Acanthamoeba are ubiquitous protists that play an environmental role in regulating microbial diversity; they also occasionally cause infections of the eye (Acanthamoeba keratitis) and brain (granulomatous amoebic encephalitis). These organisms exhibit two distinct phenotypes. The trophozoite form dominates in favorable conditions, in which the Acanthamoeba move through the extension of pseudopodia, engulfing microbes and other particles. During stressful conditions, the Acanthamoeba undergo a process of encystment, in which they build a double cell wall and become relatively inactive. The cyst form can survive years until more favorable conditions arise, at which point they may excyst. For this study, multiple laboratory encystment methods were compared to determine the percent encystment and the different viabilities of laboratory-produced cysts. Furthermore, four different encystment genes were targeted for development of a primer library for reverse-transcription, polymerase chain reaction expression studies. The library was developed using sequences accessed from various databases, including NCBI and EMBL; primers were screened through polymerase chain reaction, and those primers producing positive results were used to further screen cellular RNA that was extracted from encysting cells over various time points during the encystment process, and using various encystment media. Using these methods, target gene involvement in the encystment process was compared between species and encystment methods. These studies lay the foundation for quantitative gene expression analysis, and provide the basis for comparison of various encystment methods.

Pseudomonas aeruginosa is an opportunistic, nosocomial pathogen for which antibiotic resistance and biofilm development is common. Quorum sensing communication is known to be a major controlling factor in virulence gene expression, biofilm development, antibiotic resistance factors, and specifically MexAB-OprM multi-drug efflux pump expression in P.aeruginosa. MexAB-OprM efflux pumps contribute to antibiotic resistance of tetracycline and other antibiotics in pseudomonads and other organisms. P.aeruginosa infections are problematic in cystic fibrosis and burn patients; it is also the number one causative agent of respiratory infections for intensive care unit patients. Present day antibiotics are losing the battle against these infections. In theory, quorum sensing inhibitors (QSI) reduce pathogencity of the organism; making it less virulent, thus allowing either the host immune system to clear the infection or use of a QSI in combination with an antibiotic to clear more persistent pathogens. For these reasons two alternative modes of treatment were explored in this study: quorum sensing inhibition by folk-medicinal plant extracts and an example of combination drug therapy, the “thyme-tetracycline effect”. Fifty folk-medicinal plant extracts were screened for potential anti-quorum sensing activity using two quorum sensing inhibition (QSI) reporter strains, Pseudomonas aeruginosa QSIS2 and Chromobacterium violaceum 12725. These were used to test specifically for C4-C6 and C12 HSL quorum sensing inhibition. Of the fifty plants tested, thirty plant families were represented. Eleven plant extracts (basil, chaparral, clove, cranberry, oregano, pomegranate, rosemary, sage, sassafras, thyme and witch hazel) showed C4 HSL quorum sensing inhibition as determined by both assays. Interestingly, five of the plants were from the Lamiaceae family. Thymus vulgaris (thyme), also from the Lamiaceae family, was chosen for further assessment. Previous research has shown that thyme extract can synergistically augment tetracycline activity against tetracycline-resistant Pseudomonas aeruginos, creating the “thyme-tetracycline effect.” Disc diffusion assay, thin layer chromatography (TLC), and TLC bioassay techniques were used to show that thymol is the active component in the thyme extract that augments tetracycline activity against resistant Pseudomonas. This study also showed that thymol is a potent C4 HSL quorum sensing inhibitor. The collective data suggests a potential mode of action for the thyme-tetracycline effect: thymol appears to prevent MexAB-OprM efflux pump gene expression. By blocking MexAB-OprM expression, tetracycline antibiotic accumulation can occur within the cell, thus allowing cellular damage.

