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Thesis (Ph.D.)--Boston University. The following pages are missing: 110, 136-137, 145, and 157. / PLEASE NOTE: Boston University Libraries did not receive an Authorization To Manage form for this thesis or dissertation. It is therefore not openly accessible, though it may be available by request. If you are the author or principal advisor of this work and would like to request open access for it, please contact us at open-help@bu.edu. Thank you. / Some aspects of sterol and steroid biosynthesis were investigated to gain an insight into the control and regulatory mechanisms. In some of the initial experiments, LH was found to increase the incorporation of acetate-1-14C into DPS and cholesterol, suggesting that one of the sites of action of LH is before the formation of cholesterol. [TRUNCATED] / 2031-01-01

Thesis advisor: Evan R. Kantrowitz / Nucleotides, the building blocks for nucleic acids, are essential for cell growth and replication. In E. coli the enzyme responsible for the regulation of pyrimidine nucleotide biosynthesis is aspartate transcarbamoylase (ATCase), which catalyzes the committed step in this pathway. ATCase is allosterically inhibited by CTP and UTP in the presence of CTP, the end products of the pyrimidine pathway. ATP, the end product of the purine biosynthetic pathway, acts as an allosteric activator. ATCase undergoes the allosteric transition from the low-activity and low-affinity T state to the high-activity and high-affinity R state upon the binding of the substrates. In this work we were able to trap an intermediate ATCase along the path of the allosteric transition between the T and R states. Both the X-ray crystallography and small-angle X-ray scattering in solution clearly demonstrated that the mutant ATCase (K164E/E239K) exists in an intermediate quaternary structure shifted about one-third toward the canonical R structure from the T structure. The structure of this intermediate ATCase is helping to understand the mechanism of the allosteric transition on a molecular basis. In this work we also discovered that a metal ion, such as Mg2+, was required for the synergistic inhibition by UTP in the presence of CTP. Therefore, the metal ion also had significant influence on how other nucleotides effect the enzyme. A more physiological relevant model was proposed involving the metal ion. To better understand the allosteric transition of ATCase, time-resolved small-angle X-ray scattering was utilized to track the conformational changes of the quaternary structure of the enzyme upon reaction with the natural substrates, PALA and nucleotide effectors. The transition rate was increased with an increasing concentration of the natural substrates but became over one order of magnitude slower with addition of PALA. Addition of ATP to the substrates increased the rate of the transition whereas CTP or the combination of CTP and UTP exhibited the opposite effect. In this work we also studied E. coli dihydroorotase (DHOase), which catalyzes the following step of ATCase in the pyrimidine biosynthetic pathway. A virtual high throughput screening system was employed to screen for inhibitors of DHOase, which may become potential anti-proliferation and anti-malarial drug candidates. Upon the discovery of the different conformations of the 100's loop of DHOase when substrate or product bound at the active site, we've genetically incorporated an unnatural fluorescent amino acid to a site on this loop in the hope of obtaining a better understanding of the catalysis that may involve the movement of the 100's loop. / Thesis (PhD) — Boston College, 2012. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Chemistry.

This dissertation covers two projects linked by their involvement in the modification of tRNA bases. The first project focused on an investigation of a role for the modified base Archaeosine, the ubiquitous modification in tRNA in the archaeal domain. Initial work was performed on a set of in vitro prepared tRNA modified to feature either the canonical guanine base at position 15, preQ0 (TGT product) or Archaeosine (ArcS product). There was very little difference in the thermal stability of tRNAs containing these modifications in the halophilic H. volcanii tRNASer or E. coli tRNAGln. In tRNAGln taken from M. thermautotrophicum however, there was a 2°C increase in melting point in 50 mM MgCl2 upon modification to archaeosoine. Benefitting from the development of genetic tools for the generation of specific deletion mutants of the thermophile Thermococcus kodakarensis, it was possible to start investigation of tRNAs that have been hypomodified in vivo due to the lack of arcTGT (TK0760) and ArcS (TK2156). In vitro modified equivalents of the GlnCUG isoacceptor were also prepared. Thermal stability of these tRNAs show virtually identical melting transitions, with a biphasic denaturation occurring at all magnesium concentrations tested. Isolation of the CUG isoacceptor from the in vivo maturated total tRNA pool allowed melts of specifically hypomodified tRNAs. Those containg Archaeosine (WT) and genetically encoded guanine (∆tgt) showed identical melting profiles with Tm beyond the 98°C limit of the experiment. In the preQ0 containing in vivo RNA the shows a lag in its magnesium response, and a more persistent biphasic melting profile. At 10mM Mg2+ concentration the preQ0 containing tRNA is approaching a Tm of 98°C though the turn over point in the melt is not well defined. The second project was to investigate the product of base treatment of the oxidized cofactor NAD(P)+. This cofactor is involved in the biosynthesis of preQ1 from preQ0 in bacterial systems and at low concentrations it can be difficult to quantify enzyme activity based on direct quantitation. Under these conditions a fluorescence based method where by the production of NAD(P)+ is measured rather than the consumption of NAD(P)H. Base treatment of the oxidized cofactor generates a fluorescent species with an efficiency of 95%. The assay has been used extensively by our group to track activity of various enzymes including QueF, however the identity of the fluorophore had not been established. Purification of the fluorescent product was achieved by isocratic HPLC in water using a reverse phase column. It was found that the assay conditions previously used (7.5M NaOH for 2 hours) were actually counterproductive for maximizing fluorescence yield. Incubation at 2M NaOH gave a 35% increase in product yield. The isolated product was determined to have molecular weight of 123.0318 (3.6 ppm by accurate mass ESI MS). 1H and 13C NMR were used to confirm the structure to be that of 2-hydroxynicotinaldeyde. It was also possible to determine the quantum yield for the molecule to 0.11. Work carried out previously on pyridinium based NADP analogs is consistent with the identity of the fluorophore presented here.

