by Chin Miu Ling, Nathalie. / Thesis (M.Phil.)--Chinese University of Hong Kong, 1996. / Includes bibliographical references (leaves 130-143). / ABSTRACT --- p.i / ACKNOWLEDGEMENTS --- p.iii / LIST OF TABLES --- p.vii / LIST OF FIGURES --- p.x / INTRODUCTION --- p.1 / Chapter A --- Aminoglycosides --- p.1 / Chapter 1 --- Structure --- p.1 / Chapter 2 --- Classification --- p.1 / Chapter 3 --- Mode of action --- p.2 / Chapter 4 --- Types --- p.9 / Chapter B --- Mechanisms of aminoglycoside-resistance --- p.13 / Chapter C --- Aminoglycoside-modifying enzymes --- p.14 / Chapter 1 --- Classification --- p.19 / Chapter i --- Phosphotransferases --- p.19 / Chapter ii --- Adenylytransferases --- p.21 / Chapter iii --- Acetyltransferases --- p.22 / Chapter 2 --- Genes encoding AMEs --- p.24 / Chapter 3 --- Applications --- p.27 / Chapter D --- Prevalence of aminoglycoside-resistance --- p.28 / Chapter E --- Methods for the determination of aminoglycoside-modifying enzymes --- p.34 / Chapter 1 --- Examination of resistance phenotype --- p.35 / Chapter 2 --- Phosphocellulose paper binding assay --- p.38 / Chapter 3 --- Hybridization with specific gene probes --- p.39 / Chapter 4 --- Antibiotic inactivation --- p.44 / Chapter 5 --- High performance liquid chromatography (HPLC) --- p.44 / Chapter F --- Prevalence of aminoglycoside-modifying enzymes --- p.45 / Chapter G --- Objectives --- p.52 / MATERIALS AND METHODS --- p.53 / Materials --- p.53 / Chapter A --- Bacterial strains --- p.53 / Chapter 1 --- Standard strains --- p.53 / Chapter 2 --- Clinical isolates --- p.53 / Chapter B --- "Antibiotic, media, chemicals and instruments" --- p.55 / Methods --- p.55 / Chapter A --- Orevalence of aminoglycoside-resistance --- p.55 / Chapter B --- Susceptibility testing --- p.55 / Chapter C --- Characterization of aminoglycoside-modifying enzymes (AMEs) --- p.61 / Chapter 1 --- Extraction of enzymes --- p.61 / Chapter 2 --- Substrate profile analysis by the phosphocellulose paper binding assay --- p.62 / Chapter D --- Localization of resistance genes --- p.64 / Chapter 1 --- Genetic study --- p.64 / Chapter 2 --- Molecular studies --- p.67 / Chapter i --- Preparation of crude plasmid extracts --- p.68 / Chapter ii --- Agarose gel electrophoresis --- p.68 / Chapter E --- Plasmid profile analysis --- p.69 / Chapter F --- Plasmid fingerprinting --- p.69 / Chapter 1 --- Preparation of purified plasmid --- p.69 / Chapter 2 --- Restriction endonuclease digestion of plasmid DNA --- p.70 / Plan to achieve objectives --- p.71 / results --- p.73 / Chapter A --- Prevalence of aminoglycoside-resistant Gram-negative bacteria isolated in the Prince of Wales Hospital from 1989 to1992 --- p.73 / Chapter B --- "Susceptibility to 12 aminoglycosides of aminoglycoside-resistant E. coli, K pneumoniae and Ps. aeruginosa" --- p.78 / Chapter C --- "Aminoglycoside-modifying enzymes (AMEs) produced by E. coli, K pneumoniae and Ps. aeruginosa" --- p.88 / Chapter D --- Plasmid profile analysis --- p.93 / Chapter E --- Localization of aminoglycoside-resistance genes --- p.102 / discussion --- p.114 / Chapter A --- Aminoglycoside-resistance --- p.114 / Chapter B --- Mechanisms of aminoglycoside-resistance --- p.118 / Chapter C --- Genetic location of aminoglycoside-resistance and plasmid profiles --- p.122 / Chapter D --- Characterization of AMEs --- p.126 / Chapter E --- Areas for future research --- p.128 / references --- p.130 / appendix --- p.144

