin production is metabolically regulated by cellular C:N balance and specific growth rate. The primary importance of nitrogen and carbon was demonstrated by a simple model where only nitrogen uptake, carbon fixation and growth rate were used to predict microcystin levels. The model also explains results previously described in literature. Similarly, an artificial neural network model was used to show that the carbon fixation dependence on phosphorus allows accurate prediction of microcystin levels based on growth rate and environmental nitrogen and phosphorus. / AFRIKAANSE OPSOMMING: Verskeie genera van sianobakterieë produseer 'n verskeidenheid van toksiene. Die toename in die tempo van eutrofikasie van varswater oppervlaktes as gevolg van antropogeniese insette veroorsaak al hoe meer en al hoe erger sianobakteriële infestasies. Dit veroorsaak probleme vir ontspanninggebruik van hierdie waters en verhoog die koste van produksie van drinkbare water as gevolg van die noodsaak om die toksiene wat deur die selle gedurende die suiweringsproses vrygelaat word te verwyder. Microcystis aeruginosa is die belangrikste varswater bloeisel-vormende toksiese sianobakterium. Die konsentrasie van die hepatotoksien mikrosistien is hoogs varieerbaar in sulke bloeisels. Gepubliseerde literatuur oor die omgewingskondisies wat lei na verhoogde mikrosistienproduksie is dikwels weersprekend en neem in vele gevalle nie al die relevante parameters in ag nie. Desnieteenstaande word omgewingstikstof, fosfor, temperatuur en lig, asook groeisnelheid, geïmpliseer in die regulering van toksieninhoud. Die doel van hierdie navorsing was dus om omgewingsfaktore (spesifiek stikstof en fosfor) en sellulêre aktiwiteite (spesifiek koolstoffiskering en die snelheid van stikstofopname en van groei) betrokke by die modulering van mikrosistienproduksie in M. aeruginosa te ondersoek in 'n poging om die rol van hierdie parameters te verstaan en om regulatoriese meganismes vir mikrosistienproduksie te identifiseer. In hierdie studie is aangetoon dat omgewingstikstof en fosfor sowel as groeisnelheid mikrosistienproduksie in M. aeruginosa ko-moduleer. Genoegsame fosfor word benodig vir fotosintetiese koolstoffiksering. Fosforopname deur M. aeruginosa korreleer sterk met die snelheid van koolstoffiksering. Alhoewel mikrosistieninhoud toegeneem het met 'n toename in die stikstof:fosfor verhouding in die kultuurmedium, was die mikrosistieninhoud onder kondisies van fosforlimitering laer ongeag die stikstofkonsentrasie. Hierdie waarneming, tesame met die noodsaak van gefikseerde koolstof vir stikstofassimilering, het gelei na 'n studie van die effekte van sellulêre koolstoffiksering and stikstofopname op die modulering van mikrosistienproduksie. Dit is gevind dat mikrosistienproduksie verhoog was wanneer die snelheid van stikstofopname relatief tot die snelheid van koolstoffiksering hoër was as die waarde wat benodig word vir gebalanseerde groei. Die sellulêre stikstof:koolstof verhouding waarbo mikrosistienkonsentrasies beduidend verhoog is stem ooreen met die Redfield verhouding vir gebalanseerde groei. 'n Ondersoek na potensiële reguleringsmeganismes waarby die sianobakteriële stikstofreguleerder NtcA betrokke is het gelei na die ontdekking van moontlike NtcA bindingseteis; dit kan dui op die repressie van die mikrosistiensintetase geengroepering. Onder kultuurkondisies is gevind dat die geen vir die polipeptiedsintetase module, mcyA, en ntcA omgekeerd uitgedruk word as 'n funksie van koolstofopname:stikstofopname potensiale. Geen toename of afname in mikrosistienproduksie kon egter gekoppel word aan óf glutamien, óf glutamaat, óf a-ketoglutaraat nie, metaboliete wat betrokke is by die regulering van ntcA. Die rol van NtcA in die regulering van mikrosistienproduksie kon dus nie bevestig word nie. Die gevolgtrekking is dus gemaak dat mikrosistienproduksie metabolies gereguleer word deur die C:N balans en die spesifieke groeisnelheid. Die primêre belang van stikstof en koolstof is gedemonstreer deur 'n eenvoudige model waarin slegs stikstofopname, koolstoffiksering en groeisnelheid gebruik word om mikrosistienvlakke te voorspel. Die model verklaar ook resultate wat tevore in die literatuur beskryf is. Soortgelyk is 'n artifisiële neurale netwerkmodel gebruik om te toon dat die afhanklikheid van koolstoffiksering van fosfor akkurate voorspelling van mikrosistienvlakke gebaseer of groeisnelheid en omgewingstikstof en fosfor moontlik maak.