Cyanobacteria produce a diverse array of natural products with significant potential in many biotechnological, clinical and commercial applications. These include pharmaceuticals, such as antitumour products, antibiotics, immunosuppressants, anticholesterolemics and anti-parasitic agents, as well as veterinary therapies and agrochemicals. These compounds are synthesised by complex secondary metabolism pathways involving polyketide synthases (PKS) and non-ribosomal peptide synthetases (NRPS), both of which require an essential phosphopantetheinyl transferase (PPT) for their activity. PPTs activate the acyl, aryl and peptidyl carrier proteins within various biosynthetic pathways by the transfer of a phosphopantetheinyl moiety to an invariant serine residue. Phylogenetic analysis of the large superfamily of PPTs has revealed two separate families based on substrate specificity, which have been designated AcpS and Sfp-like. The AcpS PPT family activate acyl carrier proteins of fatty acid synthesis, while the Sfp-like PPT family, typified by the Bacillus subtilis PPT Sfp, has diverse roles in primary and secondary metabolism. The majority of cyanobacterial PPTs are of the Sfp-like PPT family and occur in genomes lacking an AcpS PPT. Phylogenetic analysis uncovered a distinct clade of cyanobacterial PPTs involved in heterocyst differentiation. Heterologous expression and functional analysis of NsPPT, the heterocyst-associated PPT in Nodularia spumigena NSOR10, represented the first characterisation of a cyanobacterial PPT. PCR-based screening was utilised to identify NsPPT and Southern hybridisation suggested this was the only PPT encoded by the N.spumigena NSOR10 genome. Enzymatic analyses demonstrated the ability of NsPPT to phosphopantetheinylate PKS and NRPS carrier proteins from a range of metabolism pathways and cyanobacterial species. Nostoc punctiforme ATCC 29133 encodes three PPTs. One of these PPTs, NgcS, is also a heterocyst-associated PPT and is homologous to NsPPT of N.spumigena NSOR10. Expression and enzymatic analysis of NgcS from N. punctiforme ATCC 29133, revealed contrasting phosphopantetheinylation activity to that seen for NsPPT, and indicated that NgcS may have evolved to have a strict specificity for the glycolipid biosynthesis pathway. Although the Sfp-like family of PPTs are normally associated with secondary metabolite biosynthesis, Synechocystis sp. PCC 6803 harbours a unique Sfp-like PPT (Sppt) but does not produce NRPS or PKS compounds. Genetic disruption of Sppt was attempted and expression of Sppt allowed the characterisation of its enzyme kinetics. Sppt displayed the ability to activate non-cognate cyanobacterial carrier proteins from NRPS and PKS biosynthetic pathways, although only at a low level of activity. This suggested that wild-type Synechocystis sp. PCC6803 would not be suitable for heterologous expression of cyanobacterial secondary metabolites. These results have important implications regarding the expression and manipulation of cyanobacterial bioactive compounds in heterologous hosts. Applications of this research may provide a biotechnological platform for the sustainable production of cyanobacterial natural products.

Natural-synthetic hydrid biomaterials have been isolated from the growth of Alcaligenes latus and Pseudomonas oleovorans in the presence of diethylene glycol (DEG). A. latus could cometabolise DEG with 10 g/L glucose, while DEG was consumed by P. oleovorans with 20 mM sodium octanoate or octanoic acid. The presence of DEG in bioprocessing systems for the production of short chain length (scl-) and medium chain length (mcl-) PHAs consequently lowered cell viability and PHA yield. Cell morphology was slightly changed, but the PHA inclusion bodies apparently were not. DEG affected the composition of the mclPHA which was confirmed to be polyhydroxyoctanoate (PHO) with a significant increase in the C8 component. Gas chromatography-mass spectrometry (GC-MS) was used to quantitatively monitor DEG in the system and revealed its cellular adsorption. Intracellularly, the DEG significantly decreased the molar weight of the mclPHA and sclPHA. P1PH NMR, 2-D COSY and HSQC spectra confirmed that the polymer samples consisted of PHA chains terminated by DEG. Similar to the cultivation of P. oleovorans with DEG, the presence of PEG200 and PEG400 also had an effect on cell growth, PHO yield and cell viability. Furthermore, a hybrid copolymer of PHO-PEG200 was synthesised. The synthesis of these natural-synthetic hybrid copolymers could lead the way for a wide variety of PHA-PEG copolymers with a range of bioactive properties. All thermal properties of PHB were higher than those of PHB-DEG. This may be due to a combination of lower PHB molecular weight and termination of the chains by DEG, i.e. ???DEGylation???. However, PHB-DEG was more elastomeric when compared to PHB, showing properties similar to its copolymer with 20 mol% 3-hydroxyvalerate. Contact angles revealed that the PHB-DEG film was slightly more hydrophilic than PHB. Despite the large difference in their respective proportions, the comparatively small DEG component exerted an influence on chain confirmation, such that solvent casting under humid conditions apparently induced self-assembly and formed a disordered microporous film. DEGylation of PHO also had noticeable effects on the physiochemical properties of the biopolymer. A major decrease in molecular weight, together with the termination of hydrophobic PHO chains with hydrophilic end-groups resulted in changes to its thermal properties when compared to PHO. In comparison to PHO, solvent cast films of PHO-DEG were apparently less flexible, but more hydrophilic.