Thesis (PhD (Biomedical Sciences. Molecular Biology and Human Genetics))--University of Stellenbosch, 2007. / The infectious disease tuberculosis (TB) is one of the leading causes of death worldwide. The idea that infectious diseases are the most important driving force in natural selection and that they sustain frequent polymorphisms in the human genome was formally suggested by Haldane in 1949. This hypothesis implicated the human genetic component in the response to infectious disease. Today the involvement of host genetics in TB has been proven unequivocally and, together with environmental factors (e.g. nutrition and crowding) and the causative bacterium, Mycobacterium tuberculosis (M.tuberculosis), may influence the outcome of disease. As is evident, TB is a complex disease and the implication for studying genetic susceptibility is that a number of genes will be involved. Interferon gamma (IFN-7) is the major macrophage-activating cytokine during infection with M.tuberculosis and its role has been well established in animal models and in humans. This cytokine is produced by activated T helper 1 (Th1) cells. These Th1 responses can best deal with intracellular pathogens such as M.tuberculosis. We selected twelve candidate genes based on the hypothesis that genes which regulate the production of IFN-7 may influence TB susceptibility. We also selected polymorphisms from 27 other candidate genes, which may affect immunological pathways involved in TB, to investigate as susceptibility factors based on the following hypotheses: 1) granulomatous diseases can share susceptibility genes; 2) gene expression studies done by DNA-array analysis experiments may reveal TB susceptibility genes; 3) genomewide linkage studies in TB can determine susceptibility loci and genes in this region are possibly susceptibility factors; and 4) functional susceptibility polymorphisms in genes involved in immune-mediated diseases other than TB may contribute to susceptibility to TB. This research tested the association of 136 genetic polymorphisms in 39 potentially important genes with TB in the South African Coloured population. Well-designed case-control association studies were used and we attempted to replicate these findings in an independent sample set using family-based case-control designs (transmission disequilibrium tests (TDTs)). In addition, haplotypes and linkage disequilibrium (LD) in the candidate genes were also investigated. During the case-control analyses we found significant associations for 6 single nucleotide polymorphisms (SNPs) in the following genes: SH2 domain protein 1A, tolllike receptor 2, class II major histocompatibility complex transactivator, interleukin 1 receptor antagonist, runt-related transcription factor 1 and tumour necrosis factor superfamily, member 1B. Discrepant results were obtained during the TDT analyses. The number of families available was small and for this reason we cannot conclude that the case-control results were spurious. We also tested the association of haplotypes with TB. Haplotypes in the interleukin 12, beta (IL12B) and toll-like receptor 4 genes were nominally associated with TB in both the case-control and TDT analyses. We observed strong LD for the genes in the South African Coloured population. In total 17 novel SNPs were identified and one novel allele was found for a microsatellite in IL12B. This research contributes to the increasing amount of information available on genes involved in TB susceptibility, which in the future may help to predict high risk individuals.

Thesis (PhD (Med))--University of Stellenbosch, 2011. / ENGLISH ABSTRACT: The nitrogen metabolic pathway is essential for growth and survival of all living organisms including prokaryotes. Certain components of the pathway, such as the enzyme glutamine synthetase (GS), have been studied; however, little information is available regarding the pathway in the mycobacteria. Our in silico studies revealed that many of the components and mechanisms involved in the pathway appear to be conserved between closely related Actinomycetales. Therefore, we investigated three aspects of nitrogen metabolic control in Mycobacterium smegmatis; namely, transcriptional regulation of nitrogen metabolism-related genes, control of enzyme activity and the signalling cascade governing the nitrogen metabolic response. At the transcriptional level, it was found that nitrogen metabolism-related genes were regulated in response to ammonium availability. Two possible transcriptional regulators, AmtR and GlnR, which are the regulators responsible for control of nitrogen-related gene transcription in Streptomyces coelicolor and Corynebacterium glutamicum respectively, were identified in M. smegmatis. Through generation of amtR and glnR deletion mutants, we found that both potential regulators played a role in the control of nitrogen-related gene expression in M. smegmatis. GlnR acted as both an activator and repressor of gene transcription whilst AmtR appeared to activate gene expression which is different to the role its homolog plays in C. glutamicum. On a protein level we found that both GS and glutamate dehydrogenase (GDH) were responsible for ammonium assimilation in M. smegmatis and were regulated in response to ammonium availability. Two GDH isoforms (NAD+- and NADP+-specific) were identified in M. smegmatis and whereas only an NAD+-GDH was detected in M. tuberculosis. The M. tuberculosis GDH also played a largely anabolic role with regard to ammonium assimilation which is in contrast to the belief that ammonium can only be assimilated via GS in this pathogen. The signaling cascade was investigated through generation of a glnD deletion mutant in M. smegmatis. We were able to show that this pivotal protein (GlnD) was able to relay the cellular nitrogen status to the transcriptional machinery as well as to GS. The data presented in this study has advanced our understanding of the nitrogen metabolic pathway in the mycobacteria. Through elucidation of such pathways, our knowledge of mycobacterial physiology and thus infection and survival improves, which could ultimately lead to the discovery of novel mechanisms to aid in