Enterohepatic Helicobacter species (EHS) are emerging infectious disease agents. Infection of the enterohepatobiliary tract of several mammals by this group of bacteria results in various pathological disorders. The availability of the Helicobacter hepaticus sequenced and annotated genome, allowed molecular characterisation of the responses of H. hepaticus to host factors such as bile. The adaptation/responses of the bacterium to bovine, porcine and human bile were investigated using proteomics and transcriptomics. Ninety-one different proteins were identified in the responses of H. hepaticus response to the three types of bile. These proteins participate in several key cellular processes including DNA replication; protein transcription, translation and folding; oxidative stress response; motility; virulence; and metabolism. In particular, the bacteria deployed several strategies such as inhibition of the TCA cycle and the electron transport chain as well as iron sequestration to ensure control of the levels of hydroxyl radicals. The results of this study revealed also the modulation by bile of the expression of H. hepaticus genes involved in response to oxidative stress and virulence. The responses of human HEp-2 and Huh7-derived cell-lines to H. hepaticus and Helicobacter bilis, respectively, were investigated employing proteomics and transcriptomics. One-hundred and twenty different proteins were differentially expressed in the responses of the human cells to the presence of Helicobacter spp. in the cell cultures. These proteins are involved in regulation of cell proliferation and structure; metabolism; protein transcription, translation and modification; stress response; and tumour induction. For example, in co-cultures of Huh7-derived cells and H. bilis, the activation of several mitochondrial and endoplasmic reticulum stress-related proteins and the dysregulation of several apoptosis effectors were suggested as mechanisms that could result in the death of the liver cells. Importantly, the differential expression of several tumour-related proteins by the Huh7 cells supported a possible role for Helicobacter spp. in liver cancer.

The dioxin receptor (DR), a transcription factor with basic-helix-loop-helix/PERARNTSIM (bHLH/PAS) homology domains, is activated by toxic xenobiotic ligands leading to severe physiological disturbances most of which are due to deregulation of receptor’s central role in normal development. Activation mechanisms of DR in the presence of exogenous or endogenous ligands are poorly understood. Elucidation of factors involved in the activation of the receptor would assist not only in development of an optimal measure for risk assessment of levels of common environmental pollutants but also in providing novel targets for therapeutic interventions. Posttranslational modifications (PTMs) play an indispensable role in all major signal transduction pathways by increasing the inventory of chemical modifications beyond those already present in the side-chains of common amino acids. Thus, by simple on/off or complex patterns generated by these PTMs, they control a myriad of different biological outcomes. Numerous studies that have suggested an important role of posttranslational modifications in DR activation has prompted a search in this direction, however, apart from phosphorylations at Ser36 and Ser68 no other PTM sites are known. Advanced mass spectrometry (MS)-based characterisation of PTMs is an established technique that can comprehensively provide an accurate cast of all PTM variants and their locations on a protein. This thesis reports the first MS-based comprehensive characterisation of all PTM sites of the purified latent DR and preliminary analysis of identified PTM sites of the activated DR in response to developmental signals (suspension-activated DR) and signals leading to toxic outcomes (ligand-activated DR). The PTM map of the latent DR revealed from this study comprises of 25 phosphorylations, 4 monomethyl-lysines, 2 dimethyl-lysines, 1 O-acetyl-serine and 2 O-sulfono-serines. Most of the phosphorylations and other PTMs were present in the conserved regions of the protein. Investigation of the activated samples of the receptor revealed loss of the above repertoire of modifications and possible presence of some rarer modifications such as O-acetyl-serines in suspension-activated instead of O-sulfonations and pyrophosphorylation at Ser716 in both suspension- as well as ligand-activated DR. A comprehensive mutagenesis study is in progress to understand the functional consequence of each of these modification sites and unravel the functional posttranslational system in DR signalling.

