Hon, Ching Yi. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2010. / Includes bibliographical references (leaves 144-157). / Abstracts in English and Chinese. / Examination Committee List --- p.i / Acknowledgements --- p.ii / Abstract --- p.iv / 摘要 --- p.vi / Table of Contents --- p.viii / List of Tables --- p.xiv / List of Figures --- p.xv / List of Abbreviations --- p.xvii / List of Chemicals --- p.xx / Chapter CHAPTER 1 --- INTRODUCTION --- p.1 / Chapter 1.1 --- Mycobacterium tuberculosis --- p.1 / Chapter 1.2 --- Tuberculosis --- p.2 / Chapter 1.3 --- Pathogenesis of TB --- p.3 / Chapter 1.3.1 --- Mycobacterial entry to the host macrophage --- p.3 / Chapter 1.3.2 --- Modulation of the host endocytic pathway --- p.4 / Chapter 1.3.2.1 --- The fusion between lysosome and mycobacterial phagosomeis blocked --- p.4 / Chapter 1.3.2.2 --- The endosomal pH of mycobacterial phagosome is preserved --- p.5 / Chapter 1.3.2.3 --- Mtb successfully mediates host cell apoptosis inhibition --- p.6 / Chapter 1.3.3 --- Cell migration and granuloma formation --- p.7 / Chapter 1.4 --- Insights from the complete genome sequence of Mtb H37Rv --- p.9 / Chapter 1.4.1 --- PE protein family --- p.9 / Chapter 1.4.2 --- PPE protein family --- p.10 / Chapter 1.5 --- Interaction between PE and PPE proteins --- p.11 / Chapter 1.5.1 --- Integrated bioinformatics prediction --- p.11 / Chapter 1.5.2 --- In vitro interaction studies of PE25/PPE41 protein complex --- p.12 / Chapter 1.5.3 --- Structural characterization of PE/PPE complex as revealed by PE25/PPE41 crystal structure --- p.14 / Chapter 1.6 --- Biological roles of PE and PPE proteins --- p.15 / Chapter 1.6.1 --- Immunological roles of PE family proteins --- p.15 / Chapter 1.6.2 --- Immunological roles of PPE family proteins --- p.16 / Chapter 1.6.3 --- Immunological roles of PE/PPE protein complex --- p.16 / Chapter 1.7 --- Sub-cellular localization of PE and PPE proteins --- p.17 / Chapter 1.8 --- PE and PPE as exported proteins --- p.18 / Chapter 1.8.1 --- Association of Mtb secreted proteins to pathogenesis of tuberculosis --- p.18 / Chapter 1.8.2 --- Exported PE and PPE proteins --- p.19 / Chapter 1.9 --- Differential expression of PE and PPE genes --- p.20 / Chapter 1.10 --- Objective of project --- p.21 / Chapter CHAPTER 2 --- "CLONING, EXPRESSION, PURIFICATION AND VERIFICATION OF PE15 AND PPE20 AS COMPLEX" --- p.24 / Chapter 2.1 --- Materials --- p.24 / Chapter 2.1.1 --- Bacterial expression plasmids for expression of PE or PPE proteins --- p.24 / Chapter 2.1.2 --- E. coli strains --- p.27 / Chapter 2.1.3 --- Reagents and buffers for molecular cloning --- p.27 / Chapter 2.1.4 --- Reagents and buffers for E. coli protein expression --- p.29 / Chapter 2.1.5 --- Buffers for protein purification --- p.30 / Chapter 2.2 --- Methods --- p.31 / Chapter 2.2.1 --- Molecular cloning --- p.31 / Chapter 2.2.1.1 --- Primers --- p.31 / Chapter 2.2.1.2 --- Gene Amplification by Polymerase Chain Reaction (PCR) --- p.33 / Chapter 2.2.1.3 --- Agarose gel electrophoresis --- p.34 / Chapter 2.2.1.4 --- Extraction and purification of DNA from agarose gel by QIAquick Gel Extraction Kit --- p.34 / Chapter 2.2.1.5 --- Restriction digestion of DNA --- p.35 / Chapter 2.2.1.6 --- Purification of DNA by QIAquick PCR Purification Kit --- p.36 / Chapter 2.2.1.7 --- Ligation of DNA and expression vector to produce recombinant plasmid --- p.37 / Chapter 2.2.1.8 --- Transformation of plasmid into E. coli competent cell --- p.38 / Chapter 2.2.1.9 --- PCR Screening of recombinant clones --- p.39 / Chapter 2.2.1.10 --- Plasmid DNA purification using the QIAprep Spin Miniprep Kit --- p.40 / Chapter 2.2.1.11 --- DNA sequencing --- p.41 / Chapter 2.2.2 --- Expression of PE15 and PPE20 proteins --- p.41 / Chapter 2.2.2.1 --- Small scale protein expression of PE 15 and PPE20 proteins --- p.41 / Chapter 2.2.2.2 --- Small scale co-expression of PE 15 and PPE20 proteins --- p.42 / Chapter 2.2.2.3 --- Protein solubility analysis --- p.43 / Chapter 2.2.2.4 --- Large scale expression of PE and PPE proteins --- p.43 / Chapter 2.2.3 --- SDS-PAGE --- p.44 / Chapter 2.2.4 --- Bradford assay --- p.45 / Chapter 2.2.5 --- Protein purification of PE15 --- p.46 / Chapter 2.2.5.1 --- Sonication and extraction of proteins --- p.46 / Chapter 2.2.5.2 --- Protein purification of PE15 by gutathione-sepharose affinity chromatography --- p.46 / Chapter 2.2.5.3 --- Protein purification of PE15 by re-binding to glutathione-sepharose --- p.47 / Chapter 2.2.5.4 --- Protein purification of PE15 by size exclusion chromatography --- p.47 / Chapter 2.2.5.5 --- Protein purification of GST-PE15 --- p.48 / Chapter 2.2.6 --- Protein purification of PPE20(PPE) --- p.49 / Chapter 2.2.6.1 --- Sonication and extraction of proteins --- p.49 / Chapter 2.2.6.2 --- Protein purification of PPE20(PPE) by glutathione-sepharose affinity chromatography --- p.49 / Chapter 2.2.6.3 --- Protein purification of PPE20(PPE) by re-binding to glutathione-sepharose --- p.49 / Chapter 2.2.6.4 --- Protein purification of PPE20(PPE) by size exclusion chromatography --- p.50 / Chapter 2.2.6.5 --- Protein purification of GST-PPE20(PPE) --- p.50 / Chapter 2.2.7 --- Verification of PEPPE protein complex --- p.50 / Chapter 2.2.7.1 --- Size exclusion