Thesis (PhD)--Stellenbosch University, 2001. / ENGLISH ABSTRACT: Bacterial canker of stone fruit, caused by Pseudomonas syringae pv. syringae, is one of the most destructive crop diseases in South Africa. Chemical control has failed completely and effective long-term management strategies will have to rely on the breeding of resistant host trees. To assist in such breeding programmes, investigations into the molecular basis of the interaction between P. s. pv. syringae and stone fruit trees have been undertaken in collaboration with the ARC-Fruit, Wine and Vine Research Institute in Stellenbosch. The aim of this dissertation was to clone and identify genes that are involved in interaction between the bacterial canker pathogen and stone fruit trees. In the first part of the study, the harpin encoding gene of a local strain of the pathogen, P. s. pv. syringae NV, was amplified in a polymerase chain reaction (PCR) strategy with primers based on the hrpAZB sequences of the bean pathogen, P. s. pv. syringae 61. Sequencing of this hrpZpssNvgene revealed a high degree of homology (96%) between the harpin encoding genes and harpin proteins of the two strains. The hrpZpssNvgene was subsequently cloned into the pMAL-c2 expression vector and expressed in Escherichia co/i. This system was used for the production of purified, biologically active, recombinant HrpZpSSNV protein. In the second part of the study, differential display (DD) technology was used to identify genes that are induced in stone fruit trees in response to P. s. pv. syringae and/or its harpin elicitor. For this purpose, actively growing shoots of two Prunus sa/icina cultivars, the moderately resistant cv. 'Laetitia' and the highly susceptible cv. 'Songold' were treated with recombinant harpinpssNvprotein or live P. s. pv. syringae NV bacteria. An untreated control and wounding control was included in the experiment. Total RNA was isolated for comparative mRNA analysis 24 hours after treatment. DD profiles were generated with fifteen primer combinations. Eight candidate bands were re-amplified, cloned and sequenced. Reverse transcription PCR was employed to verify the expression patterns of the cloned bands in the original RNA sample set. Two bands, DDc and DD4 were shown to be differentially expressed between treatments and/or cultivars, while no differences in the expression levels of the remaining six bands (DDa, DDe, DD3, DD5, DD6 and DD7) were observed. BLAST similarity searches yielded significant matches for DDe, DD4 and DD7 with plant defense-related genes. / AFRIKAANSE OPSOMMING: Bakteriese kanker van steenvrugte, wat deur Pseudomonas syringae pv. syringae veroorsaak word, is een van die mees verwoestende siektes van landbougewasse in Suid-Afrika. Chemiese beheermaatreëls het geheel en al misluk en effektiewe langtermyn beheerstrategieë sal op die teling van weerstandbiedende gasheerbome moet staatmaak. Ondersoeke na die molekulêre basis van die interaksie tussen P. s. pv. syringae en steenvrugbome is in samewerking met die LNR-Vrugte-, Wyn- en Wingerdnavorsingsinstituut in Stellenbosch van stapel gestuur om tot sulke telingsprogramme by te dra. Die doelwit van hierdie proefskrif was om gene wat betrokke is in die interaksie tussen die bakteriese kanker patogeen en steenvrugbome te kloneer en te identifiseer. In die eerste gedeelte van die studie is die harpien-koderende geen van 'n plaaslike ras van die patogeen, P. s. pv. syringae NV, geamplifiseer in 'n polimerase kettingreaksie (PKR)-strategie met peilers wat op die hrpAZB-geenopeenvolgings van die boontjiepatogeen, P. s. pv. syringae 61, gebaseer is. Volgordebepaling van hierdie hrpZpssNv-geen het 'n hoë vlak van homologie (96%) tussen die harpien-koderende gene en harpien proteïene van die twee rasse getoon. Die hrpZpssNv-geen is vervolgens in die uitdrukkingsvektor pMAL-c2 gekloneer en uitgedruk in Escherichia coli. Hierdie sisteem is vir die produksie van suiwer, biologies-aktiewe, rekombinante HrpZpssNv-proteingebruik. In die tweede gedeelte van die studie is die differensiaalvertoon (DD) tegniek gebruik om gene te identifiseer wat deur P. s. pv. syringae en/of sy harpien elisitar in steenvrugbome geïnduseer word. Vir hierdie doel is aktief-groeiende lote van twee Prunus sa/icina kultivars, die matig weerstandbiedende kv. 'Laetitia' en die hoogs vatbare kv. 'Songold', met rekombinante harpienpssNvproteïen of lewende P. s. pv. syringae NV bakterieë behandel. 'n Onbehandelde- en verwondingskontrole is in die eksperiment ingesluit. Totale RNA is 24 uur na behandeling vir vergelykende mRNA-analise geïsoleer. DD-profiele is met vyftien peilerkombinasies gegenereer. Agt kandidaatbande is geheramplifiseer en gekloneer, waarna hul DNA-opeenvolgings bepaal is. Trutranskriptase-PKR is gebruik om die ekspressiepatrone van die gekloneerde bande in die oorspronklike RNA monsters na te gaan. Daar is vasgestel dat twee van die bande, DDc en DD4, differensieel tussen kultivars en/of behandelings uitgedruk is, terwyl geen verskille in die ekspressievlakke van die oorblywende ses bande (DDa, DOe, 003, DOS, 006 en DO7) waargeneem is nie. BLAST-soektogte het betekenisvolle ooreenkomste vir DDe, DD4 en DD7 met plant weerstandsgeassosieerde gene opgelewer.