Research Doctorate - Doctor of Philosophy (PhD) / Membrane fusion events are a fundamental aspect of cellular biology and underpin important processes such as organ formation and fertilisation. Within the latter, proteins that are expressed on the egg surface which are responsible for mediating sperm recognition, binding and fusion to the egg, are yet to be fully determined. Evidence does however suggest that egg surface glycophosphatidylinositol (GPI)-anchored proteins play a role in sperm binding, whilst another class of proteins, known as tetraspanins, appear to be important in downstream events of membrane fusion. Of the tetraspanins, CD9 and CD81 have been identified as fulfilling roles in membrane fusion; identifications are however yet to obtained for the important GPI-anchored protein(s). This research aimed to identify and characterise egg surface proteins implicated in sperm-egg interaction, and embodied attempts to both identify the important GPI-anchored protein(s) as well as expand upon tetraspanin studies through investigations into mice lacking the tetraspanin CD151. Throughout this research, it was hypothesised that membrane fusion events of fertilisation parallelled those of enveloped virus – host cell fusion, for which rearrangement of surface protein thiols is essential. In vitro binding and fusion experiments were utilised as functional bioassays in the investigation of factors affecting sperm-egg interaction, such as tetraspanin deletion and the xenobiotic modification of cell surface thiols, while mass spectrometry (MS)-based proteomics and bioinformatics-based analyses were employed to compile oocyte protein databases and to identify candidate proteins responsible for mediating sperm-egg interaction, such as GPI-anchored proteins. It was determined that exposing oocytes to compounds with a capacity to alkylate cell surface thiols strongly inhibited sperm-egg binding. Additionally, while CD151 deletion had no effect on sperm-egg binding, the downstream events of membrane fusion were significantly impaired. Ovaries from CD151 null mice also exhibited abnormal phenotypes. In addition, a total of 11 identifications were obtained in the search for the GPI-anchored proteins expressed within eggs, however only 6 of these were deemed to be potential mediators of sperm-egg interaction. In conclusion, the experiments outlined herein demonstrate a novel inhibitory effect for specific xenobiotics on sperm-egg interaction, and correlate the inhibitory action of these compounds with their capacity to reduce cell surface thiol labelling. A novel role for CD151 in the mediation of sperm-egg fusion was also discovered, while at the same time the important GPI-anchored protein(s) implicated in sperm-egg binding may be among 6 identified potential candidates. Together the findings reiterate the consensus that oocytes possess a cell surface protein complex responsible for mediating sperm binding and fusion as separate events, and in light of the demonstrated importance of surface thiols, that events of sperm-egg membrane fusion parallel those of enveloped virus – host cell fusion.

Streptococcus gordonii is a primary coloniser of the tooth surface where it efficiently ferments carbohydrates at pH levels above 6.0. By not being able to maintain the pH of dental plaque to a level required for enamel dissolution, the dominance of S. gordonii in dental plaque is considered a sign of a healthy oral cavity. However, upon entering the bloodstream and encountering a rise in pH, S. gordonii may become pathogenic, being one of the major causative organisms associated with infective endocarditis. Proteome analyses of S. gordonii grown at steady state in a chemostat allowed the phenotypic changes associated with alterations in pH levels characteristic of these two environments to be determined. As an initial starting point to this study, a two-dimensional electrophoresis (2- DE) reference map of S. gordonii grown at pH 7.0 was produced. Although only 50% of the S gordonii genome was available in an annotated form during the course of this study, the closely related Streptococcus pneumoniae genome (with which S. gordonii shares 97.24% DNA sequence homology) had been completed in 2001. The use of both of these databases allowed many of the S. gordonii proteins to be identified by mass spectrometry. Four hundred and seventy six protein spots, corresponding to 250 different proteins, or 12.5% of the S. gordonii proteome, were identified, giving rise to the first comprehensive proteome reference map of this oral bacterium. Of the 250 different proteins, 196 were of cellular origin while 68 were identified from the extracellular milieu. Only 14 proteins were common to both compartments. Of particular interest among the 54 uniquely identified extracellular proteins was a homologue of a peptidoglycan hydrolase that has been associated with virulence in S. pneumoniae. Among the other proteins identified were ones involved in transport and binding, energy metabolism, translation, transformation, stress response and virulence. Twelve cell envelope proteins were identified as well as 25 others that were predicted to have a membrane association based on the presence of at least one transmembrane domain. The study also confirmed the existence of 38 proteins previously designated as �hypothetical� or with no known function. Mass spectral data for over 1000 protein spots were accumulated and archived for future analysis when sequencing of the S. gordonii genome is finally completed. Following the mapping of the proteome of S. gordonii, alterations in protein spots associated with growth of the bacterium at pH intervals of 0.5 units in the pH range 5.5 - 7.5 were determined. Only 16 protein spots were shown to be significantly altered in their level of expression despite the range of pH studied. Among the differentially expressed proteins was a manganese-dependent inorganic pyrophosphatase (PpaC), which regulates expression of adhesins required for coaggregation. The expression of PpaC was highest at pH 6.5 - 7.0, the pH of a healthy oral cavity, indicating that PpaC may play an important part in dental plaque formation. Another differentially expressed protein was the heat-inducible transcription repressor (HrcA). Alterations in HrcA were consistent with its role as a negative repressor in regulating heat-shock proteins at low pH, even though no changes in the level of heat-shock proteins were observed as the pH declined. This result gave rise to the hypothesis that the possible reason cariogenic bacteria, such as Streptococcus mutans, can out compete S. gordonii at low pH might simply be due to their ability to manipulate their proteome in a complex manner for survival and persistence at low pH, unlike S. gordonii. This may imply some prevailing level of genetic regulation that is missing in S. gordonii.