chromatography --- p.50 / Chapter 2.2.7.2 --- Cross-linking --- p.50 / Chapter 2.2.7.3 --- Pull-down assay --- p.51 / Chapter 2.3 --- Results --- p.52 / Chapter 2.3.1 --- Construction of bacterial expression plasmids for PE15 and PPE20 genes --- p.52 / Chapter 2.3.2 --- Expression of PE15 and PPE20 proteins --- p.54 / Chapter 2.3.2.1 --- Small scale protein expression of PE15 --- p.55 / Chapter 2.3.2.2 --- Small scale protein expression of PPE20 --- p.56 / Chapter 2.3.2.3 --- Small scale co-expression of PE15 and PPE20 proteins --- p.60 / Chapter 2.3.3 --- Large scale purification of PE15 and PPE20(PPE) proteins --- p.66 / Chapter 2.3.3.1 --- Large scale purification of PE15 --- p.66 / Chapter 2.3.3.2 --- Large scale purification of GST-PE15 --- p.68 / Chapter 2.3.3.3 --- Large scale purification of PPE20(PPE) --- p.69 / Chapter 2.3.3.4 --- Large scale purification of GST-PPE20(PPE) --- p.70 / Chapter 2.3.4 --- Verification of PE15/PPE20 complex --- p.71 / Chapter 2.3.4.1 --- Size exclusion chromatography --- p.71 / Chapter 2.3.4.2 --- Cross-linking study --- p.74 / Chapter 2.3.4.3 --- Pull-down assay --- p.77 / Chapter 2.4 --- Discussion --- p.79 / Chapter 2.4.1 --- Expression of PE15 and PPE20 proteins --- p.79 / Chapter 2.4.2 --- Co-expression of PE15 and PPE20 proteins --- p.81 / Chapter 2.4.3 --- Prediction of PE/PPE interaction --- p.82 / Chapter 2.4.4 --- Study ofPE15 and PPE20(PPE) interaction --- p.83 / Chapter CHAPTER 3 --- PRELIMINARY X-RAY ANALYSIS OF PPE20(PPE) PROTEIN CRYSTAL --- p.86 / Chapter 3.1 --- Materials --- p.86 / Chapter 3.1.1 --- Crystallization screening kits --- p.86 / Chapter 3.1.2 --- Crystallization chemicals --- p.86 / Chapter 3.2 --- Methods --- p.87 / Chapter 3.2.1 --- Crystallization screening using Phoenix´ёØ RE --- p.87 / Chapter 3.2.2 --- Optimization of PPE20(PPE) crystals by grid screening --- p.88 / Chapter 3.2.3 --- Optimization using Additive screen for PPE20(PPE) --- p.88 / Chapter 3.2.4 --- X-ray diffraction and data collection --- p.88 / Chapter 3.3 --- Results --- p.89 / Chapter 3.3.1 --- Crystallization screening --- p.89 / Chapter 3.3.2 --- Crystallization optimization --- p.90 / Chapter 3.3.3 --- Preliminary X-ray diffraction analysis --- p.92 / Chapter 3.3.4 --- Attempts to solve the phase by molecular replacement --- p.96 / Chapter 3.4 --- Discussion --- p.97 / Chapter CHAPTER 4 --- ISOLATION OF INTERACTING PARTNERS OF PE15 AND PPE20(PPE) FROM HUMAN MACROPHAGE U-937 --- p.99 / Chapter 4.1 --- Materials --- p.99 / Chapter 4.1.1 --- Mammalian cell line --- p.99 / Chapter 4.1.2 --- Mammalian cell growth medium --- p.99 / Chapter 4.1.3 --- Reagents and buffers for mammalian cell culture --- p.100 / Chapter 4.1.4 --- Reagents and buffers for mass spectrometry sample preparation --- p.100 / Chapter 4.2 --- Methods --- p.101 / Chapter 4.2.1 --- U-937 cell culturing --- p.101 / Chapter 4.2.1.1 --- Thawing U-937 cells --- p.101 / Chapter 4.2.1.2 --- Monitoring cell growth --- p.102 / Chapter 4.2.1.3 --- Cell differentiation --- p.102 / Chapter 4.2.1.4 --- Cell Harvesting --- p.103 / Chapter 4.2.2 --- In-vitro pull-down to identify interacting partners of PE15 or PPE20(PPE) --- p.103 / Chapter 4.2.2.1 --- Preparation of cellular proteins from U-937 cells --- p.103 / Chapter 4.2.2.2 --- Pre-clearing of U-937 supernatant --- p.104 / Chapter 4.2.2.3 --- Pull-down of U-937 cellular proteins with immobilized GST-PE15 --- p.104 / Chapter 4.2.2.4 --- Pull-down of U-937 cellular proteins with immobilized GST-PPE20(PPE) --- p.106 / Chapter 4.2.2.5 --- SDS-PAGE analysis --- p.106 / Chapter 4.2.2.6 --- Silver staining --- p.106 / Chapter 4.2.3 --- Mass- Spectrometry --- p.107 / Chapter 4.2.3.1 --- De-staining of silver stained gel spots --- p.107 / Chapter 4.2.3.2 --- Trypsin digestion --- p.108 / Chapter 4.2.3.3 --- Peptide Extraction --- p.108 / Chapter 4.2.3.4 --- Desalting and concentration of peptide mixture --- p.109 / Chapter 4.3 --- Results --- p.110 / Chapter 4.3.1 --- U-937 differentiation --- p.110 / Chapter 4.3.2 --- In-vitro pull-down --- p.113 / Chapter 4.3.2.1 --- Pull-down with immobilized GST-PE15 --- p.113 / Chapter 4.3.2.2 --- Pull-down with immobilized GST-PPE20(PPE) --- p.116 / Chapter 4.3.2.3 --- Mass spectrometry identification of protein --- p.120 / Chapter 4.4 --- Discussion --- p.122 / Chapter 4.4.1 --- Differentiation of U-937 --- p.122 / Chapter 4.4.2 --- Isolation of PE15 and PPE20(PPE) interacting partners from U-937 --- p.125 / Chapter CHAPTER 5 --- CONCLUSION AND FUTURE PERSPECTIVES --- p.133 / Chapter 5.1 --- Conclusion --- p.133 / Chapter 5.2 --- Future perspectives --- p.137