Major Histocompatibility Complex Class-II (MHC-II) molecules are critical regulators of adaptive immunity that present extracellular antigens required to activate CD4+ T cells. MHC-II are regulated at the level of transcription by master regulator, the Class II Transactivator (CIITA), whose association with the MHC-II promoter is necessary to initiate transcription. Recently, much research focused on novel mechanisms of transcriptional regulation of critical genes like MHC-II and CIITA; findings that the macromolecular complex of the 26S-proteasome is involved in transcription have been perhaps the most exciting as they impart novel functions to a well studied system. Proteasome is a multi-subunit complex composed of a 20S-core particle capped by a 19S-regulatory particle. The 19S contains six ATPases which are required for transcription initiation and elongation. We demonstrate that 19S ATPase-S6a inducibly associates with CIITA promoters. Decreased expression of S6a negatively impacts recruitment of the transcription factors STAT-1 and IRF-1 to the CIITA due to significant loss in histone H3 and H4 acetylation. S6a is robustly recruited to CIITA coding regions, where S6a binding coordinates with that of RNA polymerase II. RNAi mediated S6a knockdown significantly diminishes recruitment of Pol II and P-TEF-b components to CIITA coding regions, indicating S6a plays important roles in transcriptional elongation. Our research is focused on the ways in which accessibility to and transcription of DNA is regulated. While cancers are frequently linked to dysregulated gene expression, contribution of epigenetics to cancers remains unknown. To achieve metastatic ability, tumors alter gene expression to escape host immunosurveilance. MHC-II and CIITA expression are significantly downregulated in highly metastatic MDA-MB-435 breast cancer cells. This suppression correlates with elevated levels of the silencing modification H3K27me3 at CIITA and a significant reduction in Pol II recruitment. We observe elevated binding of the histone methyltransferase to CIITApIV and demonstrate this enzyme is a master regulator of CIITA gene expression. EZH2 knockdown results in significant increases in CIITA and MHC-II transcript levels in metastatic cells. In sum, transcriptional regulation by the 19S-proteasome and histone modifying enzymes represents novel mechanisms of control of mammalian gene expression and present novel therapeutic targets for manipulating MHC expression in disease.

Two cellular innate responses, the dsRNA protein kinase (PKR) pathway and the 2'-5' oligoadenylate synthetase (OAS)/RNase L pathway, are activated by dsRNAs produced by viruses and reduce translation of host and viral mRNAs. PKR activation results in eIF2a phosphorylation. As a consequence of eIF2a phosphorylation, stress granules (SGs) are formed by the aggregation of stalled SG proteins with pre-initiation complexes and mRNA. West Nile virus (WNV) infections do not induce eIF2a phosphorylation despite upregulation of PKR mRNA and protein suggesting an active suppression of PKR activation. Assessment of the mechanism of suppression of PKR activation in WNV-infected cells indicated that WNV infections do not induce PKR phosphorylation so that active suppression is not required. In contrast to infections with "natural" strains of WNV, infections with the chimeric W956 infectious clone (IC) virus efficiently induce SGs in infected cells. After two serial passages, the IC virus generated a mutant (IC-P) that does not induce SGs efficiently but does induce the formation of NS3 granules that persist throughout the infection. This mutant was characterized. 2'-5' oligoadenylate synthetases (OAS) are activated by viral dsRNA to produce 2-5A oligos that activate RNase L to digest viral and cellular RNAs. Resistance to flavivirus-induced disease in mice is conferred by the full-length 2'-5' oligoadenylate synthetase 1b (Oas1b) protein. Oas1b is an inactive synthetase that is able to suppress the in vitro synthetase activity of the active synthetase Oas1a. The ability of Oas1b to inhibit Oas1a synthetase activity in vivo and to form a heteromeric complex with Oas1a was investigated. Oas1b suppressed 2-5A production in vivo. Oas1a and Oas1b overexpressed in mammalian cells co-immunoprecipitated indicating the formation of heteromeric complexes by these proteins. Unlike mice, humans encode a single OAS1 gene that generates alternatively spliced transcripts encoding different isoforms. Synthetase activity has previously been reported for only three of the isoforms. The in vitro synthetase activity of additional OAS1 isoforms was analyzed. All tested isoforms synthesized higher order 2-5A oligos. However, p44A only produced 2-5A dimers which inhibit RNase L.

Neutrophil (PMN) inflammatory functions, including cell adhesion, diapedesis, and phagocyto-sis, are dependent on the mobilization and release of various intracellular granules/vesicles. In this study, I found that treating PMN with damnacanthal, a Ras family GTPase inhibitor, resulted in a specific release of secondary granules, but not primary or tertiary granules, and caused dy-sregulation of PMN chemotactic transmigration and cell surface protein interactions. Analysis of the activities of Ras members identified Ral GTPase as a key regulator during PMN activation and degranulation. In particular, Ral was active in freshly isolated PMN, while chemoattractant stimulation induced a quick deactivation of Ral that correlated with PMN degranulation. Over-expression of a constitutively active Ral (Ral23V) in PMN inhibited chemoattractant-induced secondary granule release. By subcellular fractionation, I found that Ral, which was associatedwith the plasma membrane under the resting condition, was redistributed to secondary granules after chemoattractant stimulation. Blockage of cell endocytosis appeared to inhibit Ral transloca-tion intracellularly. In conclusion, these results demonstrate that Ral is a critical regulator in PMN that specifically controls secondary granule release during PMN response to chemoattrac-tant stimulation.