Thesis (PhD)--Stellenbosch University, 2001. / ENGLISH ABSTRACT: Polygalacturonase-inhibiting proteins (PGIPs) are present in the cell walls of a variety of plant species. These proteins have been shown to specifically inhibit endopolygalacturonases (endo-PGs) secreted by invading fungal pathogens as part of the induced disease resistance mechanism of plants. This is the first report on the isolation and characterisation of a pgip gene from Vitis vinifera L., designated grapevine pgip1. A single open reading frame encoding a deduced polypeptide of 333 amino acids with a predicted molecular mass of 37.1 kOa and a calculated isoelectric point of 8.61 was identified from a 5.6 kb subgenomic fragment of V. vinifera cv Pinotage. Nucleotide and derived amino acid sequence analysis of grapevine pgip1 showed significant homology with other characterised PGIP encoding genes and revealed features characteristic of PGIPs found in several other plant families. Genomic DNA analysis showed that grapevine pgip1 belongs to a small multigene family in Vitis cultivars. From Northern blot analysis it was evident that expression of the PGIP family is both tissue- and developmental stage specific. The grapevine pgip1 was transiently expressed in Nicotiana benthamiana L. with potato virus X (PVX) as a vector. Grapevine PGIP1 isolated from crude protein extracts of PVX-infected N. benthamiana were tested and showed inhibitory activity against polygalacturonases (PGs) from Botrytis cinerea. Grapevine PGIPs have not previously been purified and characterised. Molecular analyses have confirmed that PGIPs are typically encoded by multigene families and that the inhibitor specificities and kinetics of the isolated proteins differ within and among species. In this study, two PGIP isomers from V. vinifera berries were isolated. The one isomer, designated PGIP-A, was partially purified and had a molecular mass of 39 kOa, whereas the other PGIP, designated PGIP-B, was purified and had a molecular mass of 42 kOa as determined by sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SOS-PAGE) and Western blot analysis. Both proteins were cell wall-bound. Enzymatic deglycosylation confirmed that PGIP-B is a glycosylated protein. Grapevine PGIP-A showed strong inhibitory activity against a homogeneous PG from Aspergillus niger and to a lesser extent against PG from Fusarium moniliforme, but was unable to interact with a crude PG preparation from B. cinerea. Grapevine PGIP-B was able to strongly inhibit PGs from B. cinerea as well as from Colletotrichum gleosporoides, yet showed no inhibition towards PG from A. niger. The grapevine pgip1 gene was expressed under the control of the Cauliflower mosaic virus (CaMV) 35S promoter in tobacco plants via Agrobacterium tumefaciensmediated transformation. Transgenic tobacco plants expressing the grapevine PGIP (gPGIP1) were used to demonstrate the effectiveness of this inhibitor against fungal PGs and to investigate whether gPGIP1 influences disease development. Northern blot analysis identified 19 transgenic plants expressing pgip1 transcript levels. Crude PGIP extracts from the transgenic tobacco plants inhibited PGs from B. cinerea and C. gleosporoides, but not PG from A. niger. Leaves from untransformed tobacco plants, from transgenic tobacco lines showing high and low PG inhibition, and from transgenic plants that did not express pgip1, were inoculated with B. cinerea. Transgenic leaves showed a reduction in the size of necrotic lesions of macerated tissues of approximately 45% relative to control and non-expressing transgenic leaves. The results from the heterologous expression of gPGIP1, together with the results from the protein purifications and inhibition studies, indicate that the isolated grapevine pgip1 gene encodes the isolated PGIP-B isomer. This work has ; established a good model system to study certain aspects of plant-pathogen interactions in grapevine. Heterologous expression of gPGIP1 has demonstrated that PGIP inhibition of fungal PGs slows disease development of B. cinerea in planta. / AFRIKAANSE OPSOMMING: Sien volteks vir opsomming

Thesis (PhD (Biochemistry))--University of Stellenbosch, 2010. / ENGLISH ABSTRACT: In the last decade a need arose to find a theoretical framework capable of gaining a quantitative understanding of ecosystems. Control analysis was proposed as a suitable candidate for the analysis of ecosystems with various theoretical applications being developed, i.e. trophic control analysis (TCA) and ecological control analysis (ECA). We set out to test the latter approach through experimental means by applying techniques akin to enzyme kinetics of biochemistry on a simple ecosystem between Saccharomyces cerevisiae and Gluconobacter oxydans. However, this exercise was far more complex than we originally expected due to the extra metabolic activities presented by both organisms. Nevertheless, we derived suitable kinetic equations to describe the metabolic behaviour of both organisms, with regards to the activities of interest to us, from pure culture experiments. We developed new techniques to determine ethanol and oxygen sensitivity of G. oxydans based on its obligately aerobic nature. These parameters were then used to build a simple kinetic model and a more complex model incorporating oxygen limited metabolism we observed at higher cell densities of G. oxydans. Our models could predict both situations satisfactorily for pure cultures and especially the more complex model could describe the lack of linearity observed between metabolic activity and cell density at higher cell densities of G. oxydans. Mixed populations of S. cerevisiae and G. oxydans reached quasi-steady states in terms of ethanol concentration and acetate flux, which was a positive indication for the application of control analysis on the ecosystem. However, the theoretical models based on parameters derived from pure culture experiments did not predict mixed culture steady states accurately. Careful analysis showed that these parameters were mostly under-estimated for G. oxydans and overestimated for S. cerevisiae. Hence, we calculated the kinetic parameters for mixed population assays directly from the experimental data obtained from mixed cultures. We could calculate the control coefficients directly from the experimental data of mixed population studies and compare it with those from theoretical models based on 3 different parameter sets. Our analysis showed that the yeast had all the control over the acetate flux while control over the steady-state ethanol was shared. The strength of our approach lies in designing our experiments with a control analysis approach in mind, but we have also shown