Patients who experience multiple hospitalizations over short periods of time may be at greater risk of hospital-acquired infections (HAIs). While it is known that prior hospitalizations are associated with HAIs, there is a gap in knowledge regarding which factors of prior hospitalizations have an impact on the risk of HAIs in subsequent hospitalizations. HAIs caused by gram-negative bacteria (GNB) are of particular concern due to their propensity to develop drug resistance and the limited antibiotics available to treat them. The aims of this dissertation are to: 1) examine clinical and patient risk factors associated with acquiring at least one gram-negative hospital-acquired infection in adult patients with multiple hospitalizations; 2) systematically review the literature assessing the association between repeat gram-negative bacterial infections and changes in antibiotic susceptibility patterns; and 3) assess the association between repeat infections with three common gram-negative pathogens and risk of subsequent drug resistant infections with the same species among patients with multiple hospitalizations. A retrospective cohort study was conducted to identify risk factors from prior hospitalizations associated with incident HAIs caused by three common GNB. Of the 129,372 patients with multiple hospitalizations, 1,672 (1.3%) acquired K. pneumoniae, 1,127 (0.9%) acquired P. aeruginosa, and 262 (0.2%) acquired A. baumannii infections. In survival analyses, older age, mechanical ventilation, history of chronic diseases, and increasing days of use of antibiotics decreased the time to infection for all 3 pathogens. This study highlights potential modifiable risk factors for infection control. Patients with multiple hospitalizations are also inherently at greater risk for repeat HAIs which may result in decreased antibiotic susceptibility, making them more difficult to treat. A systematic review was conducted to evaluate if there is an association between repeat GNB HAIs and drug resistance. From 2000 to 2015, only seven studies explicitly examined repeat GNB HAIs and change in antibiotic susceptibility, five of which reported decreased susceptibility in later infections. The association between repeat GNB HAIs and risk of drug resistance among patients with multiple hospitalizations was then investigated with available electronic medical record data. The risk of a drug-resistant K. pneumoniae HAI increased by 1.14 times (95%CI: 1.04-1.24) with each prior K. pneumoniae HAI, after adjusting for potential confounders and antibiotic use. Similarly, patients with repeat P. aeruginosa infections had a 1.23 times increased risk of a subsequent drug-resistant infection (95%CI: 1.12-1.36) with each prior P. aeruginosa HAI as compared to patients with only one infection. Repeat A. baumannii infections were not analyzed due to limited sample size. The studies in this dissertation demonstrate that patients with multiple hospitalizations are a high-risk population for GNB HAIs. Prevention of GNB HAIs in this group is critical in order to reduce complications to medical care and limit transmission of infections to others in healthcare facilities and the community. Patient medical history can be used for infection risk assessment and to guide future medical care to reduce risk of infection in patients with multiple hospitalizations.