結核病是由結核桿菌感染而引起的慢性傳染病，它是危害人類健康的主要殺手。根據世界衛生組織的報導，目前在全球範圍內有三分之一的人口感染了結核桿菌，每年約有915 萬人口被確診患有結核病。耐藥結核病尤其是對最有效的一線抗結核藥物異煙阱和利福平產生抗藥的耐多藥結核病的出現，令有效的控制結核病更加棘手。 / 在本研究中，我們首先用利福平誘導得到五株伴有明顯生長緩慢的高水平利褔卒耐藥的恥垢分支桿菌。通過比較基因組學研究發現，在編碼區有四個突變，其中兩個位於中rpoB 基因(N484T and 1488F) ，一個位於MSMEG_0436 (V49M) ,一個位於MSMEG_6872 (V181L)。rpoB 基因突變是該恥垢分支桿菌利福平耐藥的主要原因。而生長緩慢主要源於MSMEG_6872基因的影響。更為有趣的是，我們發現一個與MSMEG_6872具有相同的蛋白模序的結核分支桿菌蛋白質Rv1367 在不間的結核分支桿菌菌株之間存在I193V 多態性。193V 主要存在于北京株或者在耐藥的非北京株上。進一步的研究發現，過量表達MSMEG_6872或者Rv1367c 的恥垢分支桿菌形態上呈現為細長棒狀，而他們的親代則為短棒狀。 / 為獲得耐藥性，以及在高濃度的抗生素環境下生存，細菌必須付出一定的生物學代價。本研究中，恥垢分支桿菌以生長缺陷為代價獲得了對利褔平的耐藥，而這個代價可能是由於MSMEG_6872 基因的突變或者過量表達打破了細胞壁延長和分裂的平衡引起。 / Mycobacterium tuberculosis (MTB), which is the pathogen of tuberculosis (TB), remains a major human public health problem throughout the world. According to the report from the World Health Organization, currently about one third of the world's population was infected by MTB and there is globally 9.15 million recorded cases of TB annually. The occurrence of resistance to drugs used to combat TB, particularly multi-drug resistant TB (MDR-TB), defined as resistance to at least isoniazid and rifampin (RIF), has become a significant public health problem in a number of countries and an obstacle to effective global TB control. / In this project, we firstly obtained high level RIF resistant Mycobacterium smegmatis (MSM) strains with obviously growth retardation by repeated drug selection. Comparative analysis of genomic sequences revealed 4 mutations in coding sequences, including two in rpoB (N484T and I488F), one in MSMEG 0436 (y 49M), and one in MSMEG 6872 (y181L). Characterization of these four mutations showed that the two mutations in rpoB were correlated to RIF resistance. The one in MSMEG_6872 can render obviously growth retardation when MSMEG_6872 is over-expressed. Interestingly, we found an MTB protein, Rv1367c, which has the same motif with MSMEG_6872, had an I193V polymorphism in different MTB strains. The 193V variant was mainly found in Beijing/W or drug resistant non-Beijing/W family strains. The transformants, no matter MSMEG_6872 or Rv 1367 c, all exhibited slim and long rod shape compared to stocky and short rod appearance of the parental strain. / Mycobacterial cells must pay biological cost in order to obtain RIF resistance and survive in the high concentration of RIF. In our case, the growth arrest may be due to the mutation of MSMEG_6872 which disrupts the balance of cell wall elongation and cell division. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Guan, Bing. / "November 2011." / Thesis (Ph.D.)--Chinese University of Hong Kong, 2012. / Includes bibliographical references (leaves 139-143). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstract also in Chinese. / Acknowledgements --- p.I / Abstract --- p.II / Abstract in Chinese --- p.IV / List of Abbreviations --- p.V / List of Tables --- p.VI / List of Figures --- p.VII / Contents --- p.IX / Chapter CHAPTER 1 --- INTRODUCTION / Chapter 1.1 --- Overview of Tuberculosis --- p.1 / Chapter 1.1.1 --- Pathogens --- p.2 / Chapter 1.1.2 --- Syndromes --- p.2 / Chapter 1.1.3 --- Transmission --- p.3 / Chapter 1.1.4 --- Diagnosis --- p.4 / Chapter 1.1.5 --- Epidemiology --- p.6 / Chapter 1.1.6 --- Mortality --- p.8 / Chapter 1.2 --- The Anti-TB Strategies --- p.8 / Chapter 1.2.1 --- Chemotherapy Treatment for MTB --- p.8 / Chapter 1.2.2 --- Vaccine Development for MTB --- p.9 / Chapter 1.3 --- Genome Sequencing of MTB Isolates --- p.9 / Chapter 1.4 --- Drug Resistance of MTB --- p.13 / Chapter 1.4.1 --- MDR-TB and XDR-TB --- p.15 / Chapter 1.4.2 --- Mechanism of Drug Resistance --- p.18 / Chapter 1.4.2.1 --- Intrinsic Resistance of Mycobacterium Species --- p.20 / Chapter 1.4.2.2 --- Acquired Resistance of Mycobacterium Species --- p.22 / Chapter 1.4.3 --- RIF Resistant MTB --- p.24 / Chapter 1.5 --- Useful tool for MTB Research --- p.26 / Chapter 1.6 --- The Biological Cost of Antibiotic Resistance in MTB --- p.27 / Chapter 1.6.1 --- The meaning of Biological Cost --- p.27 / Chapter 1.6.2 --- Factors Involved in Biological Cost of Mycobacterium Species --- p.29 / Chapter 1.17 --- Objectives of the Project and Experimental Strategies --- p.30 / Chapter CHAPTER 2 --- MATERIALS AND METHODS / Chapter 2.1 --- Selection of RIF Resistant MSM mc²155 Strains --- p.31 / Chapter 2.1.1 --- Bacterial Strains, Media, and Growth Conditions --- p.31 / Chapter 2.1.2 --- Selection of RIF Resistant Strain --- p.31 / Chapter 2.2 --- Minimum-Inhibitory-Concentration (MIC) Assay --- p.34 / Chapter 2.3 --- Detection of Mutations in the rpoB Gene of RIF Resistance Strains --- p.36 / Chapter 2.3.1 --- Primers Design --- p.36 / Chapter 2.3.2 --- PCR and Direct Sequencing --- p.36 / Chapter 2.4 --- Characterization of the RpoB Gene --- p.38 / Chapter 2.4.1 --- Construction of Recombinant Clones --- p.38 / Chapter 2.4.2 --- Preparation of MSM competent cell. --- p.38 / Chapter 2.4.3 --- Electroporation of plasmid into MSM competent cells --- p.39 / Chapter 2.4.4 --- Site-directed Mutagenesis of the RpoB Clone --- p.39 / Chapter 2.5 --- Whole Genome Sequencing of Parental and Drug --- p.43 / Chapter 2.5.1 --- MSM Genomic DNA Extraction --- p.43 / Chapter 2.5.2 --- Genomic Sequencing --- p.44 / Chapter 2.5.3 --- Data Analysis and SNPs Identification --- p.45 / Chapter 2.6 --- Validation of Mutations by PCR and Direct Sequencing --- p.46 / Chapter 2.6.1 --- PCR Primers Design --- p.46 / Chapter 2.6.2 --- PCR and Direct Sequencing --- p.46 / Chapter 2.7 --- Characterization of MSMEG 0436 and MSMEG 6872 --- p.47 / Chapter 2.7.1 --- Construction of the recombinant clones --- p.47 / Chapter 2.8 --- Assay of Ethidium Bromide in Intact Cells --- p.48 / Chapter 2.9 --- Quantitative Real-time PCR to Expression of the Measure the ATP-binding Cassette (ABC) Superfamily Efflux Pumps --- p.49 / Chapter 2.9.1 --- RNA Extraction --- p.49 / Chapter 2.9.2 --- Synthesis of Double-stranded