the eradication of the disease. / AFRIKAANSE OPSOMMING: Stikstof metabolisme is noodsaaklik vir die oorlewing en groei van alle organismes, prokariote ingesluit. Sekere sellulêre komponente, soos die ensiem glutamine sintetase (GS), is al tevore bestudeer, maar baie min verdere inligting is beskikbaar oor stikstof metabolisme in die mycobacteria. Ons in silico studies het gewys dat baie van die komponente en meganismes gekonserveerd gebly het tussen nou-verwante Actinomycetales. Dus het ons drie aspekte in die beheer van stikstof metabolisme ondersoek; naamlik, die transkriptionele regulering van stikstof metabolisme-verwante gene, die beheer van ensiem aktiwiteit en die sein-meganisme wat die reaksie op stikstof konsentrasie reageer. Op transkripsionele vlak het ons gevind dat stikstof metabolisme-verwante gene gereguleer word in reaksie op stikstof beskikbaarheid. AmtR en GlnR is twee moontlike transkripsie reguleerders wat verantwoordelik is vir transkripsionele beheer in onderskeidelik Streptomyces coelicolor en Corynebacterium glutamicum. Beide hierdie proteïene is geïdentifiseer in M. smegmatis. Deur die konstruksie van amtR en glnR mutante, het ons gevind dat beide potensiële reguleerders ‘n rol gespeel het in die beheer van stikstof-verwante transkripsie in M. smegmatis. GlnR het opgetree as beide ‘n aktiveerder en ‘n onderdrukker van transkripsie terwyl AmtR net ‘n aktiverende rol gespeel het. Die funksie van AmtR in M. smegmatis is dus verskillend van sy homoloog in C. glutamicum. Op proteïen-vlak het ons gevind dat beide GS en glutamaat dehidrogenase (GDH) verantwoordelik was vir die assimilasie van ammonium in M. smegmatis en albei was gereguleer in reaksie op ammonium beskikbaarheid. Twee vorme van GDH (NAD+- spesifieke- en NADP+-spesifieke GDH) was geïdentifiseer in M. smegmatis terwyl net ‘n NAD+- spesifieke GDH in M. tuberculosis gevind is. Die M. tuberculosis GDH het ook ‘n anaboliesie rol gespeel met betrekking tot ammonium assimilasie wat in teenstelling is met die huidige opvatting dat ammonium alleenlik deur GS ge-assimileer kan word. Die sein-meganisme is ondersoek deur ‘n glnD M. smegmatis mutant te konstrueer. Ons het bewys dat hierdie deurslaggewende proteïen (GlnD) die sellulêre stikstof status aan die transkripsionele masjinerie, en aan GS kon oordra. Die data wat in hierdie studie voorgelê word, het ons kennis van stikstof metabolisme in die mycobacteria gevorder. Sodanige metaboliese studies verbreed ons kennis van mycobacteriële fisiologie en dus M. tuberculosis infeksie en oorlewing en kan uiteindelik lei tot die ontdekking van unieke teiken meganismes om te help met die beheer van die siekte en nuwe middelontwikkeling.

Thesis (PhD (Biomedical Sciences. Molecular Biology and Human Genetics))--University of Stellenbosch, 2007. / Tuberculosis (TB) is a global health problem and demands rigorous control management efforts. A dramatic increase in the acquisition and spread of drug resistant TB globally has been observed in recent years. A grim picture has emerged for the control program with the discovery of extreme drug-resistant TB, which is virtually untreatable and is of immense concern for the future of TB control. In the last decade strain-specific genetic markers have been identified to examine the molecular epidemiology and spread of TB, including IS6110 DNA-fingerprinting and spoligotyping. Although spoligotyping has less discriminatory power than the gold standard, IS6110 DNA-fingerprinting, it is simpler, faster and less expensive, as it is PCR-based. Spoligotyping has been applied to enhance our understanding of the dynamics of drug susceptible and drug resistant strains of Mycobacterium tuberculosis in high incidence communities, by studying 3 aspects of the TB epidemic: molecular epidemiology of drug resistant TB, recurrent TB and the evolution of M. tuberculosis. By using spoligotyping and other genotypic and phenotypic analysis of drug-resistant M. tuberculosis isolates from the Western Cape Province of South Africa showed that drug resistance is widespread and recently transmitted. An emerging drug resistant M. tuberculosis outbreak has been identified, termed DRF150, which has specific genotypic characteristics and is resistant to 5 first-line drugs in 45% of the cases. Inappropriate chemotherapy; poor adherence to treatment and prolonged periods of infectiousness due to the delay in susceptibility testing has led to the development and spread of this drug resistant genotype. The study demonstrates the ability of the spoligotyping technique to accurately determine the pathogenic mechanism of recurrent disease by spoligotyping, making it useful in large-scale intervention studies. Application of spoligotyping and a newly developed PCR-method showed that the occurrence of multiple infections was higher than what was previously assumed and also more frequent in retreatment cases than new cases. These findings have important implications for the understanding of protective immunity, and the development and testing of new vaccines and drugs. Various different molecular markers including spoligotyping has been used to reconstruct the evolutionary history of isolates with less than 6 copies of IS6110 element (termed Low Copy Clade (LCC)), which were previously poor defined. It was also shown that LCC is widely disseminated and play an important role in the global tuberculosis epidemic. Reconstruction of the evolutionary relationship of M. tuberculosis Principal Genetic Group 2 strains, identified previously unknown genetic relationships between strain families and laid the foundation to establish correlations between genotype and phenotype. Spoligotyping signatures, created by evolution of the Direct Repeat region in M. tuberculosis, were identified, which will enable the analysis of the strain population structure in different settings and will also enable the rapid identification of strain families that acquire drug-resistance or escape protective immunity in drug and vaccine trials. This study contributed to our understanding of the molecular epidemiology of drug resistant TB, recurrent TB and the evolution of M. tuberculosis in high incidence communities.