that even for simple ecosystems this approach is non-trivial. Despite the various experimental challenges, this approach was very rewarding due to the extra information obtained especially regarding control structure with regards to the steady-state ethanol concentration. / AFRIKAANSE OPSOMMING: In die afgelope dekade het daar ’n behoefte ontstaan na ‘n teoretiese raamwerk om tot ‘n kwantitatiewe begrip van ekosisteme te kom. As kandidaat vir so tipe raamwerk is kontrole analise voorgestel gepaardgaande met die ontwikkeling van verskeie teoretiese toepassings, i.e. trofiese kontrole analise en ekologiese kontrole analise. In hierdie tesis het ons laasgenoemde aanslag eksperimenteel ondersoek op ‘n eenvoudige ekosisteem, tussen Saccharomyces cerevisiae en Gluconobacter oxydans, deur gebruik te maak van tegnieke vanuit ensiemkinetika van biochemie. Hierdie strategie was egter baie meer kompleks as wat oorspronklik verwag is as gevolg van verdere metabolise aktiwiteite aanwesig in beide organismes. Ons het egter steeds daarin geslaag om kinetiese vergelykings af te lei, vanuit suiwer kulture, wat die metaboliese gedrag van beide organismes beskryf vir die aktiwiteite van belang vir ons studie. Ons het nuwe tegnieke, gebaseer op die aerobiese natuur van G. oxydans, ontwikkel om die sensitiwiteit van G. oxydans vir etanol en suurstof te bepaal. Hierdie parameters is gebruik om eers ’n eenvoudige model en toe ‘n meer gevorderde model, wat die suurstof-beperkte metabolisme van G. oxydans by hoër biomassa te beskryf, op te stel. Beide modelle was baie effektief in die voorspelling van die situasies waarvoor hulle ontwikkel is vir die suiwer kulture waar veral die meer gevorderde model die gebrek aan ‘n linieêre verband tussen die metabolisme van G. oxydans en biomassa by hoër biomassa kon beskryf. ’n Bemoedigende aanduiding dat kontrole analise toegepas kon word op die ekosisteem was dat mengkulture van S. cerevisiae en G. oxydans het quasi-bestendige toestande bereik het in terme van etanol konsentrasies en asetaat-fluksie. Die teoretiese modelle gebaseer op die parameters afgelei vanaf suiwer kulture kon egter nie die bestendige toestande in mengkulture akkuraat voorspel nie. Nadere ondersoek het aangedui dat die parameters meesal onderskat is vir G. oxydans en oorskat is vir S. cerevisiae. Gevolglik het ons die kinetiese parameters vir mengkulture direk van eksperimentele data van die mengkulture bereken. Verder kon ons die kontrole koeffisiente ook direk vanaf die eksperimentele data van mengkulture bereken en vergelyk met dié bereken vanuit die teoretiese modelle gebaseer op drie verskillende paremeter-stelle. Ons analise het gewys dat die gis alle beheer op die asetaat-fluksie uitoefen en dat die beheer oor die etanol-konsnetrasie gedeel is tussen die twee organismes. Die krag van ons aanslag lê daarin dat die eksperimente ontwerp is met ‘n kontrole analise in gedagte, maar ons het ook bewys dat hierdie aanslag selfs vir eenvoudige ekosisteme nie triviaal is nie. Ten spyte van die eksperimentele uitdagings, was die aanslag baie waardevol as gevolg van die ekstra inligting verkry met spesifieke klem op die kontrole-struktuur met betrekking tot die etanol konsentrasie by bestendige toestand.

Thesis (PhD (Biochemistry))--University of Stellenbosch, 2011. / ENGLISH ABSTRACT: Metabolic Control Analysis (MCA) provides a powerful quantitative framework for understanding and explaining the control and regulation within a cellular system. MCA allows the global control of a steady-state system to be quantified in terms of control coeficients, which we can express in terms of the local properties referred to as elasticity coeficients. MCA relates elasticities to control coeficients through a matrix inversion, thus allowing scientists to predict and quantify how the kinetics of the individual enzymes affect the systemic behaviour of cellular systems. Traditionally we solved this problem numerically, while we used algebraic and symbolic control analysis techniques less frequently. By using symbolic algebraic computation we present a general implementation of the symbolic matrix inversion of MCA, known as SymCA, which requires only the description of any allosteric modifier interactions and the stoichiometry of a cellular system. The algebraic expressions generated allow an in-depth analysis of the distribution of the control within a system and also of the parameters which exhibit the greatest effect on this control distribution. This also applies when the exact values for the elasticities or control coeficients are unknown. We have demonstrated that by quantifying the control patterns, referred to as `routes of regulation', inherent in all control coeficient expressions, we can gain insight into how perturbations are propagated through a cellular system and which regulatory pathways are favoured under changing conditions. / AFRIKAANSE OPSOMMING: Metaboliese Kontrole-Analise (MKA) bied 'n kragtige kwantitatiewe raamwerk om die beheer en regulering binne sellulere sisteme te verstaan en te verduidelik. 'n Sleutelaspek van MKA is dat die globale beheer van 'n sisteem met 'n bestendige toestand gekwantifiseer kan word in terme van kontrole-koefisente en dat hierdie koefisente uitgedruk kan word in terme van die sisteem se lokale eienskappe, genaamd elastisiteitskoefisente. Deur van matriksinversie gebruik te maak kan MKA die verband tussen elastisiteitskoefisente en kontrole-koefisente aflei wat mens in staat stel om te sien hoe die kinetika van die individuele ensiemreaksies die sisteemgedrag op sellulere vlak beinvloed. Die probleem word tradisioneel hoofsaaklik op numeriese wyse bereken terwyl die gebruik van algebraiese en simboliese kontrole-analise minder gereeld gebruik word. In hierdie proefskrif verskaf ons, deur van simboliese algebraiese metodes gebruik te maak, 'n generiese implementasie van die simboliese matriksinversie van MKA, genaamd SymCA, wat slegs 'n beskrywing van 'n sellulere sisteem se allosetriese interaksies en die stoichiometrie benodig. Die algebraiese uitdrukkings sodanig gegenereer stel mens in staat om 'n in-diepte analise te doen om vas te stel waar die beheer binne 'n sisteem le, asook watter parameters die grootste effek op die kontrole-verspreiding het. Dit geld selfs in die geval waar die presiese waardes van die elastisiteitskoefisente of kontrole-koefisente onbekend is. Hierdie proefskrif demonstreer hoe die kwantifisering van kontrole-patrone, ook gesien as 'roetes van regulering', wat inherent is aan kontrole-koefisent vergelykings, mens in staat stel om te sien hoe perturbasies in 'n sellulere sisteem voortplant en watter regulatoriese paaie bevoordeel word onder veranderde kondisies.