cDNA from Total RNA --- p.49 / Chapter 2.9.3 --- Real-time PCR to Quantify the Efflux Pump Gene Expression Level --- p.49 / Chapter 2.10 --- The construction of the Growth Curve --- p.53 / Chapter 2.11 --- Generation of ΔMSMEG_6872 Mutant Strain --- p.54 / Chapter 2.11.1 --- Preparation of Recombination Strain Stocks --- p.54 / Chapter 2.11.2 --- Preparation of the Electrocompetent Cells of the Recombination Strain --- p.54 / Chapter 2.11.3 --- Preparation of Allelic Exchange Substrate (AES) for Generating Gene Replacement Mutants --- p.55 / Chapter 2.12 --- Validation of Rv1367c (MT1414) in MTB --- p.60 / Chapter 2.12.1 --- Primer Design --- p.60 / Chapter 2.12.2 --- Strain Selection --- p.60 / Chapter 2.12.3 --- PCR and Direct Sequencing --- p.60 / Chapter 2.12.4 --- Alignment the Gene Sequence of Rv1367c of Different MTB Strains --- p.61 / Chapter 2.13 --- Model building of the RpoB protein --- p.62 / Chapter 2.14 --- MSM staining method --- p.63 / Chapter CHAPTER 3 --- RESULTS / Chapter 3.1 --- dentification of RIF Resistant Related-genes Using Induced RIF Resistant MSM Model --- p.64 / Chapter 3.1.1 --- Emergence ofRIF Resistant Strains after the Prolonged Drug Exposure --- p.64 / Chapter 3.1.2 --- Induced RIF Resistance Were Stable In the Absence of Selection --- p.66 / Chapter 3.1.3 --- The Growth State of 5 RIF Resistance MSM mc²155 Strain --- p.68 / Chapter 3.1.4 --- Involvement of RpoB in the Mechanisms of the Emergence of RIF Resistance in MSM --- p.71 / Chapter 3.1.4.1 --- Mutations in the RpoB Gene --- p.71 / Chapter 3.1.4.2 --- Identical Mutations of RpoB Gene in Different RIF Resistance Isolates from Different Generation --- p.74 / Chapter 3.1.4.3 --- Characterization of RpoB in MSM strains --- p.76 / Chapter 3.1.4.4 --- Rifampin-Binding Pockets of RpoB Protein Model --- p.80 / Chapter 3.1.5 --- Other Genetic Alternations possibly Involved in RIF Resistance --- p.83 / Chapter 3.1.5.1 --- Whole Genome Sequencing of the Patental and P5 MSM mc²155 Strains --- p.83 / Chapter 3.1.5.2 --- Validation of the 32 Selected Alterations --- p.88 / Chapter 3.1.5.3 --- Characterization of MSMEG_0436 and MSMEG_6872 in RIF Resistance --- p.91 / Chapter 3.1.5.4 --- Characterization of MSMEG_0436 in the Growth Rate of MSM --- p.93 / Chapter 3.1.5.5 --- Characterization of MSMEG_6872 in the Growth Rate of MSM --- p.95 / Chapter 3.1.5.6 --- MSMEG_6872 Knock-out Strain Exhibited Normal Phenotype as its Parent --- p.98 / Chapter 3.1.5.7 --- Identification of Mutations in the Beta-Iactamase Gene of Mycobacterium Tuberculosis (MTB) --- p.101 / Chapter 3.1.5.8 --- Characterization of Rv 1367 c in Mycobacterium Growth Rate --- p.108 / Chapter 3.1.5.9 --- Morphology Changes of the Rv1367c and MSMEG_6872 Transformants --- p.110 / Chapter 3.2 --- Genetic Alterations in Non-coding Sequence --- p.112 / Chapter 3.2.1 --- ATP-binding Cassette (ABC) Superfamily Efflux Pumps Up-regulated in Drug Resistant M Smegmatis Strain --- p.112 / Chapter 3.2.2 --- RIF Resistant M smegmatis mc²155 Strain exhibited Low Level Cross-drug Resistance to INH --- p.115 / Chapter 3.2.3 --- RIF Resistant M smegmatis mc²155 Strain Showed Low level Accumulation of Ethidium Bromide --- p.117 / Chapter CHAPTER 4 --- DISCUSSION / Chapter 4.1 --- The Protocol for the Preparation RIF Resistant Strains --- p.121 / Chapter 4.2 --- RIF Induced Stable Chromosomal Mutations in RIF Resistant MSM Strains --- p.123 / Chapter 4.3 --- MIC Levels of the RIF Resistant Strains --- p.125 / Chapter 4.4 --- Factors May involved in RIF Resistant MSM Strains --- p.128 / Chapter 4.5 --- Cell Shape and Growth Regulation --- p.129 / Chapter 4.6 --- MSMEG _6872 and Twin-Arginine Translocase (TAT) Secretion System --- p.135 / Chapter 4.7 --- Conclusion --- p.137 / Chapter 4.8 --- Future Perspectives --- p.138 / REFERENCES --- p.139

Thesis (MScMedSc (Biomedical Sciences))--University of Stellenbosch, 2010. / Thesis presented in partial fulfillment of the requirements for the degree Master of Science in Medical Biochemistry at the University of Stellenbosch. / Bibliography / ENGLISH ABSTRACT: Tuberculosis (TB) is an infectious disease which has plagued society for thousands of years. Despite public health programs, anti-TB drugs and a vaccine, the absolute numbers of people infected with TB each year continue to rise as populations grow. The high TB-burden areas are also plagued by other debilitating factors including HIV/AIDS infection, poverty and malnutrition. Nutrition has been implicated in TB susceptibility in a number of studies. While most are observational reports made during times of war, famine or natural disaster, multiple studies provide convincing evidence for poor nutritional status increasing the morbidity and mortality of TB. Numerous approaches are currently utilized in TB research, and there has been convincing evidence to support the role of host genetics in TB susceptibility. Based on previous linkage studies and a search of current literature, three genes were selected for this case-control study. Subsequently, variations located in cathepsin Z (CTSZ), melanocortin 3 receptor (MC3R) and melanocortin 4 receptor (MC4R) were genotyped in the South African Coloured (SAC) population to determine the existence of an association with TB