Doctor of Philosophy (PhD) / Proteomics is rapidly achieving recognition as a complimentary and perhaps superior approach to examine global changes in protein abundance in complex biological systems and the value of these techniques in neuropsychiatry is beginning to be acknowledged. Characterizing the brain’s regional proteomes provides a foundation for the detection of proteins that may be involved in disease-related processes. Firstly, optimal conditions were achieved for the application of two dimensional-gel electrophoresis (2D-GE)-based proteomics with postmortem human brain tissue. These optimized techniques were then applied to soluble fractions of adjacent grey and white matter of a single cytoarchitecturally defined area (Brodmann area 9; BA9) and of two adjacent regions of frontal white matter (BA9 and CC body) from healthy individuals. These normative proteomic comparisons highlighted the importance of correct tissue sampling, i.e. proper separation of regional white matter, as heterogeneity in the respective proteomes was demonstrated. Furthermore, they stressed the necessity for future molecular brain mapping studies. The main focus of this thesis however, was to examine the proteomes of brain regions specifically vulnerable to alcohol-induced damage underlying cognitive dysfunction. Alcoholic patients commonly experience mild to severe cognitive decline. It is postulated that cognitive dysfunction is caused by an alcohol-induced region selective brain damage, particularly to the prefrontal cortex. The cerebellum is increasingly recognized for its role in various aspects of cognition and alcohol–induced damage to the cerebellar vermis could indirectly affect neurocognitive functions attributed to the frontal lobe. We used a 2D-GE-based proteomics approach to compare protein abundance profiles of BA9 grey and white matter and the cerebellar vermis from human alcoholics (neurologically uncomplicated and alcoholics complicated with liver cirrhosis) and healthy control brains. Among the protein level changes observed are disturbances in the levels of a number of thiamine-dependent enzymes. A derangement in energy metabolism perhaps related to thiamine deficiency seems to be important in all regions analysed, even where there are no clinical or pathological findings of Wernicke-Korsakoff Syndrome. Evidence of oxidative changes was also seen in all regions and effects of liver dysfunction in the vermis found. However, overall, these results highlight the complexity of this disease process in that a number of different proteins from different cellular pathways appear to be affected. By identifying changes in protein abundance levels in the prefrontal grey and white matter and the cerebellar vermis, hypotheses may draw upon more mechanistic explanations as to how chronic ethanol consumption causes the structural and functional alterations associated with alcohol-related brain damage. Furthermore, by comparing these results, we may be able to isolate disturbances in molecular pathways specific to the brain damage caused by alcohol, severe liver dysfunction and thiamine deficiency.

[Formulae and special characters can only be approximated. Please see the pdf version of this abstract for an accurate reproduction.] Tumor necrosis factor (TNF) is a pleiotropic cytokine that mediates a long list of immunological and pathophysiological processes. TNF is produced by a wide variety of cells including immune and non-immune cells, however in most cell types TNF is not expressed prior to stimulation. The function of TNF is mediated via its trimeric domain by binding to TNF receptors that are found on most types of cells, especially of the haematopoietic systems, hence transpiring its effects on a wide variety of cells and organ systems. The cytotoxic (apoptosis) and pro-inflammatory (differentiation, proliferation and activation) functions of TNF are protective but can also result in pathological or deleterious consequences. A biallelic G to A transition polymorphism in the promoter region of TNF at nucleotide position 308 from the transcription start site is suggested to be involved in differential transcriptional regulation of TNF expression. The high TNF producing 308A allele is associated with susceptibility to or worse outcome of many infectious diseases in addition to autoimmune and other pathophysiological conditions. A previous study in our laboratory observed a selective affinity towards the polymorphic 308A allele by an EMSA protein(s) complex, named E. Several other protein complexes were found along with complex E and one of them was identified as Sp1. The identification of complex E was unsuccessful but it was hypothesized to play a major role as transcriptional activator in 308A allele individuals hence transpiring its effect in various pathophysiological states. In this study, the EMSA complexes observed in the TNF promoter region between nucleotides 322 to 283, encompassing the 308 polymorphism, is characterized. EMSA using mutated oligonucleotides mapped the binding sites of complexes B, C, D and E. TRANSFAC database search in addition to previous work revealed the identity of complex C as Sp1 but the rest of complexes remained unknown. Moreover, in contrast to our previous study, the protein(s) in the complex E was found to preferentially bind 308G nucleotide hence posing as a transcriptional repressor, resulting in decreased production state of TNF in 308G allele individuals than 308A allele individuals. In order to characterize putative transcription factors binding to the promoter region, first the biochemical characteristics such as the effects of temperature, salts and cations on DNA binding ability of EMSA complexes were studied. EMSA complexes B, C, DI and E required cations, probably Zn+2, to bind DNA. By optimizing a technique that couples EMSA with SDS-PAGE, the molecular weight of C, DI and E was determined. A novel technique that couples EMSA with IEF determined the pI of complexes B, C, D, DI and E. Although a commonly used technique of identifying unknown DNA-binding protein of interest, Yeast One-Hybrid assay, did not identify complex E, the novel identification method involving chromatography, two-dimensional electrophoresis, EMSA, mass spectrometry and database interrogation successfully identified TNF EMSA complex E as transcription factor Ying Yang 1 (YY1). Supershift EMSA confirmed complex E as YY1. In addition, the supershift assay showed presence of Sp1 and Sp3 in complex C. Similarly, complex DI is identified as Sp3. The novel method in identifying DNA-binding proteins is particularly useful as this technique allows identification of protein seen in EMSA without the need of extensive identification process. YY1 binds to a 6 base pair sequence, 5? TTGAGG 3?, from nt 295 to 290 of TNF promoter. The loss of affinity in 308A allele is caused by transition of underlined G nucleotide to A. The determined and described molecular weight of YY1 in literature is 60 kDa while the theoretical weight is 45 kDa. Both the determined and theoretical pI of YY1 is 5.8. YY1 is a multifunctional transcription factor implicated in both positive and negative regulation of gene expression as well as in initiation of transcription. It is ubiquitously expressed in growing, differentiated, and growth-arrested cells. Although future experiment is yet to establish in vivo presence of YY1 in TNF promoter, our study so far provides convincing evidence that the putative transcription factor that has selective affinity towards 308G allele is indeed YY1.