FundaÃÃo Cearense de Apoio ao Desenvolvimento Cientifico e TecnolÃgico / O Streptococcus (S.) pneumoniae à considerado como o principal agente causador de morbidade e mortalidade em crianÃas menores de cinco anos de idade. Todas as doenÃas pneumocÃcicas comeÃam com o estabelecimento da colonizaÃÃo do S. pneumoniae na nasofaringe, podendo progredir para doenÃa invasiva se as barreiras naturais forem cruzadas. Nas Ãltimas dÃcadas, o aumento do nÃmero de cepas de S. pneumoniae resistentes à antibiÃticos β-lactÃmicos e a outras classes de antimicrobianos tem dificultado o tratamento da infecÃÃo pneumocÃcica. Atualmente cerca de 13 sorotipos de S. pneumoniae respondem por mais de 85% dos isolados invasivos. A vacina pneumocÃcica polissacarÃdica conjugada 7-valente tem sido amplamente recomendada para crianÃas menores de cinco anos. Os objetivos desse estudo foram determinar a prevalÃncia de S. pneumoniae em crianÃas portadoras, a frequÃncia de isolados de S. pneumoniae de indivÃduos com infecÃÃo sistÃmica, o perfil de sensibilidade a antimicrobianos e os sorotipos mais comuns, em Fortaleza, Brasil. Os isolados de portadores foram recuperados a partir de swabs de nasofaringe de crianÃas usuÃrias de creches, enquanto que os isolados de infecÃÃo sistÃmica foram cedidos pelo LACEN-CE. Foram realizadas as ConcentraÃÃes InibitÃrias MÃnimas (CIM) para penicilina e ceftriaxona para todos os isolados, e levofloxacina apenas para os isolados de nasofaringe. Os pontos de corte das CIM foram determinados de acordo com o CLSI (2007). As sorotipagens dos isolados sistÃmicos foram realizadas pela reaÃÃo de Quellung, enquanto que a genotipagem capsular dos isolados de portadores foi realizada pela tÃcnica de multiplex PCR. De 215 crianÃas usuÃrias de creches, foram isolados S. pneumoniae em 152 (71%). As CIM de 137 isolados de portadores mostraram uma taxa resistÃncia de 71% para penicilina e de 21% para ceftriaxona. NÃo houve resistÃncia nos testes com levofloxacina. Comparado a um estudo similar, realizado hà 10 anos, em Fortaleza, nossos resultados apresentaram um aumento significativo nas taxas de resistÃncia à penicilina e ceftriaxona. De 26 isolados de nasofaringe que apresentaram resistÃncia plena, apenas, seis isolados (23%) tiveram a genotipagem capsular identificada por multiplex PCR. A incidÃncia de isolados invasivos neste estudo por ano, foi de, aproximadamente, 1 caso/100.000 hab. Dos 52 isolados, 42% apresentaram resistÃncia à penicilina e 13,5% à ceftriaxona. Os sorotipos mais comuns dos isolados sistÃmicos foram 19F (12%), 14, 3, 6A (8% cada), 4, 18C e 9V (6% cada), com cobertura estimada, tanto para vacina pneumocÃcica conjugada 7-valente quanto para a 10-valente, de 31,8%. / Streptococcus (S.) pneumoniae is considered the principal causative agent of morbidity and mortality in children younger than five years of age. All pneumococcal diseases are initiated by establishing a S. pneumoniae colonization in nasopharynx, the disease progressing to systemic disease if natural barrier are crossed. During the last decades, the increasing amount of resistant S. pneumoniae strains to beta-lactams and other classes of antimicrobials has modified the treatment of pneumococcal infection. At present, nearly 13 serotypes respond for more than 85% of invasive isolates. The 7-valent polysaccharide-conjugated pneumococcal vaccine has been widely recommended for use in children younger than five years. The aims of this study were to determine the S. pneumoniae carrier in children, the frequence of serotypes from systemic infection patients, the susceptibility profile to antimicrobials in Fortaleza, Brazil. Carrier state isolates were recovered from nasopharyngeal swabs from children attending day-care center facilities, while the isolates from systemic infection fournished by LACEN-CE. Minimal Inhibitory Concentrations (MIC) to penicillin and ceftriaxone were assessed for all isolates, and levofloxacin MIC only from nasopharyngeal isolates. MIC cut-offs were determined according to CLSI standards (2007). Serotyping of systemic isolates was performed by Quellung reaction, while capsular genotyping of carrier isolates was performed by multiplex PCR assay. OF 215 children attending day-care centers, 152 S. pneumoniae isolates were identified (71%). Penicillin MIC showed 71% of resistance, and for ceftriaxone, 21% of resistance. No resistance was found for levofloxacin MIC testing. When compared to a 10-year old similar study in Fortaleza, our results have shown a significant increase of penicillin and ceftriaxone resistance rates. Of 26 isolates tested, only six nasopharyngeal isolates (23%) were positively genotyped by multiplex PCR. The incidence of invasive isolates was 1/100,000 inhab. per year. Of 52 systemic isolates serotyped, 42% were penicillin-resistant, and 13.5% were ceftriaxone-resistant. Systemic serotypes identified were 19F, 3, 6A, 4, 18C and 9V, with a estimated coverage by the 7-valent and 10-v pneumococcal polysaccharide conjugated vaccines of 31.8%.