disease. CTSZ is a lysosomal cysteine protease expressed in cells of the immune system. Interaction between this 303 amino acid protein and β2 integrin receptors lymphocyte function-associated antigen-1 (LFA-1) and macrophage antigen-1 (MAC-1) leads to altered lymphocyte proliferation. As a result, a single exonic variant in CTSZ, rs34069356, the same identified in a previous linkage study, showed strong evidence for association with TB susceptibility in cases (n = 410) and controls (n = 301) in the SAC population (p< 0.0001). MC3R and MC4R are two of 5 melanocortin receptors. MC3R has been found to be a key regulator in energy expenditure and host metabolism while activation of MC4R leads to a decrease in food intake. Activation of these two receptors is regulated by leptin, a hormone released by adipose tissue. A variant located upstream of the MC3R gene, rs6127698, also showed evidence of disease association with the less frequent allele, T, being under-represented in cases (n = 540) compared to controls (n = 541) (genotypic frequency, p = 0.0039), suggesting a possible resistance phenotype. Functional analysis of this variant revealed an increase in MC3R expression when stimulated with BCG, with individuals homozygous for the T allele exhibiting an even larger upregulation of MC3R expression than individuals homozygous for the G allele, though this difference was not statistically significant. A single haplotype in MC3R was found to be associated with TB susceptibility (p = 0.0008) and this association remained after permutation testing to correct for multiple testing (p = 0.0061) Three variants were selected for genotyping in MC4R and while none of these showed a statistically significant difference between cases (n = 510) and controls (n = 487), this gene should not be ruled out as both MC3R and MC4R have been found to work closely though not redundantly and double knockout experiments result in exacerbated obesity, suggesting that these proteins have a synergistic effect. The results of this study support both a role of host genetics and nutritional status in TB and strongly motivate further research in both of these fields. / AFRIKAANSE OPSOMMING: Tuberkulose (TB) is ‘n aansteeklike siekte wat reeds vir eeue die gesondheid van die publiek bedreig. Ten spyte van publieke gesondheidsprogramme en verskeie anti-TB medikasie middele, groei die aantal van mense wat hiermee ge-infekteer word steeds jaarliks. Dit is veral in areas waar TB steeds groei, waar ook ander neerdrukkende faktore soos HIV/Vigs, armoede en wanvoeding hoogty vier. Na aanleiding van verskeie verslae tydens oorloë, hongersnood en ander natuulike rampe is dit veral duidelik dat swak nutriënt inname morbiditeit en sterftes wat met TB gepaard gaan verhoog. Talle benaderings word tans gebruik in TB-navorsing, Bewyse is oortuigend om die rol van genetika van die gaheer met vatbaarheid vir TB te verbind. Op grond van vorige studies en die huidige literatuur, het ons drie gene gekies vir hierdie pasiënt-kontrole studie. Variante geleë in cathepsin Z (CTSZ), melanocortin 3 receptor (MC3R) en melanocortin 4 receptor (MC4R) is ge-genotipeer in die Suid-Afrikaanse Kleurling bevolking (SAK) (540 gevalle en 540 kontrole) om sodoende die assosiasie met TB te bepaal. CTSZ is ‘n lisosomale sisteïen protease wat uitgedruk word in immuunselle. Interaksie tussen hierdie 303 aminosuur protein en β2 integrin reseptore nl. LFA-1 en MAK-1 bring veranderde limfosiet proliferasie mee. ‘n Enkele eksoniese variant in CTSZ, rs34069356, dieselfde soos ge-identifiseer in ‘n vorige studie, verskaf sterk bewys vir assosiasie met TB vatbaarheid in gevalle (n = 410) en kontrole (n = 301) in die SAK bevolking. MC3R en MC4R is twee van 5 melanokortien reseptore. Daar is gevind dat MC3R 'n sleutelrol speel in die energie regulering van gasheer metabolisme, terwyl die aktivering van MC4R eindelik lei tot 'n afname in voedsel inname. Aktivering van hierdie twee reseptore word gereguleer deur Leptien, 'n hormoon wat vrygestel word deur adipose weefsel, ‘n Variant, stroomop geleë vanaf MC3R, rs6127698, is ook bewys om met TB ge-assosieer te wees, met die T-alleel meer seldsaam in gevalle (n = 540) as in kontroles (n = 541) wat dui op 'n moontlike weerstandsfenotipe. Funksionele analise van hierdie variant onthul 'n toename in MC3R uitdrukking wanneer gestimuleer met BCG, met individue homosigoties vir die T-alleel wat selfs groter opregulation veroorsaak wanneer vergelyk word met individue homosigoties vir die G allele. Hierdie resultaat was egter nie statisties beduidend nie. 'n Enkele haplotiepe in MC3R is ge-assosieer met TB vatbaarheid en die assosiasie is onveranderd nadat ‘n permutasie korreksie aangebring is (p = .0061). Voorts is drie variante gekies vir genotipering in MC4R en ten spyte daarvan dat nie een daarvan 'n statisties beduidende verskil getoon het tussen pasiënte (n = 510) en kontroles (n = 487) nie, behoort hierdie geen nie uitgesluit word nie, Die rede hiervoor is dat beide MC3R en MC4R verskeie kere gevind is om in samewerking ‘n rol te speel om vetsug te voorkom of te vererger. Die resultate van hierdie studie beaam beide 'n rol van gasheer genetika en voedingstatus in TB en motiveer veral verdere navorsing in beide van hierdie vakgebiede.