Thesis (PhD (Biomedical Sciences. Molecular Biology and Human Genetics))--University of Stellenbosch, 2009. / Dissertation presented for the degree of Doctor of Philosophy in Medical Biochemistry at Stellenbosch University. / ENGLISH ABSTRACT: The infectious disease tuberculosis (TB) still represents a global threat due to its devastating effect on health and the subsequent high mortality rate. Previous studies have indicated that host genetic factors are implicated in host susceptibility to TB. Since TB is a complex disease, it can be assumed that susceptibility to M. tuberculosis has multiple genetic causative factors (as well as environmental causes). The current study focussed on a number of South African Coloured (SAC) individuals, some of whom were TB cases and others controls. Population substructure was tested in the admixed SAC population as it can be a strong confounding factor for association studies. Our results using the programme STRUCTURE indicated no population substructure in the SAC population. We further investigated the population structure of the SAC group using Affymetrix 500k SNP chip data which showed that the SAC population group has 4 major ancestral components: the Khoesan, European, African and Asian (Indian). A number of candidate polymorphisms in eight genes, previously indicated to play an important role in TB susceptibility, were tested in case-control associations studies. We found statistically significant associations between IFNGR1, IL-8, IL-1Ra and NRAMP1 polymorphisms and TB susceptibility in the SAC population. It has become increasingly evident that gene-gene interactions play a far more important part in an individual’s susceptibility to a complex disease than single polymorphisms would on their own. The importance of epistasis was clearly identifiable in this study with only four associations found between the individual variants and TB susceptibility, but eight instances of statistically significant gene-gene interactions. A combined data set consisting of 106 variants constructed from our database and also used for gene-gene interaction analysis yielded numerous statistically significant interactions. The interaction between the genotype of the human host and the bacterial strain genotype was also investigated and yielded interesting results. Owing to various polymorphisms in several cytokine genes, the protein levels of the main modulators of the immune system, cytokines and chemokines, are changed in several diseases such as infectious diseases and may affect susceptibility or resistance to TB. The functional polymorphisms or haplotype patterns in some of these cytokine genes might be vital for protective immune responses and may serve as biomarkers of protection or susceptibility to TB. The present study investigated 18 cytokines including pro-inflammatory, anti-inflammatory and chemokine factors in healthy (mantoux positive or negative) children using the Linco-plex immunoassay, and investigated potential interactions. The basic research will one day contribute to personalised genetics which may benefit infectious diseases such as TB. If individuals can be identified as potentially more vulnerable, they may require different vaccination strategies, a higher index of suspicion if exposed to TB, and prophylactic treatment. / AFRIKAANSE OPSOMMING: Die infektiewe siekte tuberkulose (TB) is steeds ‘n gevaar wat die hele wêreld bedreig weens die groot impak op gesondheid en die gevolglike hoë mortaliteit. Vorige studies het bevind dat die gasheer se genetiese faktore wel betrokke mag wees by die gasheer se vatbaarheid vir TB. Aangesien TB ‘n komplekse siekte is, kan dit aanvaar word dat vatbaarheid tot M. tuberculosis veelvuldige genetiese oorsaaklike faktore (sowel as omgewingsoorsake) het. Hierdie studie het gefokus op ‘n aantal Suid-Afrikaanse Kleurling (SAC) individue, waarvan sommige TB pasiënte en ander kontroles was. Die gemengde SAC populasie is getoets vir populasie-stratifikasie, aangesien stratifikasie ‘n sterk verwarrende invloed op pasiënt-kontrole studies kan hê. Ons resultate is verkry met behulp van die program STRUCTURE en het aangedui dat daar geen populasie sub-struktuur tussen die pasiënte en kontroles was nie. Ons het ook die populasiesamestelling van die SAC groep ondersoek met data verkrygbaar van die Affymetrix 500k enkel nukleotied polimorfisme mikroskyfie. Hierdie data het getoon dat die SAC populasie uit 4 hoof voorouerlike komponente bestaan naamlik die Khoesan, Europeërs, Afrikane en Asiate (Indiërs). ‘n Aantal kandidaat polimorfismes in agt gene, wat volgens vorige studies ‘n belangrike rol in TB vatbaarheid te speel, was