Pulmonary surfactant is a critical surface-active substance consisting of dipalmitoylphosphatidylcholine (DPPtdCho) and key apoproteins that are produced and secreted into the airspace from alveolar type II epithelial cells. Surfactant deficiency leads to severe lung atelectasis, ventilatory impairment, and gas-exchange abnormalities. These are features of the acute lung injury syndrome, characterized by a strong pro-inflammatory component where cytokines or bacteria infections greatly impair surfactant DPPtdCho biosynthesis. The key enzyme needed to produce surfactant DPPtdCho is a rate-limiting enzyme CTP: phosphocholine cytidylyltransferase (CCTalpha). Calmodulin (CaM), rather than disruption of an NH2-terminal PEST sequence, stabilizes CCTalpha from actions of the proteinase, calpain. Mapping and site-directed mutagenesis of CCTalpha uncovered a motif (LQERVDKVK) harboring a vital recognition site, Q243, whereby CaM directly binds to the enzyme. Mutagenesis of CCTalpha Q243 not only resulted in loss of CaM binding, but also led to complete calpain resistance in vitro and in vivo. These data suggest that CaM, by antagonizing calpain, serves as a novel binding partner for CCTalpha that stabilizes the enzyme under pro-inflammatory stress. We further show that CCTalpha does not undergo polyubiquitination and proteasomal degradation. Rather, the enzyme is monoubiquitinated at a molecular site (K57) juxtaposed near its NLS resulting in disruption of its interaction with importin, nuclear exclusion, and subsequent degradation within the lysosome. Importantly, by using CCTalpha-ubiquitin hybrid constructs that vary in the intermolecular distance between ubiquitin and the NLS, we show that CCTalpha monoubiquitination masks its NLS resulting in cytoplasmic retention. These results unravel a unique molecular mechanism whereby monoubiquitination governs the trafficking of a critical regulatory enzyme in vivo. Last, we identify FBXL2 as a novel F-box E3 ubiquitin ligase that targets CCTalpha for degradation. Interestingly, FBXL2 also interacts with CaM, and CaM directly disrupts CCTalpha and FBXL2 interaction. This study demonstrates in the first time that adenoviral gene transfer of CaM attenuates the deleterious effects of P. aeruginosa infection by improving several parameters of pulmonary mechanics in animal models of sepsis-induced acute pulmonary injury. Collectively, these studies reveal a novel regulatory mechanism for phosphatidylcholine synthesis that may provide important clues to understanding the pathobiology of acute lung injury.

Although arsenic is ubiquitous in the environment, certain forms of arsenic are added deliberately in ever increasing quantities. The addition of large quantities of the trivalent inorganic form (arsenite) could pose a serious hazard because of the toxicity of this form explicable in terms of its action of sulfhydryl containing enzymes and/or coenzymes. In the environment B.rsenite is rapidly converted to arsenate (the pentavalent inorganic form). Since a biological explanation for the oxidation of arsenite to arsenate was available only for cattle dips (a unique environment), this study was undertaken to examine sewage for the presence of arsenite oxidizing bacteria. The isolation of bacteria capable of arsenite oxidation would allow a study of cultural and physiological properties and thus provide information useful in making rational decisions regarding the continued use of inorganic arsenicals as pesticides; as well as elucidating one segment of the arsenic cycle. Thirty-four different strains of arsenite oxidizing pseudomonads were isolated from sewage and classified into two major groups, Pseudomonas fluorescens-arsenoxydans and Pseudomonas acidovorans-arsenoxydans, with three and four ecotypes in each group. One particularily rapid arsenite oxidizing strain (designated Pseudomonas acidovorans-arsenoxydans YE56) was extensively studied. A minimal, defined medium was used to study the relationship of temperature, pH, aeration and nutrition to growth of this organism versus the ability of the organism to convert arsenite to arsenate under the same conditions. The conversion of arsenite to arsenate in YE56 was shown to be due to the appearance at stationary phase of an enzyme and/or component of the electron transport system when the organism is grown in chemically defined medium. In contrast, induction of the arsenite oxidizing system occurs in late exponential growth phase when the organism is grown in a rich medium. Thus, even though cell populations may never reach stationary phase in sewage, the ability of organisms to oxidize arsenite is probably constant. No energy could be detected from the oxidation of arsenite as measured by increase in growth rate or total cell yield. The adaptability of this organism to the changing environmental conditions of a sewage plant helps explain the findings that pseudomonads are the predominant species in sewage. A simple, unambiguous method for the separation of arsenite, arsenate and phosphate, using a combination of thin layer chromatography and paper chromatography, is described which makes it possible for investigators to define arsenic determinations to include the form (organic or inorganic), oxidation state (trivalent or pentavalent) and the quantity present in the samples.