Thesis (PhD)--Stellenbosch University, 2014. / ENGLISH ABSTRACT: Tuberculosis (TB) disease results in approximately 2 million deaths annually and is the leading cause of death due to a single infectious agent. Previous studies have indicated that host genetics play an important role in the development of TB. This together with pathogen and environmental factors intensifies the complexity of this disease. The Major Histocompatibility Complex (MHC) and Leukocyte Receptor Complex (LRC) comprise several genes which are known to be important modulators of the host immune response. The human leukocyte antigen (HLA) class-I genes of the MHC are involved in the presentation of pathogenic antigens on the surfaces of infected cells, while the killer cell immunoglobulin-like receptors (KIRs) of the LRC are involved in the recognition of self and non-self cells. Natural Killer (NK) cells through their KIRs are thus able to kill non-self cells through recognition of the class-I molecules expressed. Additionally, HLAs and KIRs are extremely polymorphic and differ markedly across populations of different ethnicities. Here we studied these genes and their polymorphisms in the South African Coloured (SAC) population to determine their involvement in susceptibility to TB, susceptibility to disease caused by specific Mycobacterium tuberculosis subtypes, and understanding their ancestral contribution to the SAC with regards to the development of TB. We showed that the KIR3DS1 gene and KIR genotypes with five or more activating KIRs, and the presence of 3DS1, protected against the development of active TB in the SAC population. Several HLA class-I alleles were identified as susceptibility factors for TB disease. With regards to genes of the MHC and LRC, several loci were found to alter susceptibility to TB in the SAC population, including MDC1, BTNL2, HLA-DOA, HLA-DOB, C6orf10, TAP2, LILRA5, NCR1, NLRP7 and the intergenic regions between HLA-C/WASF5P and LAIR1/TTYH1. We showed that the Beijing strain occurred more frequently in individuals with multiple disease episodes, with the HLA-B27 allele lowering the odds of having an additional episode. Associations were identified for specific HLA types and disease caused by the Beijing, Latin America-Mediterranean (LAM), Low-Copy Clade (LCC), and Quebec strains. HLA types were associated with disease caused by strains from the Euro-American or East Asian lineages, and the frequencies of these alleles in their sympatric human populations identified potential co-evolutionary events between host and pathogen. Finally, we showed that the SAC population is the most diverse SA population with regards to HLA alleles and KIR genotypes, as would be expected given the admixture of the SAC. Based on the HLA allele class-I profiles across SA populations, we noted that the Ag85BESAT- 6, Ag85B-TB10.4 and Mtb72f vaccines currently undergoing clinical trials would have low efficacy across most SA populations. We showed that the MHC and LRC regions in SAC healthy controls are predominantly of European ancestry, and that SAC TB cases are more closely related to Khoisan and black SA population groups. Our work highlights the importance of investigating both host and pathogen genetics when studying TB disease development and that understanding the genetic ancestral contributions to the SAC population can contribute to the identification of true and novel TB causing variants. / AFRIKAANSE OPSOMMING: Tuberkulose (TB) is jaarliks verantwoordelik vir ongeveer 2 miljoen sterftes en is die hoofoorsaak van dood as gevolg van „n aansteeklike siekte. Vorige navorsingstudies het aangedui dat die genetiese samestelling van die gasheer „n beduidende rol speel in die ontwikkeling van TB. Die kompleksiteit van hierdie siekte word vererger deur die betrokkenheid van die gasheer genoom sowel as bakteriële en omgewings faktore. Die Major Histocompatibility Complex (MHC) en Leukocyte Receptor Complex (LRC) bestaan uit verskeie gene wat die gasheer immuunrespons verstel. Die human leukocyte antigen (HLA) klas I gene van die MHC is betrokke by die aanbieding van patogeniese antigene op die oppervlak van geïnfekteerde selle, terwyl die killer cell immunoglobulin-like receptors (KIRs), geleë in die LRC, betrokke is by die herkenning van eie en vreemde selle. NK selle, deur middel van hul KIRs, kan dus vreemde selle uitwis aangesien hulle die uitgedrukte klas I molekules kan herken. Beide HLA en KIRs is hoogs polimorfies en verskil beduidend tussen etniese groepe. In hierdie studie is die bogenoemde gene en hul polimorfismes in die Suid Afrikaanse Kleurling bevolking (SAC) ondersoek om vas te stel tot watter mate dit genetiese vatbaarheid vir TB, asook vatbaarheid vir TB wat deur spesifieke Mycobacterium tuberculosis subtipes veroorsaak word, beïnvloed. Daar is ook gepoog om te verstaan hoe die voorouerlike bydrae van hierdie gene die SAC met betrekking tot TB vatbaarheid affekteer. Die resultate van die studie het aangedui dat die KIR3DS1 geen en KIR genotipes met vyf of meer aktiewe KIRs en die teenwoordigheid van 3DS1, die SAC bevolking beskerm teen die ontwikkeling van aktiewe TB. Verskeie HLA klas I allele is geïdentifiseer as vatbaarheidsfaktore vir TB. Talle lokusse van die MHC en LRC gene is