Thesis (PhD (Biochemistry))--University of Stellenbosch, 2011. / ENGLISH ABSTRACT: Antagonism of antimicrobial action represents an alternative survival strategy for cohabiting soil organisms. Under competitive conditions, our group previously showed that surfactin (Srf) produced by Bacillus subtilis acts antagonistically toward gramicidin S (GS) from a cohabiting bacillus, Aneurinibacillus migulanus, causing the loss the antimicrobial activity of GS. This antagonism appeared to be caused by inactive complex formation. This study aimed to elucidate whether the previously observed antagonism of GS activity by Srf is a general resistance mechanism that also extends to related peptides such as the tyrocidines (Trcs) and linear gramicidins (Grcs) from Bacillus aneurinolyticus. Molecular interaction between the antagonistic peptide pairs was investigated using biophysical analytical methods such as electrospray mass spectrometry (ESMS), circular dichroism (CD), fluorescence spectroscopy (FS) and nuclear magnetic resonance (NMR). Results from this study corroborated the previous findings, namely that Srf antagonised the activity of GS towards Gram positive bacteria. However, for Micrococcus luteus synergism of GS action was observed at low Srf concentrations, while antagonism only occurred at Srf concentrations above the critical micelle concentration (CMC) of Srf when the bacteria were pre-incubated with Srf. This result and an ultra-performance liquid chromatography massspectrometry (UPLC-MS) study indicated that Srf pre-absorbed to cells, as well as Srf micelles interacted with GS, preventing GS from reaching the membrane target. Antagonism of GS action by Srf was also observed towards the Srf producer B. subtilis ATCC21332 and B. subtilis OKB120, a non-producer. The Srf producer was less sensitive than the nonproducer towards GS, possibly due to Srf production. Pre-incubation of Srf at different concentrations caused a dose-dependent antagonism, from as low as 0.9 μM Srf of GS activity towards B. subtilis OKB120. This antagonism at the low Srf concentration may be related to the induction of more resistant biofilms by Srf in B. subtilis. It was also found that Srf significantly improved the survival of B. subtilis OKB120 above that of M luteus in a mixed culture. In addition, the Srf producer B. subtilis ATCC21332 grew in the inhibition zone of the GS producer A. migulanus ATCC9999 during co-culturing, while B. subtilis OKB120 growth was inhibited. Srf induced biofilm formation in B. subtilis may be important in protecting the bacteria in solution, but not on solid phase such as on or in agar plates. Also, the protection of various cell types (previous studies by our group) by Srf from GS indicated a directed antagonistic Srf mode of action. Srf formed complexes that are visible and stable under ESMS conditions with GS, with the peptide bonds in the Val-Orn-Leu-D-Phe moiety of GS and the Val-Asp- D-Leu-Leu moiety of Srf protected from fragmentation. 1H-NMR titration studies strongly indicated that the molecular interaction of Srf and GS involved the re-orientation of the DPhe4,9 and Orn2,7 residues in GS. From CD spectra it was observed that Srf induced a concentration dependent decrease in the β-turn component and increase in β-sheet structures of the GS-Srf mixture. Diffusion orientated NMR (DOSY) indicated that Srf and GS formed homo-oligomers with the Srf-GS mixture having a slightly higher diffusion coefficient indicating the formation of smaller homo-oligomers or more compact hetero-oligomers. These hetero-oligomers involve intermolecular interaction at <5Å between the Orn2,7 residue of GS with Asp residue of Srf, as observed with ROESY-NMR. These results strongly indicate that inactive complex formation between Srf and GS is part of the antagonistic mechanism of action of Srf towards GS. Two high performance liquid chromatography (HPLC) methods was developed to purify peptides from the tyrothricin complex, namely the Trcs (contains one GS Val-Orn-Leu-DPhe- Pro moiety) and Grcs. These peptides were used to assess if Srf has an antagonistic activity beyond that of GS. Srf indeed showed antagonistic action against the antimicrobial activity of Trcs towards B. subtilis ATCC21332 and OKB120, with the tyrocidine C (TrcC) being more sensitive to antagonism than tyrocidine B (TrcB). Srf had an ambiguous effect on the linear gramicidin A (GA) that is co-produced with Trcs in tyrothricin. GA acted synergistically with Srf at low GA concentrations, but slight antagonism was observed at high GA concentrations. In contrast, GA showed pronounced synergism with TrcB towards the M. luteus. However, Srf at 30 μM, antagonised the synergistic action of a lethal mixture of 25 μM GA and TrcB. The Srf producer was also able to withstand and grow in the presence of the tyrothricin producer B. aneurinolyticus ATCC10068, indicating that antagonism of peptide action may allow different organisms to cohabit. Basic NMR and ESMS studies failed to show complex formation between Srf and the Trcs. However, CD presented clear evidence of Srf induced changes in secondary structures and/or higher order self-assembled structures of the Trcs-Srf mixture. FS also provided evidence of the reorientation/exposure of the Trp6 residue of the Trcs in the presence of Srf. These results corroborated the previous findings that complexation between Srf and GS or peptides analogous to GS may be part of the mechanism of Srf antagonistic action. In conclusion, this study showed that the antagonism of GS activity by Srf, conferred in part by inactive complex formation, is a putative resistance mechanism that also extends to other peptides containing the Val-Orn-Leu-D-Phe-Pro moiety such as the Trcs from B. aneurinolyticus. / AFRIKAANSE OPSOMMING: Antagonisme van antimikrobiese aksie verteenwoordig ʼn alternatiewe oorlewingstrategie vir grondorganismes wat in dieselfde habitat gevestig is. Ons