Drug resistance is one of the most medically relevant forms of pathogen evolution. To date, vaccines have not failed with the same depressing regularity as drugs. Does that then make vaccines evolution-proof? In the face of vaccination, pathogens are thought to evolve in two ways: by evolving epitope changes at the antigenic target of vaccination (epitope evolution); or by evolving changes at other antigenic loci, some of which may involve virulence (virulence evolution). The fundamental difference between these two forms of evolution is that virulence evolution could lead to disease outcomes in unvaccinated people that are more severe than would have been seen prior to evolution. One of the theoretical assumptions of virulence evolution is that more virulent parasites will have a selective advantage over less virulent parasites in an immunized host, and are thus more likely to be transmitted. The assumption is that more virulent parasites may be competitively more superior in mixed infections, or may be better able to evade/modulate the host immune response. Thus, the aim of this thesis was to experimentally test whether more virulent parasites have a within-host selective advantage in an immunized host or whether vaccine efficacy is more likely to depend on genetic differences at the targeted sites of vaccination. I used clones (genotypes) of the rodent malaria Plasmodium chabaudi originally derived from wild-caught Thicket (Thamnomys rutilans) rats to infect laboratory mice and a rodent analogue of the candidate blood-stage malaria vaccine apical membrane antigen 1 (AMA-1). I found that within-host selection did not depend on parasite virulence, and that protective efficacy depended on genotype-specific differences at the vaccine target. Vaccine-induced protection was not enhanced by including a number of allelic variants. However, such genotype-specific responses were only observed when the vaccine was tested against genetically distinct P. chabaudi parasites. When one P. chabaudi genotype was serially passaged through naïve mice the derived line was more virulent and was subsequently less well controlled by vaccine-induced immunity. In other experiments I found within host competition not to be immune-mediated. Thus my results suggest that vaccination has the potential to select for more virulent parasites but that the selective advantage is likely to be independent of competition. The selective advantage may be attributable to the enhanced immune evasion of more virulent parasites. However, without genetic markers of virulence, the mechanisms that mediate this selection remain unknown. My thesis contributes towards a growing body of evidence that vaccines have the potential to differently alter the within-host parasite dynamics of particular pathogen genotypes and that the selection imposed is likely to be system specific, depending on the fine specificity of the vaccine-induced responses and the identity of infecting parasites. Although vaccine potency may not be enhanced by including more than one allelic variant of an antigen, multi-valent vaccines may be one of the best ways to avoid the inadvertent selection for more virulent malaria parasites.