Research Doctorate - Doctor of Philosophy (PhD) / Membrane fusion events are a fundamental aspect of cellular biology and underpin important processes such as organ formation and fertilisation. Within the latter, proteins that are expressed on the egg surface which are responsible for mediating sperm recognition, binding and fusion to the egg, are yet to be fully determined. Evidence does however suggest that egg surface glycophosphatidylinositol (GPI)-anchored proteins play a role in sperm binding, whilst another class of proteins, known as tetraspanins, appear to be important in downstream events of membrane fusion. Of the tetraspanins, CD9 and CD81 have been identified as fulfilling roles in membrane fusion; identifications are however yet to obtained for the important GPI-anchored protein(s). This research aimed to identify and characterise egg surface proteins implicated in sperm-egg interaction, and embodied attempts to both identify the important GPI-anchored protein(s) as well as expand upon tetraspanin studies through investigations into mice lacking the tetraspanin CD151. Throughout this research, it was hypothesised that membrane fusion events of fertilisation parallelled those of enveloped virus – host cell fusion, for which rearrangement of surface protein thiols is essential. In vitro binding and fusion experiments were utilised as functional bioassays in the investigation of factors affecting sperm-egg interaction, such as tetraspanin deletion and the xenobiotic modification of cell surface thiols, while mass spectrometry (MS)-based proteomics and bioinformatics-based analyses were employed to compile oocyte protein databases and to identify candidate proteins responsible for mediating sperm-egg interaction, such as GPI-anchored proteins. It was determined that exposing oocytes to compounds with a capacity to alkylate cell surface thiols strongly inhibited sperm-egg binding. Additionally, while CD151 deletion had no effect on sperm-egg binding, the downstream events of membrane fusion were significantly impaired. Ovaries from CD151 null mice also exhibited abnormal phenotypes. In addition, a total of 11 identifications were obtained in the search for the GPI-anchored proteins expressed within eggs, however only 6 of these were deemed to be potential mediators of sperm-egg interaction. In conclusion, the experiments outlined herein demonstrate a novel inhibitory effect for specific xenobiotics on sperm-egg interaction, and correlate the inhibitory action of these compounds with their capacity to reduce cell surface thiol labelling. A novel role for CD151 in the mediation of sperm-egg fusion was also discovered, while at the same time the important GPI-anchored protein(s) implicated in sperm-egg binding may be among 6 identified potential candidates. Together the findings reiterate the consensus that oocytes possess a cell surface protein complex responsible for mediating sperm binding and fusion as separate events, and in light of the demonstrated importance of surface thiols, that events of sperm-egg membrane fusion parallel those of enveloped virus – host cell fusion.

Diss. (sammanfattning) Stockholm : Karol inst., 2004. / Härtill 4 uppsatser.

Thesis (Ph.D.)--University of Western Australia, 2004.

Thesis (Ph.D.)--University of Wollongong, School of Biological Sciences. / Typescript. Includes bibliographical references: leaf 269-331.