in hierdie pasiënt-kontrole assosiasie studie bestudeer. Ons het statistiese beduidende verwantskappe tussen IFNGR1, IL-8, IL-1Ra en NRAMP1 polimorfismes en TB vatbaarheid in die SAC populasie gevind. Dit het al hoe meer duidelik geword dat geen-geen interaksies ‘n baie belangriker rol in ‘n individu se vatbaarheid vir ‘n komplekse siekte speel as enkel polimorfismes op hul eie. Die belang van epistase kon duidelik in hierdie studie geïdentifiseer word met slegs vier assosiasies wat tussen die individuele variante en TB vatbaarheid gevind is, in vergelyking met agt statisties beduidende geen-geen interaksies. ‘n Gekombineerde datastel wat uit ons databasis saamgestel is en wat 106 variante bevat is ook in ‘n aparte geen-geen interaksie analise gebruik, wat verskeie statisties beduidende interaksies getoon het. Die interaksie tussen die menslike gasheer genotipe en die bakteriese stam genotipe is ook in hierdie studie ondersoek en het interessante resultate opgelewer. Veranderde proteïen uitdrukking van die hoofmoduleerders van die immuunsisteem, sitokine en chemokine, kom voor in verskeie siektes soos infektiewe siektes weens verskillende polimorfismes in verskeie sitokien-gene. Sulke polimorfismes kan ook vatbaarheid vir of weerstandigheid teen TB beïnvloed. Die funksionele polimorfismes of haplotipe patrone in sommige van hierdie sitokien-gene mag noodsaaklik wees vir beskermende immuunresponse en mag ook as biomerkers vir beskerming teen of vatbaarheid vir TB dien. Hierdie studie het 18 sitokiene (insluitend pro-inflammatoriese-, anti-inflammatoriese- en chemokiene faktore), sowel as potensiële interaksies in gesonde (mantoux positiewe of negatiewe) kinders, ondersoek met behulp van die Linco-plex immuno-analise. Hierdie basiese navorsing sal eendag in die toekoms bydrae tot persoonlike genetiese analises wat tot voordeel kan wees vir infektiewe siektes soos TB. Indien individue as potensieël meer vatbaar vir TB geïdentifiseer kan word, kan sulke persone ander vaksineringstrategieë sowel as voorkomende behandeling vereis.

Thesis (PhD (MedSc))--University of Stellenbosch, 2011. / ENGLISH ABSTRACT: Fumonisins are carcinogenic mycotoxins which occur world-wide in maize and maize-based products intended for human consumption. Consumption of fumonisin contaminated maize as a staple diet has been associated with oesophageal and liver cancer incidence as well as neural tube defects. This study has confirmed the State of Santa Catarina, Brazil as another region where the consumption of maize contaminated with fumonisins and high oesophageal cancer incidence co-occur. Since fumonisins exert their main biochemical effect by disruption of the sphingolipid biosynthetic pathway and are implicated in cancer, the role of fumonisin B1 (FB1) in FB1–induced rat hepatocyte nodules was investigated. The current study showed that FB1 exposure activated sphingosine accumulation in the nodules which could induce the bio-active sphingosine 1-phosphate to provide a selective growth stimulus on subsequent FB1 exposure. Since the FB1-induced hepatocyte nodules were not resistant to the disruption of sphingolipid biosynthesis, it was not the mechanism whereby the altered hepatocytes escaped the mitoinhibition of FB1 and selectively proliferated into hepatocyte nodules. A study in maize subsistence farming communities investigated the sphingosine and sphinganine levels in blood and urine of participants. Fumonisin exposure was assessed in these communities based on fumonisin levels in maize that was concurrently collected from the areas where the participants resided. Subsequently fumonisin exposure was assessed in individuals based on the fumonisin levels in maize collected from each household and by acquiring weighed food records for each member of the household. It was confirmed in both these studies that communities are chronically exposed to fumonisin levels well above the provisional maximum tolerable daily intake determined by the Joint FAO/WHO Expert Committee on Food Additives. Since the sphinganine and sphingosine levels in blood and urine of the participants exposed to various levels of fumonisin were not significantly different, the sphingoid bases and their ratios could not be established as a biomarker of fumonisin exposure. Therefore, an alternative biomarker of exposure was investigated during studies into a practical cost effective method to reduce fumonisin. The customary maize food preparation practices were assessed in a maize subsistence farming community and subsequently optimised to reduce the fumonisin levels in the maize under laboratory-controlled conditions. Implementation of this optimised