ook as vatbaarheidsfaktore vir TB in die SAC bevolking geïdentifiseer, insluitende MDC1, BTNL2, HLA-DOA, HLA-DOB, C6orf10, TAP2, LILRA5, NCR1, NLRP7 en die intergeniese areas tussen HLA-C/WASF5P en LAIR1/TTYH1. Die studie het aangedui dat die Beijing stam meer voorkom in individue wat verskeie kere TB gehad het en dat die HLA-B27 alleel die kanse om „n verdere episode te hê, verlaag het. Assosiasies is geïdentifiseer tussen spesifieke HLA tipes en siekte veroorsaak deur die Beijing, LAM, LCC, en Quebec TB stamme. HLA tipes was geassosieer met siekte veroorsaak deur TB stamme van Euro-Amerikaanse en Oos-Asiëse afkoms. Die frekwensies van hierdie allele, in hul ooreenstemmende mensbevolkings, dui op „n potensïele koevolusionêre gebeurtenis tussen die gasheer en patogeen. Die studie het ook vasgestel dat die SAC populasie die mees diverse SA bevolking is met betrekking tot die HLA allele en KIR genotipes, soos verwag sou word gegewe die gemengde genetiese herkoms van die SAC. Gebaseer op die HLA allele klas I profiel van verskillende SA bevolkings merk ons op dat die Ag85B-ESAT-6, Ag85B-TB10.4 en Mtb72f vaksiene, wat huidiglik kliniese toetsing ondergaan, nie so effektief in die meeste SA bevolkings sal wees nie. Die studie het ook bewys dat die MHC en LRC streke in gesonde SAC kontroles, grootliks afkomstig was van „n Europese nalatenskap en dat die SAC TB gevalle meer verwant is aan die Khoisan en swart SA bevolkings. Hierdie studie beklemtoon die noodsaaklikheid om beide gasheer en patogeen genetika te bestudeer wanneer die ontwikkeling van TB ondersoek word en dat die verstaan van die genetiese voorouerlike bydrae van die SAC bevolking kan bydra tot die identifisering van ware en nuwe TB-veroorsakende variante.

Doctorat en Sciences médicales / info:eu-repo/semantics/nonPublished

Thesis (PhD (Biomedical Sciences. Molecular Biology and Human Genetics))--Stellenbosch University, 2008. / This series of studies includes both methodological analyses, aimed at furthering our understanding of, and improving the tools used in molecular epidemiology, and investigative projects which have used these tools to add to our knowledge of the M. tuberculosis epidemic. Using serial isolates from tuberculosis patients, we have investigated the evolutionary rate of the IS6110 RFLP pattern. In accordance with other studies, we determined a ½-life for this epidemiological marker of 10.69 years, confirming its appropriateness for this purpose. We also identified an initial, much higher apparent rate which we proposed was the result of pre-diagnostic evolution. In support of this, our investigations in the context of household transmission of M. tuberculosis revealed that IS6110-based evolution is closely associated with transmission of the organism, resulting in a strain population rate of change of 2.9% per annum. To accommodate evolution within estimates of transmission, we proposed that calculations incorporate the concept of Nearest Genetic Distance (cases most similar in RFLP pattern and most closely associated in time). We used this to create transmission chains which allowed for limited evolution of the IS6110 marker. As a result, in our study community, the estimated level of disease attributable to ongoing transmission was increased to between 73 and 88% depending on the Genetic Distance allowed. We identified the duration of a study as a further source of under-estimation of transmission. This results from the artefactual abridgement of transmission chains caused by the loss of cases at the temporal boundaries of a study. Using both real and simulated data, we showed that viewing a 12-year study through shorter window periods dramatically lowered estimates of transmission. This effect was negatively correlated with the size of a cluster. Various combinations of MIRU-VNTR loci have been proposed as an alternative epidemiological marker. Our investigations showed that, while this method yielded estimates of transmission similar to those of IS6110, there was discordance between the two markers in the epidemiological linking of cases as a result of their independent evolution. Attempting to compensate for this by allowing for evolution during transmission improved the performance of IS6110, but generally had a deleterious effect of that of MIRU-VNTR. However, this marker remains a valuable tool for higher phylogenetic analysis and we used it to demonstrate a correlation between sublineages of the Beijing clade and the regions in which they are found. We proposed that, either the host population had selected for a particular sublineage, or that specific sublineages had adapted to be more successful in particular human populations. We further explored the dynamics of the epidemic over a 12-year period in terms of the five predominant M. tuberculosis clades. We found that, while four of these clades remained relatively stable, the incidence of cases from the Beijing clade increased exponentially. This growth was attributed to drug-sensitive cases although drug-resistant Beijing cases also appeared to be more successful than their non-Beijing counterparts. Possible factors contributing to this clade’s success were a greater proportion of positive sputum smears and a lower rate of successful treatment.