Utilization of toluene by Pseudomonas putida as its sole carbon and energy source affects morphology, outer membrane protein composition, and glycolipid production. Two strains of P. putida were found to utilize toluene and to coexist in continuous and batch culture. The two strains were designated translucent and opaque, based upon their readily identifiable coloration when grown on Luria agar. The translucent strain was the dominant strain in continuous culture conditions. The outer membrane proteins of P. putida were separated by sodium dodecyl sulphate polyacrylamide gel electrophoresis. When toluene is the carbon and energy source, the trend in protein composition was towards a general increase in concentration of lower molecular weight proteins (wt). A similar decrease occurred in the concentration of higher molecular weight proteins in the range of 70X104-9X104 mol wt. P. putida produces glycolipids when grown on toluene as a sole carbon and energy source. Three glycolipids have been isolated from chemostat and batch culture spent media, using thin layer chromatography on silica gel GF254· The glycolipids are believed to be previously reported mono- and di-rhamnolipids that function as biosurfactants. The release of glycolipid into the media is believed to function to emulsify toluene, aiding in toluene uptake.

Pseudomonas aeruginosa et Candida albicans sont deux pathogènes fréquemment isolés dans les communautés microbiennes des unités de soins intensif. Nous avons auparavant montré que la colonisation des voies aériennes par C. albicans protégeait contre les lésions pulmonaires induites par P. aeruginosa. Le but de cette étude était de caractériser les mécanismes cellulaires et moléculaires responsables de la protection des voies aériennes induite par C. albicans. La colonisation des voies aériennes par C. albicans permet le recrutement et l'activation de cellules NK, de cellules lymphoïdes innées, de macrophages et de cellules dendritiques. Ce recrutement est associé à la sécrétion d'IL-22. L'inhibition de l'IL-22 est responsable d'une perte de la protection conférée par C. albicans. Nous avons identifié par cytométrie en flux que les cellules lymphoïdes innées étaient la seule source cellulaire d'IL-22. La déplétion spécifique des cellules lymphoïdes innées par des anticorps anti-CD90.2 était responsable d'une diminution de la sécrétion d'IL-22 et d'une diminution de la survie lors de la pneumonie à P. aeruginosa. Nos résultats démontrent que la production d'IL-22, principalement par les cellules lymphoïdes innées, est une étape inductible majeure dans la protection contre les lésions pulmonaires induites par P. aeruginosa. Cette cytokine pourrait ainsi représenter une cible thérapeutique pour prévenir les lésions pulmonaires induites par P. aeruginosa. / Pseudomonas aeruginosa and Candida albicans are two pathogens frequently encountered in the intensive care unit microbial community. We have demonstrated that C. albicans airway exposure protected against P. aeruginosa-induced lung injury. The goal of this study was to characterize the cellular and molecular mechanisms associated to C. albicans-induced protection. Airway exposure by C. albicans led to the recruitment and activation of NK cells, innate lymphoid cells (ILC), macrophages and dendritic cells. This recruitment was associated with the secretion of IL-22 whose neutralization abolished C. albicans-induced protection. We identified, by flow cytometry, ILCs as the only cellular source of IL-22. Depletion of ILCs by anti-CD90.2 antibodies was associated with a decreased IL-22 secretion and an impaired survival after P. aeruginosa challenge. Our results demonstrate that production of IL-22, mainly by ILCs, is a major and inducible step in protection against P. aeruginosa-induced lung injury. This cytokine may represent a clinical target in Pseudomonas aeruginosa induced lung injury.