groep het gewys dat surfaktien (Srf), geproduseer deur Bacillus subtilis, antagonistiese werking teenoor gramisidien S (GS) vanaf die bacillus Aneurinibacillus migulanus, onder kompeterende kondisies, toon. Die antagonistiese werking, wat moontlik veroorsaak word deur vorming van onaktiewe komplekse, lei tot die verlies van die antimikrobiese aktiwiteit van GS. Hierdie studie se doel was die ontrafeling van die moontlikheid dat die antagonisme van GS aktiwiteit deur Srf, soos deur vorige studies uitgewys, ʼn algemene weerstandsmeganisme is wat moontlik ook verwante peptiede soos die tirosidiene (Trcs) en lineêre gramisidiene (Grcs), afkomstig vanaf Bacillus aneurinolyticus, insluit. In hierdie studie is die molekulêre interaksie tussen antagonistiese peptiedpare ondersoek met biofisiese analitiese metodes wat elektrosproeimassaspektroskopie (ESMS), sirkulêre dichroïsme (SD), fluoressensie-spektroskopie (FS) en kernmagnetiese resonansspektroskopie (KMR) insluit. Die resultate wat tydens hierdie studie verkry is, het gewys dat Srf die werking van GS teenoor Gram-positiewe bakterie teenwerk, en het die vorige waarnemings ondersteun. Daar is egter sinergisme tussen Srf en GS werking by lae Srf-konsentrasies teenoor Micrococcus luteus waargeneem, terwyl antagonisme slegs waargeneem is by Srf-konsentrasies hoër as die kritiese miselêre Srf konsentrasie wanneer bakterieë vooraf met Srf met inkubeer is. Hierdie resultaat, tesame met ʼn ultra-hoë verrigting vloeistofchromatografie gekoppelde massaspektroskopie (UPLC-MS) studie, het daarop gedui dat Srf wat voorheen op selle geabsorbeer het, sowel as Srf-miselle in die media, met GS interaksie het en sodanig kan voorkom dat GS die membraanteiken bereik. Antagonisme deur Srf op die GS aktiwiteit is ook waargeneem teenoor die Srf-produseerder B. subtilis ATCC21332 en B. subtilis OKB120, ʼn nie-produseerder. Hierdie tipe antagonisme by ʼn lae konsentrasie van Srf mag verwant wees aan die induksie van meer weerstandige biofilms deur Srf in B. subtilis. Dit is ook gevind dat Srf die oorlewing van B. subtilis OKB120 aansienlik verhoog teenoor dié van M luteus in ʼn gemengde kultuur. Daar is verder bevind dat die Srf-produseerder, B. subtilis ATCC21332, in die inhibisiesone van die GS-produseerder, A. migulanus ATCC9999, gegroei het tydens kokultivering, terwyl die groei van B. subtilis OKB120 geïnhibeer is. Srf induseer biofilm-vorming in B. subtilis wat moontlik belangrik kan wees om die bakterieë in suspensie te beskerm, maar nie op soliede fase soos byvoorbeeld agar plate nie. Verder dui die beskerming van ʼn verskeidenheid sel-tipes (vorige studies deur ons groep) deur Srf teen GS, ʼn direkte antagonistiese aksie van Srf. Sigbare en stabiele komplekse tussen Srf en GS is waargeneem onder ESMS kondisies, waar die peptiedbindings in die Val-Orn-Leu-D-Phe-Pro eenheid van GS en die Val-Asp-Leu-D-Leu eenheid van Srf beskerm is teen fragmentering in die komplese. 1H-KMR titrasiestudies het duidelik aangetoon dat die molekulêre interaksie van Srf en GS die D-Phe4,9 en Om2, 7 residue in GS heroriënteer. SD-spektra van GS-Srf mengsels het daarop gedui dat Srf ʼn konsentrasieafhanklike vermindering in die β-draai komponente van die mengsel veroorsaak, maar dat β- plaat komponent van die mengsel vermeerder. Diffusie-georiënteerde KMR spektrometrie (DOSY) toon dat Srf en GS homo-oligomere vorm, maar ʼn hoër diffusie koeffisiënt vir die mengsel het aangedui dat die Srf-GS mengsel kleiner of meer kompakte hetero-oligomere. ROESY-KMR toon dat hierdie oligomere intermolekulêre interaksie(s) van <5Å tussen die Om2, 7 residue van GS en die Asp residu van Srf het. Die resultate gee ʼn sterk aanduiding dat die onaktiewe kompleks-vorming tussen Srf en GS deelneem in die antagonistiese werking van Srf teenoor GS. Twee hoë verrigting vloeistofchromatografie metodes is ontwikkel om peptiede uit die tirotrisienkompleks, naamlik die Trcs (bevat een GS Val-Om-Leu-D-Phe-Pro eenheid) en die gramisidiene (Grcs), te suiwer. Hierdie peptiede is gebruik om te bepaal of Srf antagonistiese aktiwiteit het wat verder strek as net dié van GS. Dit was inderdaad die geval en daar is gevind dat Srf antagonisties is teenoor die antimikrobiese aktiwiteit van Trcs met B. subtilis ATCC21332 en OKB120 as teikens, met tirosidien C (TrcC) wat meer sensitief vir antagonistiese werking van Srf was as tyrosidien B (TrcB). Srf het ʼn gemengde effek getoon teenoor lineêre gramisidien A (GA) wat saam met die Trcs in tirotrisien gekoproduseer word. GA het sinergisties met Srf gewerk by lae GA konsentrasies, maar milde antagonistiese werking getoon by hoë GA konsentrasies. Daarteenoor het GA en TrcB uitgesproke sinergisme getoon teenoor M. luteus. In teenstelling het Srf by 30 μM die sinergistiese aksie van die dodelike mengsel van 25 μM GA en TrcB elk geantagoniseer. Die Srf produseerder was ook bestand en kon in die teenwoordigheid van die tirotrisien produseerder B. aneurinolyticus ATCC10068 groei wat aangedui het dat die antagonisme van antibiotiese peptiedaktiwiteit die kohabitasie van organismes toelaat. Basiese KMR en ESMS studies kon nie kompleksvorming tussen Srf en die Trcs aantoon nie, terwyl SD duidelike bewyse gelewer het dat Srf verandering geïnduseer het in die sekondêre strukture en/of hoër orde/self-geassosieerde strukture van die Trc-Srf mengsel. FS het ook bewyse gelewer van die reoriëntasie/blootstelling van die Trp6 residu in die Trcs in die teenwoordigheid van Srf. Hierdie resultate ondersteun die vorige bevindinge dat kompleksvorming tussen Srf en GS of GS-peptiedanaloë deel van die meganisme van Srf se antagonistiese aksie uitmaak. Samevattend het hierdie studie getoon dat die antagonisme van GS aktiwiteit deur Srf deels toegeken kan word aan onaktiewe kompleksvorming tussen die twee peptiede en dat die voorgestelde weerstandsmeganisme ook ander peptiede wat die Val-Orn-Leu-D-Phe-Pro eenheid, soos die Trcs van B. aneurinolyticus, insluit.