Multiple Myeloma (MM) is an incurable plasma cell malignancy and, although novel treatment regimes in the past decade have improved patient outcome, long-term treatment leads to relapse and refractory disease. The centrosomal kinase NEK2 is found overexpressed in MM and promotes chromosomal instability, drug resistance and increased proliferation. Although much research shows NEK2 having a detrimental effect in cancer, much of its mechanisms of overexpression and drug resistance has not been studied in detail. In this work we expand our understanding of NEK2 in MM. Using Tandem Affinity Purification coupled with Mass Spectrometry, we show that NEK2 directly interacts with the de-ubiquitinase USP7. We confirm this interaction in cell lines of MM and lung cancer. Since USP7 has been shown to have important cancer-promoting roles we tested if USP7 was necessary for NEK2-driven bortezomib resistance. We found that USP7 shRNA was sufficient to sensitize the bortezomib resistant NEK2 overexpressing cells to bortezomib. Surprisingly, we found that USP7 inhibition with shRNA or by treatment with the small molecule USP7 inhibitor P5091 led to depletion of NEK2 protein in every cell line tested. Previous research shows USP7’s main function is a de-ubiquitinase and, since NEK2 is a target of the ubiquitin-proteasome system, we hypothesized USP7 may be de-ubiquitinating NEK2. Through western blots and immunoprecipitations, we show the NEK2-USP7 interaction promotes the de-ubiquitination and subsequent stabilization of NEK2, presenting USP7 as the first discovered de-ubiquitinating enzyme of NEK2. To understand how NEK2 promotes drug resistance in cancer we studied a previously published list of NEK2-regulated genes and, using the UCSC genome browser (Track Name:GM12878+TNFa RELA) ChIP-seq data, we found approximately half of these genes have the NF-κB transcription factor p65 bound throughout the gene sequence. We also produced a signaling score using an average of 11 known targets of NF-κB and patients with high NEK2 showed a significantly increased score of NF-κB signaling. Additionally, through western blots and immunofluorescence, we found that patients with high NEK2 protein levels consisitently had activation higher signal of p65 protein and phosphorylated p65 at Serine 536, indicative of increased activity. We then causally show NEK2 activates canonical NF-κB by performing western blots and a dual-luciferase reporter assay on control and NEK2 overexpressing cells. Using AKT and PP1α inhibitors, we found that NEK2 drives NF-κB by phosphorylating and inactivating PP1α, leading to hyperactive AKT. Using this model of NEK2-NF-κB activation, we aimed at targeting NEK2 directly with the small molecule drugs INH1 (depletes NEK2 protein) and P5091 (inhibits USP7 activity) in empty vector control cells, NEK2 overexpressing cells or cells with an acquired drug resistance phenotype. Our results show that both INH1 and P5091 can overcome bortezomib resistance in cell lines and in vivo. Another aspect of MM disease we targeted in this work was bone disease. Bone disease in MM is common and causes bone pain and fractures but a much is still regarding what drives these lesions. We found that NEK2 expression in patients correlates with a presence of bone lesions, based on FDG-PET scan and MRI. Using our previously published list of NEK2 regulated genes, we found Heparanase (HPSE) is directly correlated to NEK2 expression. HPSE is an extracellular protein shown to promote differentiation of the bone destroying cell, osteoclast. Using western blots, RT-qPCR and ELISA, we found NEK2 increases HPSE expression and extracellular release. HPSE was also on the list of genes upregulated by NEK2 found to have p65 bound to the gene, thus we tested if NEK2 was driving HPSE through the NF-κB. Accordingly, we found NEK2 drives HPSE through the NF-κB pathway and, consistent with our previous results, in a USP7-dependent manner. Using bone marrow macrophages and conditioned media from empty vector control or NEK2 overexpressing cells, we found NEK2 promtoes increased differentiation of osteoclasts and inhibition of HPSE blocked this effect, strongly suggesting HPSE is the mediator of this effects. Importantly these findings were recapitulated in vivo. Empty vector or NEK2 overexpressing cells were injected through the tail vein to allow dissemination to the bone marrow. microCT and Xray revealed mice injected with NEK2 overexpressing cells showed reduced bone density, compared to empty vector cells. Additionally, H&E and TRAP staining confirmed our in vitro results by showing higher osteoclast levels in bone sections of mice injected with NEK2 overexpressing cells. Lastly, we show a novel role for the ATPase TRIP13 as a cofactor for USP7 de-ubiquitinating activity. TRIP13 is overexpressed in cancer, has been shown to be an oncogene and promotes drug resistance. By systematically targeting TRIP13 overexpressing cells with drugs that inhibit different pathways we found TRIP13 drug resistance is diminished by inhibiting USP7. We found that TRIP13 binds with USP7 and by western blots and immunoprecipitations we show it is necessary for the de-ubiquitination of NEK2. Furthermore, we also found TRIP13 shows a hyperactive USP7 phenotype, shuttling PTEN out of the nucleus and stabilizing MDM2, in a USP7 dependent manner. In summary, this work shows the de-ubiquitinase USP7, coupled with the ATPase TRIP13 stabilizes NEK2 by de-ubiquitination, this leads to accumulation of NEK2 and activation of the canonical NF-κB pathway through PP1α/AKT, which promotes drug resistance and activates HPSE, increasing osteoclast differentiation and bone destruction.