and culturally acceptable intervention method of sorting and washing maize in a rural community reduced fumonisin contamination in home-grown maize by 84%. The intervention study attained a 62% reduction in fumonisin exposure based on fumonisin levels in maize-based food and consumption as assessed by 24-h dietary recall questionnaires. The alternative biomarker of fumonisin exposure, urinary FB1, was investigated during the intervention study. The FB1 urinary biomarker measured fumonisin intake at the individual level and confirmed the reduction achieved as assessed by food analysis and food intake data. The biomarker was thus well correlated with fumonisin exposure and confirmed the efficacy of the simple and culturally acceptable intervention method. Utilisation of the urinary FB1 biomarker and the customised hand-sorting and washing of maize to reduce fumonisin exposures has the potential to improve food safety and health in subsistence maize farming communities. / AFRIKAANSE OPSOMMING: Fumonisien is kankerverwekkende mikotoksiene wat wêreldwyd voorkom op mielies en mielie-verwante produkte bestem vir menslike verbruik. Daar is ‘n verband tussen die voorkoms van slukderm en lewer kanker, sowel as neuraalbuisdefekte, in gemeenskappe waar fumonisien-gekontamineerde mielies die stapel voedsel is. Die Brasiliaanse Staat, Santa Catarina is uitgewys as nog 'n area waar hoë voorkoms van slukdermkanker en hoë fumonisin vlakke in mielies gesamentlik voorkom. Aangesien fumonisien verbind word met van kanker en die hoof biochemiese effek die ontwrigting van die sfingolipiedbiosintese weg is, is die rol van fumonisien B1 (FB1) in FB1-geinduseerde rot hepatosietnodules ondersoek. Die studie het getoon dat FB1 blootstelling aktiveer sfingosien ophoping in die hepatosietnodules wat moontlik die bio-aktiewe sfingosien 1-fosfaat aktiveer om op daaropvolgende FB1 blootstellings geselekteerde groei stimulasie te ondergaan. Die FB1-geïnduseerde hepatosietnodules was nie bestand teen die inhibisie van die sfingolipied biosintese nie en dus nie die meganisme waardeur die veranderde hepatosiete mito- inhibisie van FB1 vryspring, en selektief ontwikkel in hepatosietnodules nie. ‘n Studie in bestaansboerdery gemeenskappe het die sfingosien en sfinganien vlakke in bloed en uriene vergelyk met individuele fumonisien blootstelling. Laasgenoemde is gebaseer op fumonisien vlakke in gekolleekterde mielies vanuit die deelnemers se huise en aannames vanuit die literatuur. Die opvolg studie in die areas het individuele fumonisien blootstelling bepaal gebaseer op fumonisien vlakke in die mielies van elke huishouding en die inname van mielies deur die voedsel van elke individu te weeg. Albei hierdie studies het bevestig dat die gemeenskappe blootgestel is aan kroniese fumonisien vlakke wat die maksimum toelaatbare daaglikse inname wat deur die gesamentlike FAO/WHO deskundige komitee op voedsel toevoegsels vasgestel is, oorskei. Aangesien die sfingosien en sfinganien vlakke nie beduidend verskil in bloed of uriene van mense wat aan verskillende fumonisien-kontaminasie vlakke blootgestel is nie, kan die lipiedbasisse en hul verhouding nie as ‘n biologiese merker vir fumonisien blootstelling bevestig word nie. Dus is ‘n alternatiewe biologiese merker vir fumonisien blootstelling ondersoek gedurende ‘n studie oor praktiese bekostigbare maniere om fumonisin blootstelling te verlaag. Die tradisionele voedsel voorbereidingspraktyke in ‘n bestaansboerdery gemeenskap is bestudeer en onder laboratorium-gekontroleerde toestande aangepas om fumonisien vlakke in die mielies optimaal te verlaag. Die kultureel aanvaarbare intervensie metode, sortering en was van die mielies, is in ‘n bestaansboerdery gemeenskap toegepas waar ‘n 84% verlaging in fumonisien vlakke van die mielies verkry is. Die intervensie metode het ‘n 62% verlaging in fumonisien blootstelling te weeggebring deur fumonisien vlakke in die mieliegebasserde disse te meet en inname daarvan deur die deelnemers met 24-h diëetkundige vraelyste vas t e stel. Gedurende die intervensie studie is urienêre FB1, die alternatiwe biologiese merker van fumonisien blootstelling, ondersoek. Individuele fumonisien blootstelling data, bepaal met die urienêre FB1 biomerker, het goed ooreengestem met die voedsel analise en voedsel inname data en het dus die doeltreffendheid van die praktiese kultuur aanvaarbare intervensie metode bevestig. Benutting van die FB1 urienêre biologies merker en die optimale sortering en was van die mielies om die fumonisien blootstelling te verlaag het die potensiaal om voedselveiligheid en gesondheid in hierdie bestaansboerdery gemeenskappe aansienlik te verbeter.