Thesis (PhD)--Stellenbosch University, 2011. / See also the post-print version of the article that was published from the PhD - http://hdl.handle.net/10019.1/19557 / ENGLISH ABSTRACT: Glucocorticoid receptor (GR) levels, which modulate the response to glucocorticoids (GCs), vary between tissues and individuals and are altered by physiological and pharmacological effectors. In this study we set out to investigate the effects and implications of differences in GR concentration. Firstly, we established conditions that resulted in three statistically different GR populations in transiently transfected COS-1 cells. We demonstrated, using whole cell saturation ligand binding experiments, that high levels of wild type GR, but not of dimerization deficient GR, exhibited positive cooperative ligand binding with a concomitant increased ligand binding affinity. Furthermore, we established, through co-immunoprecipitation and fluorescent resonance energy transfer, that ligand independent dimerization correlates with positive cooperative ligand binding. This is the first time that positive cooperative ligand binding and increased ligand binding affinity have been explicitly correlated and linked to increased ligand independent dimerization of the GR. The downstream consequences of variation in GR concentration and dimerization included modulation of GR import and export rates, as investigated through live cell as well as immunofluorescent analysis. Furthermore, the nuclear distribution of GR was also influenced by GR dimerization. The major function of the GR is as a transcription factor, which mediates the response to GCs via activation or repression of genes. We have revealed direct influences of GR concentration and dimerization in a number of promoter reporter assays as well as in the transactivation of an endogenous gene. Specifically, cooperative ligand binding was found to be responsible for the GR level dependent potency shift in transrepression of an NF B containing promoter reporter construct via dexamethasone and the shift in the bio-character of Compound A, a dissociative GR agonist. Transactivation potency of dexamethasone as well as the partial agonist bio-character of medroxyprogesterone and mifepristone via a multiple GRE containing promoter reporter construct were influenced directly by cooperative ligand binding. Dimerization of the GR was shown to be crucial for ligand dependent transactivation of a single GRE containing promoter reporter construct, while ligand independent transactivation of both single and multiple GRE containing constructs was significantly increased due to an increase in GR concentration. The endogenous GC responsive glucocorticoid induced leucine zipper (GILZ) gene demonstrated significant ligand independent transactivation at GR levels, which displayed ligand independent dimerization. An increase in GR concentration resulted in an increase in efficacy through all promoter reporter constructs as well as the endogenous GILZ gene. Positive cooperative binding and the concomitant increase in ligand binding affinity to the GR at high levels may be a crucial factor in determining both the efficacy and potency of the GC response. Considering the significant differences in GR concentrations expressed by different tissues and by individuals within the same tissue, our findings may explain the interindividual as well as tissue specific responses to GC treatment and suggest an important mechanism of action through which the GR is primed to responsed to subsaturating GC concentrations and displays a significant level of ligand independent activity. / AFRIKAANSE OPSOMMING: Glukokortikoïed reseptor (GR) vlakke, wat die gedrag van glukokortikoïede (GCs) moduleer, wissel tussen weefsels en onder individue en word verander deur fisiologiese en farmakologiese effektore. In hierdie studie ondersoek ons die gevolge en implikasies van verskille in GR konsentrasie. Eerstens het ons die kondisies vasgestel wat benodig word om drie statisties verskillende GR populasies te vestig in kortstondige getransfekteerde COS-1 selle. Ons het getoon, met behulp van die heel sel versadigings ligand bindings eksperimente, dat hoë vlakke van wilde-tipe GR, maar nie van dimeriserings gebrekkige GR, positiewe koöperatiewe ligand binding, met 'n gepaardgaande toename in ligand bindings affiniteit, toon. Verder het ons bevestig, deur ko-immunopresipitasie en fluoressente resonansie energie-oordrag, dat ligand onafhanklike dimerisering korreleer met positiewe koöperatiewe ligand binding. Dit is die eerste keer dat positiewe koöperatiewe ligand binding en verhoogde ligand bindings affiniteit uitdruklik gekorreleer en gekoppel word aan verhoogde ligand onafhanklike dimerisering van die GR. Die daarop nagevolge van variasie in GR konsentrasie en dimerisering sluit in modulasie van die invoer en uitvoer tempo van die GR, soos ondersoek deur lewendige sel sowel as immunofluorescente analise. Verder is die verspreiding van die GR in die kern ook beïnvloed deur GR dimerisering. Die belangrikste funksie van die GR is as 'n transkripsie faktor, wat die respons van GCS bemiddel via aktivering of onderdrukking van gene. Ons het die direkte invloed van GR konsentrasie en dimerisering in 'n aantal promotor verslaggewer essais sowel as in die transaktivering van endogene gene onthul. Spesifiek, is gevind dat koöperatiewe ligand binding verantwoordelik is vir die GR vlak afhanklike verskuiwing in transrepressie potensie van 'n NF B bevattende promotor verslaggewer konstruk via deksametasoon en die verskuiwing van die biokarakter van verbinding A,' dissosiatiewe GR agonis. Transaktiverings potensie van deksametasoon, asook die gedeeltelike agonis bio-karakter van medroksie-progesteroon en mifepristoon, via 'n veelvoudige GRE bevattende promotor verslaggewer konstruk is direk beïnvloed deur koöperatiewe ligand binding. Dimerisering van die GR is getoon om deurslaggewend vir ligand afhanklike transaktivering van 'n enkele GRE bevattende promotor verslaggewer konstruk te wees, terwyl ligand onafhanklike transaktivering van beide enkel-en veelvoudige GRE bevattende konstrukte aansienlik toegeneem het as gevolg van toename in GR konsentrasie. Die endogene GC responsiewe glukokortikoïed geïnduseerde leusien rits (GILZ) gene het beduidende ligand onafhanklike transaktivering gedemonstreer op GR vlakke wat ligand onafhanklike dimerisering toon. 'n toename in GR konsentrasie het gelei tot toename in die effektiwiteit van al die promotor verslaggewer konstrukte, sowel as die endogene GILZ gene. Positiewe koöperatiewe ligand binding en die gepaardgaande toename in ligand bindings affiniteit van die GR by hoë vlakke kan 'n belangrike faktor wees in die bepaling van sowel die effektiwiteit as die potensie van die GC respons. As die aansienlike verskille in GR konsentrasies van verskillende weefsels en tussen verskillende individue in dieselfde weefsel in ag geneem word, kan ons bevindings die inter-individuele sowel as weefsel spesifieke response op GC behandeling verduidelik en stel dit 'n belangrike meganisme van aksie voor waardeur die GR voorberei word om op sub-versadigings konsentrasies van GC te reageer deur 'n beduidende vlak van ligand onafhanklike aktiwiteit te toon.