Malaria is a mosquito borne infectious disease caused by a unicellular Apicomplexan parasite of the Plasmodia genus. The emergence and subsequent spread of drug resistance in the highly virulent Plasmodium falciparum parasite has been a major setback in eradicating malaria, which affects an estimated 216 million individuals and causes 445,000 deaths annually worldwide. Chloroquine (CQ) was once used as the first-line antimalarial drug treatment, until CQ-resistant parasites emerged in endemic regions including Africa, Southeast Asia, and South America. More recently, parasites have developed resistance to the current first line drug piperaquine (PPQ), used in combination with dihydroartemisinin (DHA) in Southeast Asia. Plasmodium falciparum chloroquine resistance transporter (PfCRT), a member of the drug/metabolite transporter (DMT) superfamily, is a 49-kDa integral transmembrane protein localized in the digestive vacuole (DV) of the pathogenic parasite. Mutations in PfCRT have been identified as the core determinants of Plasmodium falciparum resistance to CQ and PPQ by mediating the efflux of these antimalarial drugs. All CQ resistance-conferring PfCRT isoforms share the K76T mutation, which is widely used as a molecular marker for CQ resistance. Despite the significance in the impact of drug-resistant malaria, a detailed understanding of PfCRT physiological function and the molecular basis of PfCRT-mediated drug resistance have been hampered by a lack of high-resolution structural information. This dissertation describes the first structure of PfCRT and reveals the interaction of drugs with the purified and reconstituted protein. We determined the structure of the 49-kDa PfCRT 7G8, a clinically relevant CQ-resistant isoform found in South America, to 3.2 Å resolution by single-particle cryo-electron microscopy (cryo-EM), in complex with a specific antigen-binding fragment (Fab) to overcome current size limitations in cryo-EM. Our PfCRT structure displays an inward-open conformation, consists of 10 transmembrane (TM) helices with an inverted topology, and has unique elements including two juxtamembrane helices and a highly conserved cysteine-rich loop between TM helix 7 and 8. The architecture of PfCRT is similar to other members of the DMT superfamily. TM helices 1-4 and 6-9 in PfCRT form a central cavity which is a potential binding site for both CQ and PPQ. A striking feature is that virtually all the CQ resistance mutations, identified from decades of investigation into PfCRT variants that have evolved independently across the malaria-endemic world, map around this central, negatively-charged cavity. Distinct mutations that have been proposed to cause high-level PPQ resistance in parasites, which cause a loss of CQ resistance, form a planar ring that also lines this cavity. Functional experiments with various purified PfCRT isoforms or mutants provide evidence that drug resistance is possibly due to pH- and membrane potential-dependent drug transport. We also show that PfCRT CQ-resistant isoforms bind and transport arginine, suggesting that positively charged amino acids may be putative transport substrates for CQ-resistant PfCRT. This work provides a structural and functional framework to understand the mechanism of PfCRT-mediated drug resistance in the malaria parasite.