Thesis (MScMedSc)--Stellenbosch University, 2012. / ENGLISH ABSTRACT: Mycobacterium tuberculosis is a pathogenic organism that infects a third of the world’s population and causes approximately 2 million deaths per year. Extensive research has been done on this pathogen, however our knowledge of the mechanisms of pathogenicity remain limited. The M. tuberculosis genome contains five ESAT-6 gene cluster regions, ESX-1 to 5, which encode specialized type VII secretion systems. These secretion systems are known to secrete members of the ESAT-6/CFP-10 and PE/PPE protein families, some of which contribute to the pathogenicity and phagosomal escape of the pathogen. ESX-3 has been shown to be essential for in vitro growth and survival of M. tuberculosis. The expression of ESX-3 in M. tuberculosis is regulated by IdeR and Zur, in response to intracellular iron and zinc concentrations, respectively. Interestingly, ESX-3 is not essential for the growth and survival of the saprophytic organism M. smegmatis. In this study, we aimed to identify the subcellular localisation of the individual components of the ESX-3 secretion system in the non-pathogenic, fast-growing organism M. smegmatis. The esx conserved component (ecc) genes from ESX-3 were expressed from the episomal expression vector pDMNI as fusion proteins with green fluorescent protein (GFP). MSMEG_0615 (eccA3), MSMEG_0616 (eccB3), MSMEG_0623 (eccD3) and MSMEG_0626 (eccE3) were successfully cloned into pDMNI and expression of fusion proteins was confirmed by Western blotting for MSMEG_0615-GFP, MSMEG_0616-GFP and MSMEG_0626-GFP in M. smegmatis. In the M. smegmatis ESX-3 knock-out (with MSMEG_0615 to MSMEG_0626 deleted) expression was confirmed for MSMEG_0615-GFP and MSMEG0626-GFP. Fluorescent microscopy determined that MSMEG_0615-GFP localised to a single mycobacterial pole in both strains. MSMEG_0616-GFP and MSMEG_0626-GFP were found to be membrane associated in M. smegmatis, while MSMEG_0626-GFP was found to be membrane associated in the M. smegmatis ESX-3 knock-out. The unipolar localisation of MSMEG_0615-GFP suggests that the assembled ESX-3 secretion system apparatus is situated at a single pole in M. smegmatis. Therefore, we hypothesize that MSMEG_0615 might act as a recruiter protein that is involved in the assembly of ESX-3 at the mycobacterial pole. / AFRIKAANSE OPSOMMING: Mycobacterium tuberculosis is ‘n patogene organisme wat ‘n derde van die wêreld se bevolking infekteer en eis jaarliks 2 miljoen lewens deur tuberkulose. Ten spyte van uitgebreide navorsing, is daar min kennis oor die meganismes van patogenisiteit van hierdie organisme. Die M. tuberculosis genoom bevat vyf duplikasies van die ESAT-6 geen groep gebiede, ESX-1 tot 5, wat kodeer vir gespesialiseerde Tipe VII sekresie sisteme. Hierdie sekresie sisteme is bekend vir die sekresie van lede van die ESAT-6/CFP-10 en PE/PPE proteïen families, waarvan sommige bydra tot die patogenisieit en fagosomale ontsnapping van hierdie organisme. ESX-3 is noodsaaklik vir die in vitro groei en oorlewing van M. tuberculosis. Die uitdrukking van ESX-3 in M. tuberculosis word gereguleer deur IdeR en Zur in reaksie op intrasellulêre yster en sink konsentrasies, onderskeidelik. ESX-3 word nie benodig vir die groei en oorlewing van die saprofitiese organisme M. smegmatis nie. Hierdie studie was gemik om die sub-sellulêre lokalisering van ESX-3 te identifiseer in die niepatogeniese en vinnig-groeiende organisme, M. smegmatis. Die “esx conserved component” (ecc) gene van ESX-3 is uitgedruk vanaf die episomale uitdrukkingsvektor pDMNI as gekombineerde proteïene met die groen fluoreserende proteïen (GFP). MSMEG_0615 (eccA3), MSMEG_0616 (eccB3), MSMEG_0623 (eccD3) en MSMEG_0626 (eccE3) is suksesvol gekloneer en die uitdrukking van die gekombineerde proteïene is bevestig deur Western oordrag vir MSMEG_0615-GFP, MSMEG_0616-GFP en MSMEG_0626-GFP in M. smegmatis. In die M. smegmatis ESX-3 uitklopmutant (met MSMEG_0615 tot MSMEG_0626 uitgeslaan) is uitdrukking bevestig vir MSMEG_0615-GFP en MSMEG0626-GFP. Fluoresensie mikroskopie het bepaal dat MSMEG_0615-GFP gelokaliseer is by ‘n enkele mikobakteriese pool in beide stamme. MSMEG_0616-GFP en MSMEG_0626-GFP was membraan-geassosieerd in M. smegmatis, terwyl en MSMEG_0626-GFP geassosieer het met die membraan in die M. smegmatis uitklopmutant. MSMEG_0615 het gelokaliseer by ‘n enkele pool in M. smegmatis en dit dui aan dat die saamgestelde ESX-3 sekresie sisteem apparaat slegs by ‘n enkele pool voorkom in M. smegmatis. Ons hipotiseer dat MSMEG_0615 dalk mag optree as ‘n werwer proteïen wat betrokke is by die samestelling van die ESX-3 sekresie sisteem by die mikrobakteriese pool. / Stellenbosch University

Thesis (PhD (Biomedical Sciences. Molecular Biology and Human Genetics))--University of Stellenbosch, 2007. / Despite the ongoing global tuberculosis (TB) problem and extensive research into protective immunity against this intracellular pathogen, mechanisms of protective immunity against Mycobacterium tuberculosis (Mtb) in humans have not been fully clarified. Numerous reports have addressed the potential immunological defect(s) in infected individuals that have developed active TB in comparison to those who have remained healthy in spite of infection. Markers of treatment response phenotypes are still elusive. The aims of this study were to define lymphocyte subsets in the peripheral blood of TB patients and controls, to determine intracellular interferon-γ (IFN-γ) and interleukin-4 (IL-4) production and to find correlations of these data with microbiologically-defined treatment response. Methods Whole blood tests were