Mollicutes (mycoplasmas) are pathogenic in a wide range of mammals (including humans), reptiles, fish, arthropods, and plants. Of the medically important mollicutes, Mycoplasma gallisepticum is of particular relevance to avian agriculture and veterinary science, causing chronic respiratory disease in poultry and turkey. Using two-dimensional electrophoresis based quantitative expression proteomics, the current study investigated the molecular mechanisms behind the phenotypic variability between a M. gallisepticum vaccine strain (6/85) and a competitive, virulent field strain (K5234), two strains which were indistinguishable using commonly accepted genetic methods of identification. Twenty-nine proteins showed a significant variation in abundance (fold change > 1.5, p-value < 0.01). Among others, the levels of putative virulence determinants were increased in the virulent K5234, while the levels of several proteins involved with pyruvate metabolism were decreased. It is hoped that the data generated will further the understanding of M. gallisepticum virulence determinants and mechanisms of infection, and that this may contribute to the optimization of diagnostic methodologies and control strategies.

Choline oxidase catalyzes the four-electron oxidation of choline to glycine betaine, a limited number of compounds that accumulate to high levels in cytoplasm to prevent dehydration and plasmolysis in adverse hyperosmotic environments. With this respect, the study of choline oxidase has potential for the development of therapeutic agents that inhibit the biosynthesis of glycine betaine, thereby rendering pathogenic bacteria susceptible to either conventional treatments or the immune system. In this study, the highly GC rich codA gene encoding for choline oxidase was cloned, expressed. The resulting enzyme was purified to high levels, allowing for detailed biochemical, mechanistic and structural characterizations. A chemical mechanism for the reaction catalyzed by choline oxidase was established by using kinetic isotope effects and viscosity effects as probes, in which the choline hydroxyl proton is not in flight in the transition state for CH bond cleavage. Furthermore, these experiments indicated that chemical steps of flavin reduction by choline and betaine aldehyde are rate limiting for the overall turnover of the enzyme. Further mechanistic characterization clearly suggested a hydride transfer mechanism that is fully quantum mechanical. The structure of choline oxidase was resolved at 1.86 Å resolution in collaboration with the group of Dr. Allen O. Orville, at the Georgia Institute of Technology, providing a structural framework that is consistent with the mechanistic studies. The results of these studies will be presented and discussed in the context of the Glucose-Methanol-Choline oxidoreductase enzyme superfamily, of which choline oxidase is a member. Previous structural and mechanistic studies of alcohol- and aldehyde-oxidizing enzymes with different cofactors, as well as the biotechnological and biomedical relevance of choline oxidase are presented in Chapter 1. Chapter 3-8 illustrate my studies on choline oxidase, including cloning, expression, purification and preliminary characterizations (Chapter 3), spectroscopic and steady state kinetics (Chapter 4), the determination of the chemical mechanism for alcohol oxidation and the investigation of the involvement of quantum mechanical tunneling (Chapter 5 and 6), the study of aldehyde oxidation (Chapter 7), and the structural determination of choline oxidase by x-ray crystallography (Chapter 8). Chapter 9 presents a general discussion of the data presented.

Obesity is a growing disorder in the United States, affecting over 60% of the population. We previously defined sympathetic nervous system (SNS) outflow from brain to white adipose tissue (WAT) using a viral transneuronal tract tracer. SNS innervation of WAT is the principle initiator of lipolysis, whereas decreases in sympathetic drive promote lipid accumulation. Which of the many origins of SNS outflow from brain to WAT results in SNS-mediated changes in lipid mobilization (increases in drive) or accumulation (decrease in drive) is unknown. Previous research indicates that sympathetic denervation blocks lipid mobilization; thus, rostral sites in the neuroaxis connected to WAT via the SNS may promote WAT lipid mobilization. The hypothalamic paraventricular nucleus (PVN) may play a role via its descending projections to the intermediolateral horn of the spinal cord. Therefore, the consequences of PVN lesions (PVNx) on WAT mobilization or accumulation were tested. PVNx resulted in increased lipid accumulation, indicated by increases in retroperitoneal (RWAT) , epididymal (EWAT) , and inguinal WAT (IWAT) pad masses, in fed hamsters, but PVNx did not block fasting (56 h)-induced lipid mobilization. Because adrenal medullary catecholamines, especially epinephrine, also play a minor role in lipid mobilization, we tested the contribution of catecholamine release on lipid mobilization through adrenal demedullation (ADMEDx), with and without PVNx, and found fastinginduced lipid mobilization was not blocked. There was, however, a suggestion that distal denervation of IWAT, with and without ADMEDx, partially blocked lipid mobilization. In addition, evidence suggests SNS also may be an important controller of fat cell proliferation. Surgical denervation of WAT triggers increases in fat cell number (FCN), but have not determined if this FCN increase is due to preadipocyte proliferation or differentiation of preadipocytes into mature fat cells. We also have not demonstrated what role sensory innervation may have in regulating white adipocyte proliferation. Therefore, the role of WAT sympathetic or sensory innervation on adipocyte proliferation was tested. The SNS but not sensory denervation triggered bona fide proliferation as indicated by bromodeoxyuridine plus AD3, a specific adipocyte membrane protein, colabeling. These and previous data suggest that the SNS plays a role in regulating adiposity.