Peptidomimetics can mimic hierarchical structures of peptides and proteins. Thus, they are extensively studied for therapeutic applications. To break the limitation of backbones and frameworks and expand the peptidomimetics family, a new class of peptidomimetics - “γ-AApeptides” was developed. Design of γ-AApeptides is based on the chiral peptide nucleic acids (PNAs) backbone. The World Health Organization estimates that one -third of all deaths in the world are on account of infectious diseases. AMPs are important because of their high activity against broad spectrum microbes, less susceptible to grow resistance and selectivity in binding to bacterial cells over human cells. γ-AApeptides as a new class of peptidomimetics have increased stability and enhanced chemical diversity. We have developed polymyxin mimic cyclic peptides, small linear molecules and hydantoin derivatives as potent antibiotic agents with γ-AApeptides. They have good bioactivity and selectivity. Combinatorial library is key technology for accelerating the discovery of novel therapeutic agents. One-bead-two-compound γ-AApeptides-based library was developed and screened against SMYD2 protein which is essential for tumor growing.

Developing treatments for antibiotic resistant bacterial infections is among the most urgent public health challenges worldwide. Tetracyclines are one of the most important classes of antibiotics, but like other antibiotics classes, have fallen prey to antibiotic resistance. Key small changes in the tetracycline structure can lead to major and distinct pharmaceutically essential improvements. Thus, the development of new synthetic capabilities has repeatedly been the enabling tool for powerful new tetracyclines that combatted tetracycline-resistance. Traditionally, tetracycline antibiotics were accessed through bacterial natural products or semisynthetic analogs derived from these products or their intermediates. More recently, total synthesis provided an additional route as well. Importantly however, key promising antibiotic candidates remained inaccessible through existing synthetic approaches. Heterologous biosynthesis is tackling the production of medicinally important and structurally intriguing natural products and their unnatural analogs in tractable hosts such as Saccharomyces cerevisiae. Recently, the heterologous biosynthesis of several tetracyclines was achieved in Streptomyces lividans through the expression of their respective biosynthetic pathways. In addition, the heterologous biosynthesis of fungal anhydrotetracyclines was shown in S. cerevisiae. This dissertation describes the use of Saccharomyces cerevisiae towards the biosynthesis of target tetracyclines that have promising prospects as antibiotics based on the established structure-activity relationship of tetracyclines but have been previously synthetically inaccessible. Chapter 1 provides an introduction to the pursuit of tetracycline antibiotics using S. cerevisiae. Following an overview of tetracycline drugs, the chapter describes the methods for making tetracyclines and their limitations in accessing the tetracycline analogs targeted in this study. The desirability of making these target analogs as well as key desired properties are then exemplified by natural products, totally synthetic and semisynthetic derivatives. The target tetracycline analogs pursued in this study are then outlined and the considerations in choosing their desired properties are discussed, as well as the reasons for employing S. cerevisiae in their synthesis. Chapter 2 describes the use of Saccharomyces cerevisiae for the final steps of tetracycline biosynthesis, setting the stage for total biosynthesis of tetracyclines in Saccharomyces cerevisiae. Chapter 3 describes the work towards biosynthesis of the target tetracycline analogs using Saccharomyces cerevisiae, utilizing successful expression optimization and gene biomining approaches. Chapter 4 describes the work towards the target tetracycline analogs from fungal anhydrotetracyclines in Saccharomyces cerevisiae. The challenge of enzyme evolution towards unnatural substrates and the complex environment of cells require metabolic engineering efforts to be performed in libraries, as it is currently impossible to predetermine which modifications will prove beneficial. Traditional methods in DNA mutagenesis and increasingly, advances in DNA synthesis, DNA assembly and genome engineering are enabling high throughput strain construction. Thus, there is a need for a general, high-throughput, versatile and readily implemented assay for the detection of target molecule biosynthesis. The development of such an assay is described in Chapter 5. The assay is demonstrated to detect tetracycline derivatives, and differentiate a producer and a nonproducer strain of the fungal anhydrotetracycline TAN-1612. The yeast three hybrid assay for metabolic engineering of tetracycline derivatives described in this chapter could be used in the next steps towards the heterologous biosynthesis of the target tetracycline analogs in S. cerevisiae and beyond.

No description available.

Abstract not available