done on 30 HIV-negative, smear-positive pulmonary TB patients and 18 healthy skin test positive volunteers resident in the same community. Immunophenotyping was performed by flow cytometry, combined with routine haematology, for the enumeration of peripheral blood immune cell subtypes. Whole blood was also stimulated in vitro with anti-CD3 monoclonal antibody and intracellular IFN-γ and IL-4 determined by flow cytometry. Lymphocyte proliferation in response to heat-killed Mtb was determined by tritiated thymidine incorporation. Routine microbiological monitoring by sputum smears and culture was done throughout the patients’ 26 weeks of treatment. Results Compared to healthy controls, absolute numbers of peripheral blood lymphocytes and lymphocyte subsets were significantly depressed in patients at diagnosis but normalized during treatment with the exception of natural killer (NK) cells and natural killer T (NKT) cells. A novel subset of the latter was found to correlate significantly with treatment response. IFN-γ-producing T cells after a 4-hour T cell receptor stimulation were significantly higher in patients at diagnosis and normalized during treatment. Supplementary kinetic experiments showed that IFN-γ production in patients at diagnosis seemed to be accelerated. Lymphocyte proliferation was lower in patients at diagnosis and normalized during treatment. Neither IFN-γ production nor lymphocyte proliferation correlated with treatment response. Low intracellular IL-4 production was constitutive in patients and controls, was insignificantly lower in patients at diagnosis than in controls and, in the slow responder patient group, it was significantly lower than in the fast responder group. High IL-4 expression was found in low numbers of T cells in patients and controls and supplementary experiments showed co-expression of active caspase-3 in these cells, which signified apoptosis. Conclusions Lymphocyte subset phenotypes associated with TB are largely abnormal only during active infection and only a novel subset of NKT cells showed correlation with treatment response. Intracellular IFN-γ production and lymphocyte proliferation is increased and decreased, respectively, only during active infection and does not correlate with treatment response. The T helper 1/T helper 2 (Th1/Th2) hypothesis could not be confirmed in the context of tuberculosis but instead constitutive IL-4 production may play a role as a growth factor.

Thesis (PhD (Biomedical Sciences. Molecular Biology and Human Genetics))--University of Stellenbosch, 2009.

Thesis (MScMed (Biomedical Sciences. Molecular Biology and Human Genetics))--University of Stellenbosch, 2005. / Tuberculosis (TB) is one of the most serious infectious diseases known to mankind, with devastating outcomes in the poorest countries in the world. Isoniazid is the cornerstone of all first-line anti-TB regimens. Forty-eight percent of all drug resistant TB isolates in the Western Cape are Isoniazid mono-resistant, and the majority of these isolates belong to the Beijing/W strain family. Currently, the known molecular mechanisms which confer Isoniazid resistance in these isolates are attributed to mutations within the katG gene and account for up to 70% of all drug resistant TB isolates. Risk factors for the development of Isoniazid resistance can be attributed to either pathogen or host related factors and may partially account for the other 30% of Isoniazid resistant isolates. In this study, three aspects which may contribute to Isoniazid resistance were investigated: DNA repair in the bacterium, host response to anti-TB treatment and socioeconomic factors. A PCR based dot-blot strategy was used to screen for previously reported missense mutations in the mutT2, Rv3908 and ogt DNA repair genes of different strains of M. tuberculosis. All the Beijing isolates (drug resistant and susceptible), in contrast to the Atypical Beijing strains and other dominant strain families, exhibited missense mutations in all three base excision repair genes. It is therefore speculated that defects in the DNA repair genes (mutator phenotypes) of the Beijing isolates may contribute to the development of drug resistance and hence, may account for the large proportion of isolates that are Isoniazid mono-resistant. A novel method, based on primer extension, was initially developed to screen the NAT2 gene and then used to type individuals into fast, intermediate and slow acetylators of Isoniazid. The newly develop method, which is sensitive and accurate, improves the detection of Single Nucleotide Polymorphisms within the NAT2 gene, in contrast to the traditionally used methods. Utilising this method, it was found that the combination of fast and intermediate acetylators was significantly associated with Isoniazid resistance in the study community. This finding may have an important impact on TB control programmes, since it may allow for the administration of higher dosages of Isoniazid to fast/intermediate acetylators and a lower dose for slow acetylators. Clinical factors (compliance and retreatment after cure) and socio-economic factors (education, employment and income) were found to be significantly associated with the development of INH resistance. Diagnostic delay was also found to be a risk factor, since it may allow for transmission of TB during this period. The HIV prevalence in the study population is low and subsequently HIV status was not associated with the development of INH resistance. This study indicates that a combination of risk factors, both pathogen and host related, are involved in the development of Isoniazid resistance.