Cytoplasmic membrane proteins CvaB and CvaA and the outer membrane protein TolC form the bacteriocin colicin V (ColV) secretion system in Escherichia coli. CvaB functions as an ATP-binding cassette transporter with nucleotide-binding motifs in the C-terminal domain (CTD). To study the role of CvaB-CTD in the ColV secretion, a truncated construct of this domain was made and over-expressed. Different forms of CvaB-CTD were obtained during purification, and were identified as monomer, dimer, and oligomer on gel filtration. Nucleotide binding was shown critical for the CvaB-CTD dimerization: oligomers could be converted into dimers by nucleotide bindings; the removal of nucleotide from dimers resulted in transient monomers followed by CTD oligomerization and aggregation; no dimer form could be cross-linked from the nucleotide-binding deficient mutant D654H. The spatial proximity of the Walker A site and ABC signature motif in CTD dimer was identified through disulfide cross-linking of mixed CvaB-CTD with mutants A530C and L630C, while mutations did not dimerize individually. Those results indicated that the CvaB-CTD formed a nucleotide-dependent head-to-tail dimer. Molecular basis of differential nucleotide bindings was also studied through bioinformatics prediction and biochemical verification. Through sequence alignment and homology modeling with bound ATP or GTP, it was found that the Ser503 and Gln504 on aromatic stacking region (Y501DSQ-loop) of CvaB-CTD provided two additional hydrogen-bonds to GTP, but not to ATP. Site-directed mutations of the S503A and/or Q504L were designed based on the model. While site-directed mutagenesis studies of Walker A&B sites or the ABC signature motif affected little on the GTP-binding preference, the double mutation (S503A/Q504L) on the Y501DSQ-loop increased both ATP-binding and ATPase activity at low temperatures. The double mutant showed slight decrease of GTP-binding and about 10-fold increase of the ATP/GTP-binding ratio. Similar temperature sensitivity in nucleotide-binding and activity assays were identified in the double mutant at the same time. Mutations on the Y501DSQ-loop did not affect the ColV secretion level in vivo. Together, the Y501DSQ-loop is structurally involved in the differential binding of GTP over ATP.

A limited understanding of iron uptake mechanisms is available for Streptococcus pyogenes, a hemolytic human pathogen capable of using a variety of hemoproteins in addition to ferric and ferrous iron. This study characterizes the transporters of iron-complexes siuADBG (for streptococcal iron uptake) and siaABC (for streptococcal iron acquisition). These ABC-type transporters are encoded by iron regulated operons and their protein products are homologous to components of heme and siderophore transporters found in both Gram-positive and Gram-negative bacteria. Mutants of the membrane permeases siuG and siaB were constructed and characterized. Mutations in both transporters demonstrated growth reduction in comparison to the parent strain when grown in complex medium containing iron in the form of hemoglobin. The addition of heme to the growth medium inhibited ferric uptake by the wild-type while the addition of protoporphyrin IX did not, suggesting that heme utilization as an iron source is responsible for the inhibition of ferric accumulation. Inactivation of siuG reduced the ability of heme to inhibit ferric incorporation by the cells. Inactivation of siaB in addition to siuG had a cumulative effect, indicating that both siu and sia transporters are involved in heme utilization. We also demonstrated that purified rSiaA, the surface receptor of SiaABC, binds heme and hemoglobin in vitro, and we propose a mechanism of heme binding by SiaA. Studies in a zebrafish infection model revealed that the siuG mutant was attenuated in producing disease. While the siaB mutant also presented virulence attenuation, infection by this mutant was characterized by an increase in the host inflammatory response. These observations show that iron acquisition is important for S. pyogenes virulence. We propose that the SiaABC and SiuADBG, together with the multi-metal transporter MtsABC, are involved in iron acquisition from different iron sources present in the human body, thus contributing to the survival and pathogenesis of S. pyogenes.