Psychotrophic bacteria produce heat-stable lipase, protease, and phospholipase. Pervious studies indicate the production of multiple enzymes in several strains of Pseudomonas fluorescens, but conclusive evidence is lacking. The influence of culture conditions on the production and thermostability of phospholipase, protease, and lipase was investigated in 17 raw milk and environmental isolates. Production and thermostability of the enzymes were influenced by strain, stage of growth, and the culture medium. Cross-reactivity of antibodies raised to a purified protease and a commercial lipase indicated the immunological diversity of the enzymes. Protease purification was undertaken to investigate the production of multiple proteases within a single strain. A single monomeric protease with a molecular weight of 52 kDa was purified from P. fluorescens RO98. Biochemical characterization of the enzyme revealed that it was a zinc-metallo acidprotease with pH and temperature optima of 5.0 35°C, respectively. The enzyme was thermostable with a D55 of 41 min and a D62.5 of 18 h. Although sensitive assays exist for proteases, they are not suitable for detection of protease activity in milk in the presence of milk proteins. Existing immunoassays approach the required sensitivity but take about 6 h and cannot distinguish between active and inactive enzyme. An immunoassay that can be completed within 2 h and that can detect and distinguish both total and active enzyme was explored. The ratio of these two forms gives insight into the history of the milk. The ability of the purified protease to hydrolyze hydrophobic peptides associated with bitterness in Cheddar cheese was also investigated. Results demonstrated that the protease had the potential to debitter Cheddar cheese because it was able to hydrolyze the bitter peptides commonly found during aging. Two lipolytic enzymes with molecular weights of 50 (Pf-lip1) and 12 kDa (Pf-lip2) were purified from P. fluorescens RO98. Differences were observed in their biochemical properties. D62.5-values of 12.7 and 29.9 h were determined for Pf-lip1 and Pf-lip2, respectively. Pf-lip1 preferred longer chain length fatty acids, and Pf-lip2 preferred shorter chain length substrates. Pf-lip1 hydrolyzed milk fat and emulsified triolein, but Pf-lip2 did not, indicating that the latter was an esterase. This information is of significance to the dairy industry because activity tests that assay both the lipolytic enzymes need to be used in order to direct raw milk to short shelf-life products during processing and ensure quality of long shelf-life products

Doctor of Philosophy / Cystic fibrosis (CF) is the most common inherited lethal disorder among Caucasian populations. Chronic pulmonary infections, particularly from Pseudomonas aeruginosa, are the major determinant of the morbidity and mortality of people with CF. It is generally accepted that people with CF acquire this pathogen independently from their surrounding environment, and that individual CF patients carry unique strains different from others. The spread of this pathogen from patient to patient is thought to be rare and occurs particularly among closely contacted cases such as CF siblings. However, over the past decade, there have been several reports of an emergence of clonal P. aeruginosa strains commonly found infecting a number of CF patients. One such report is from the CF paediatric clinic at the Royal Children’s Hospital in Melbourne in which more than half of the patients were infected with a single strain or clone, subsequently called Australian epidemic strain 1 or AES-1. A preliminary survey showed that AES-1 had spread extensively along the Australian eastern seaboard among CF patients attending other CF centres in Melbourne, Sydney and Brisbane, including adult patients at the Royal Prince Alfred Hospital (RPAH), Sydney. Another clonal strain, subsequently called AES-2, was identified in both CF adults and children at the Prince Charles Hospital and the Royal Children’s Hospital, in Brisbane. The total extent of prevalence of the AES-1 and AES-2 strains at the RPAH as well as the clinical status of patients who carried these strains was unknown. Moreover, the pathogenicity of these two clonal strains had not been investigated. The studies presented in this thesis investigated the prevalence of these clonal strains among CF patients attending the adult CF clinic at RPAH, Sydney by using pulsed-field gel electrophoresis. Overall, 50% of 112 patients with P. aeruginosa were found to be infected with clonal strains. The AES-1 and AES-2 strains were identified in 38% and 5% of the patients respectively. Two new clonal strains, called Sydney-1 and Sydney-2, were also identified. Patients with clonal strains had a significant increase in their number of exacerbations and hospitalisation days, and tended to have lower pulmonary functions when compared to patients infected with non-clonal strains. By using a variety of bioassays to examine the pathogenicity of the clonal and non-clonal strains, it was found that both AES-1 and AES-2 produced more virulence factors and were more resistant to antibiotics when compared to the non-clonal strains. AES-1 and AES-2 were associated with increased production of proteases, including