Thesis (PhD)--Stellenbosch University, 2012. / ENGLISH ABSTRACT: The causative agent of human tuberculosis, Mycobacterium tuberculosis, is an intracellular pathogen that secretes virulence factors, namely ESAT-6 and CFP-10, as substrates of the ESX-1 secretion system. It is hypothesised that these substrates interact with host proteins in a targeted manner in order to elicit a required immune response, and they have been shown to be involved in processes related to pro-inflammatory responses, necrosis, apoptosis, membrane lysis and cytolysis. However, the biological function of ESX-1 substrates during host-pathogen interactions remains poorly and incompletely understood. Therefore, the present study was designed to gain insight into the role of the ESX-1 secretion system substrates in host-pathogen interactions and to identify how M. tuberculosis mediates the response of the human host. In this study, a cDNA yeast two-hybrid library was constructed from human lung mRNA, to identify mycobacterial-host protein-protein interactions that occur within the lung alveoli. The ESX-1 secretion system substrates, ESAT-6 and CFP-10, were cloned in-frame into the pGBKT7 vector, which was used in the yeast two-hybrid system to screen the lung cDNA library in Saccharomyces cerevisiae. The ESAT-6 and CFP-10 screens identified 79 and 19 positive colonies, respectively. Of the total number of clones characterised, only two in-frame inserts were identified with the ESAT-6 screen, corresponding to the human proteins filamin A and complement component 1, q subcomponent, A chain (C1QA). In addition, the screen with CFP-10 also identified C1QA as binding partner. Subsequent in vitro and in vivo experiments were unable to confirm the putative interactions of C1QA with ESAT-6 and CFP-10. However, the interaction between filamin A and ESAT-6 was demonstrated and confirmed by both in vivo co-localisation and co-immunoprecipitation. Furthermore, the degradation of filamin A in the presence of ESAT-6 was shown to be reflective of cytoskeleton remodelling and the induction of cell death. The work presented here suggests that as ESAT-6 gains access to the cytosol, it initiates cell death by inducing destabilisation of the cytoskeleton cell structure. This may possibly be driven by the interaction of ESAT-6 and filamin A. Finally, we also initiated an investigation of the identified putative binding partners (filamin A and C1QA) as possible genetic markers for genetic susceptibility studies to tuberculosis. A case-control analysis was performed involving 604 cases, of which 109 were Tuberculous Meningitis (TBM), and 486 were controls from the South African Coloured (SAC) population within the Ravensmead-Uitsig catchment area. The results of this analysis demonstrated a novel association of a regulatory variant (rs587585) located upstream of the C1QA gene and demonstrated an increasing trend towards increased values in tuberculosis patients with the associated genotype. This study has contributed significantly to our understanding of human-mycobacterial hostpathogen protein-protein interactions and has opened the way for future studies further exploring the consequences and function of the identified ESAT-6-filamin A interaction. It has also led to the identification of a novel genetic association with tuberculosis. Finally, it demonstrates the usefulness of the yeast two-hybrid system to identify potential proteinprotein (host-pathogen) interactions that can lead to additional important and exciting research. / AFRIKAANSE OPSOMMING: Die organisme wat tuberkulose veroorsaak, Mycobacterium tuberculosis, is `n intrasellulȇre patogeen wat virulensie faktore afskei, naamlik ESAT-6 en CFP-10, as substrate van die ESX-1 sekresiesisteem. Daar word vermoed dat hierdie substrate met gasheerproteïene in „n teiken wyse interaksie het om `n vereiste immuunreaksie voort te bring. Hierdie substrate is betrokke by prosesse soos pro-inflammatoriese reaksies, nekrose, apoptose, membraanlise en sitolise. Die biologiese funksie van die ESX-1 substrate tydens gasheer-patogeen interaksies word egter tans swak en onvolledig verstaan. Daarom was die huidige studie ontwerp om insig te bekom oor die rol hiervan in gasheer-patogeen interaksies en om te identifiseer hoe M. tuberculosis die reaksie teenoor die gasheer bemiddel. In hierdie studie was `n komplementȇre deoksiribonukleïensuur (kDNS) gis twee-hibried biblioteek gemaak vanaf long boodskapper ribonukleïensuur (bRNS) om proteïen-proteïen interaksies wat in die long plaasvind, te identifiseer. Die substrate van die ESX-1 sekresiesisteem, ESAT-6 en CFP-10, is in volgorde gekloneer in die pGBKT7 vektor en is gebruik om die long kDNS biblioteek in Saccharomyces cerevisiae te ondersoek. In die soeke na interaksies met ESAT-6 and CFP-10, was 79 en 19 positiewe kolonies onderskeidelik geïdentifiseer. Van die aantal klone, was slegs twee volgordes in-leesraam geïdentifiseer met ESAT-6. Hierdie proteïene het ooreengestem met filamin A en “complement component 1, q subcomponent, A chain” (C1QA). Bykomend hiertoe, is C1QA ook geïdentifiseer as „n bindende vennoot met CFP-10. Daaropvolgende in vitro and in vivo eksperimente kon nie die vermeende interaksie van C1QA met ESAT-6 en CFP-10 bevestig nie. Maar die interaksie tussen filamin A en ESAT-6 kon wel gedemonstreer word deur die gebruik van mede-lokalisering en medeimunopresipitasie. Die afbreek van filamin A in die teenwoordigheid van ESAT-6 is ook aangetoon en blyk „n weerspieëling te wees van sitoskelet hermodellering en die induksie van seldood. Die werk wat hier aangebied word, dui daarop dat soos ESAT-6 toegang kry tot die sitosol, inisieër dit seldood deur die destabilisaisie van die sitoskelet selstruktuur. Dit word moontlik aangedryf deur die interaksie van ESAT-6 met filamin A. Laastens het ons `n ondersoek van die geïdentifiseerde bindingsvennote (filamin A and C1QA) as moontlike genetiese merkers vir genetiese vatbaarheidsstudies vir tuberkulose uitgevoer. `n Pasiënt-kontrole studie is gedoen waarby 604 individue ingesluit is, waarvan 109 gediagnoseer is met Tuberculosis Meningitis (TBM), en die ander 486 kontrole individue was van die Suid Afrikaanse Kleurling (SAC) bevolking binne die Ravenmead-Uitsig opvanggebied. Die resultate het „n nuwe assosiasie van „n regulerende variant (rs587585) wat stroomop van die C1QA geen gelokaliseer is, getoon. Hierdie variant het `n verhoogde neiging in tuberkulose pasiënte met die geassosieërde genotipe getoon. Hierdie studie het `n beduidende bydrae gemaak tot ons begrip van menslike-mikobakteriese gasheer-patogeen proteïen-proteïen interaksies. Hierdie resultate het die weg oopgemaak om die gevolge en funksie van die geïdentifiseerde ESAT-6-filamin A interaksie verder te ondersoek. Dit het ook aanleiding gegee tot die identifikasie van `n genetiese assosiasie met tuberkulose. Om saam te vat, hierdie werk bewys die bruikbaarheid van die gis twee-hibriede sisteem, om potensiële proteïen-proteïen interaksies te ontdek wat die moontlikheid het om aanleiding te gee tot addisionele navorsingsvrae. / The National Research Foundation, / Harry Crossley Foundation / Medical Research Council of South Africa / Stellenbosch University Postgraduate bursary / Prof. Paul van Helden