Thesis (PhD)--Stellenbosch University, 2012. / ENGLISH ABSTRACT: This study describes: - the characterization and comparison of the enzymatic activity of both Angora and ovine 3βHSD expressed in non-steroidogenic COS-1 cells. The apparent Km and Vmax values for the metabolism of PREG, 17-OHPREG and DHEA were determined; - the characterization of steroid metabolites produced by COS-1 cells coexpressing either Angora or ovine 3βHSD together with Angora CYP17, in the presence and absence of overexpressed Cyt-b5, following the metabolism of PREG and 17-OHPREG. 3βHSD was identified as an additional factor in causing hypocortisolism in the South African Angora goat; - the influence of Cyt-b5 on the enzymatic activity of both Angora and ovine 3βHSD coexpressed in non-steroidogenic COS-1 cells; - the influence of purified ovine live Cyt-b5 and anti-Cyt-b5 IgG on adrenal microsomal 3βHSD activity. Cyt-b5 was shown to specifically augment 3βHSD activity which represents the first documentation of such augmentation in any species; - the overexpression and purification of Angora 3βHSD using a baculovirus expression system coupled with a detergent based enzyme purification method; - the characterization of both substrate and co-factor kinetics for the individual dehydrogenase and isomerase activities of purified 3βHSD, in the presence and absence of purified ovine liver Cyt-b5. Cyt-b5 was shown to increase the affinity of 3βHSD towards NAD+ during the dehydrogenase reaction whilst having no significant influence on the isomerase reaction. This represents the first documentation of Cyt-b5 influencing co-factor binding in any member of the -ydroxysteroid dehydrogenases; - the FRET analysis of COS-1 cells coexpressing 3βHSD-eCFP and Cyt-b5-eYFP fusion proteins, suggesting an allosteric interaction between 3βHSD and Cyt-b5. / AFRIKAANSE OPSOMMING: Hierdie studie beskryf: - die karakterisering en vergelyking van die ensiematiese aktiwiteit van beide Angora en skaap 3βHSD, wat uitgedruk was in nie-steroïed genererende COS-1 selle. Die Km en Vmax waardes tydens die metabolisme van PREG, 17-OHPREG en DHEA was bepaal; - die karakterisering van steroïed metaboliete gegenereer deur COS-1 selle wat Angora of skaap 3βHSD uitdruk saam met Angora CYP17, in die aanwesigheid of afwesigheid van sitochroom b5, na die metaboliseering van PREG en 17-OHPREG. 3βHSD was geïdentifiseer as ‘n bydraende faktor in die oorsaak van hipokortisolisme in die Suid-Afrikaanse Angorabok; - die invloed van sitochroom b5 op die ensiematiese aktiwiteit van beide Angora en skaap 3βHSD wat saam uitgedruk was in nie-steroïed genererende COS-1 selle; - die invloed van gesuiwerde skaap lewer sitochroom b5 en sitochroom b5 teenstof op mikrosomale 3βHSD aktiwiteit. Dit is getoon dat sitochroom b5 die aktiwiteit van 3βHSD spesifiek verhoog. Hierdie studie verteenwoordig die eerste dokumentasie van so ‘n verhoging in enige spesie; - die uitdrukking en suiwering van Angora 3βHSD deur middel van ‘n bakulo-virus sisteem gekoppel aan ‘n detergent gebaseerde ensiem suiwerings metode; - die karakterisering van beide substraat en ko-faktor kinetika vir die afsonderlike dehidrogenase en isomerase aktiwiteite van gesuiwerde 3βHSD, in die aanwesigheid of afwesigheid van gesuiwerde sitochroom b5. Dit is getoon dat sitochroom b5 die affiniteit van 3βHSD teenoor NAD+ tydens die dehidrogenase reaksie verhoog sonder om ‘n beduidende invloed op die isomerase reaksie te hê. Hierdie studie verteenwoordig die eerste dokumentasie van sitochroom b5 wat ko-faktor binding beïnvloed in enige lid van die hidroksisteroïed dehidrogenase familie van ensieme; - die analise van FRET sein in COS-1 selle wat beide 3βHSD-eCFP en Cyt-b5- eYFP fusie proteïene uitdruk. Die resultate stel voor dat sitochroom b5 3βHSD aktiwiteit beïnvloed deur middel van ‘n allosteriese meganisme.