Thesis (MScMed (Biomedical Sciences. Molecular Biology and Human Genetics))--University of Stellenbosch, 2006. / The ESAT-6 gene cluster regions are duplicated 5 times in the genome of Mycobacterium tuberculosis. ESAT-6 gene cluster region 1 is the most frequently studied region as it contains RD1 (region of difference 1). RD1 is a 9.5 Kb deletion region confirmed to be involved in mycobacterial virulence and pathogenesis, and is present in virulent M. bovis strains, yet absent in all attenuated M. bovis BCG vaccine strains. The antigens CFP-10 and ESAT-6, which both evoke strong T-cell responses in experimental animals and humans, are situated in the RD1 region, and are thought to be key antigens in mycobacterial virulence. The absence of this region from the genomes of all BCG vaccine strains, led to the conclusion that the mechanism of attenuation of M. bovis BCG was due to the loss of RD1. Studies have shown that this attenuation is attributed to the loss of cytolytic activity mediated by secreted ESAT-6 (and some of the genes responsible for its secretion), which in turn results in reduced tissue invasiveness. The potent T-cell antigens ESAT-6 and CFP-10 are secreted without ordinary sec-dependent secretion signals. A study of the potential functions of the proteins encoded by the ESAT-6 gene clusters shows that most of these proteins have a potential to function in a protein-dependent ATP-binding cassette active transport system. It has been shown that ESAT-6 gene cluster region 1 is responsible for the secretion of the ESAT-6 and CFP-10 genes contained in this region, explaining the absence of any ordinary sec-dependent secretion signals in the amino acid sequences of members of this family. In order to elucidate the regulation of expression of the ESAT-6 gene cluster region 1, shown to encode for a secretion system for ESAT-6 and CFP-10 and to be involved in virulence, an operon analysis and promoter identification experiments were carried out in this study. The analysis of the ESAT-6 gene cluster region 1 showed the existence of more than one operon in this region and three constitutively-expressed promoters driving the expression of the genes in the operons. These results provide insight into the functional relationship (regulatory and secretory mechanisms) between the genes contained within ESAT-6 gene cluster region 1.None of the other four ESAT-6 gene cluster regions have been proven to also encode secretion systems. Preliminary studies indicated that the ESAT-6 gene cluster region 3 is expressed in its entirety as one single operon and a strong promoter involved in the expression of this region was identified. Mtb9.9A (the ESAT-6 antigen of the ESAT-6 gene cluster region 5) have also been shown to evoke strong T cell responses and to be secreted without any ordinary secretion signal. During the present study, we thus aimed to investigate the secretion of Mtb9.9A in order to determine whether it is also secreted by a dedicated secretion system encoded by ESAT-6 gene cluster region 5. The fact that region 5 was shown to be the last of the four duplications is important, as a positive result with this region would indicate whether the other four gene clusters share a similar secretion function. ESAT-6 gene cluster regions 2, 4 and 5 were isolated in the present study to form part of subsequent ESAT-6 gene cluster region secretion studies. Mtb9.9A was cloned, expressed and purified for antibody-generation, Resulting antibodies were used in an antigen secretion analysis. The secretion analysis entailed the integration of the isolated ESAT-6 gene cluster region 5 into the genome of M. smegmatis and investigation of the influence of the genes (contained in region 5) on the secretion of a heterologously expressed Mtb9.9A-HA-tagged fusion protein. We therefore attempted to show whether the proteins encoded by the ESAT-6 gene cluster region 5 also function together as a mycobacterial membrane-bound complex involved in protein-dependent transport and if so, whether this transport system is responsible for the active secretion of the native ESAT-6 antigen (designated Mtb9.9A) of region 5. This study opens the way for the understanding of the regulation, transport- and secretion mechanisms of important T-cell antigens of the mycobacteria, thereby giving insight into and building onto our understanding of the pathogenicity of Mycobacterium tuberculosis. A better understanding of these mechanisms could lead to the development of efficient strategies to either terminate or enhance secretion of antigens, which in turn will have an impact on drug and vaccine design and development.