elastase, alkaline protease and protease IV. Overall the results presented in this thesis suggest that there may be a link between virulence and transmissibility of this pathogen. The studies presented in this thesis also compared the biofilm forming capacities of the AES-1 and non-clonal isolates. AES-1 was shown to have greater biofilm-forming capacity than the non-clonal strains, when they were grown on a glass surface, suggesting a possible association between clonality and biofilm formation. A model for the study of bacteria grown in conditions similar to CF sputum was also developed. P. aeruginosa grown in this model was found to develop into clumps which may be comparable to the biofilm structure in the CF lung. This model was shown to be beneficial for transcriptomic and proteomic studies which are underway within the research group. AES-1 was also found to have phenotypic variations between isolates. By applying the amplified fragment length polymorphism technique, more subtypes of this clone were revealed. However, these detected subtypes did not correlate with the different phenotypes, suggesting minor mutations such as single point polymorphisms may be responsible for the phenotypic diversity within the clone. The final part of this thesis was devoted to examining the safety of a novel CF treatment: hypertonic saline (HS) inhalation. HS was shown to increase airway mucociliary clearance, while increased osmolarity associated with the use of HS was also shown to have an inhibitory effect on the formation of biofilms. Findings in this study proved that there was no evidence of strain selection in patients who received the long-term treatment with HS. The study also demonstrated that AES-1 was significantly more persistent in the CF lung than the non-clonal strains. The present thesis not only defines the clonal strains of P. aeruginosa and their implications for infected patients, but also provides a general understanding into the pathogenesis of both clonal and non-clonal strains infecting CF lungs.

The pathogenic bacterium Pseudomonas aeruginosa uses a variety of highly efficient chelating compounds (siderophores) to acquire sufficient iron for growth and virulence. These siderophores can either be endogenous or acquired from exogenous sources such as other bacteria or fungi. The transport of the endogenous siderophore pyoverdine activates a signal-transduction pathway that increases the synthesis of both the ferripyoverdine receptor protein (FpvA) and pyoverdine itself. Signal-transduction systems similar to this have three specific proteins involved: a receptor protein specific for one siderophore in the outer membrane, an anti-sigma factor in the cytoplasmic membrane and a sigma factor that activates gene expression in the cytoplasm. The aim of the research presented in this thesis was to study the roles of the proteins in three different iron uptake and signalling pathways of P. aeruginosa. The substrates for each receptor protein were confirmed and the roles of each protein in the pathways were compared to the P. aeruginosa pyoverdine signalling pathway. The pyoverdine, desferrioxamine and ferrichrome transport pathways were studied to find whether interactions occur between them and if so, the mechanism(s) for that interaction. Furthermore, a technique for analysing gene expression of P. aeruginosa in sputum from the cystic fibrosis (CF) lung was developed. This technique was subsequently used to study the levels of iron responsive gene expression. The receptor, sigma factor and anti-sigma factors were all found to have a role in the siderophore-induced expression of their own signalling pathway. The experimental data provide evidence of similarities in the roles of the sigma and receptor proteins within each pathway but different roles for the anti-sigma factors. In the absence of the cognate sigma factor or anti-sigma factor the expression of the desferrioxamine and ferrichrome receptors could not be upregulated. Without its cognate sigma factor fpvA could no longer be upregulated in the presence of pyoverdine. However, unlike the other systems, in the absence of the cognate anti-sigma factor, expression of fpvA was always observed. This is consistent with the anti-sigma factors being required for the activity of the cognate sigma factor in the ferrichrome and desferrioxamine signalling pathways but not the pyoverdine signalling pathway. The siderophore signalling pathways were found to be upregulated in the presence of multiple siderophores, but generally to a lesser extent than if only one siderophore was available. This suggests that in the presence of multiple siderophores, P. aeruginosa uses all available iron chelators. The study of the role of the receptor, sigma factor and anti-sigma factor into these effects indicate sigma factor competition for RNA polymerase has a major role in the effects of multiple siderophores on pathways upregulation. The gene expression studies of P. aeruginosa in sputum from the lungs of CF patients provided support for the hypothesis that the bacteria were growing in an environment where iron levels were sufficient for bacterial growth, but not storage of iron. The expression of the sigma factor gene pvdS that is required for pyoverdine synthesis was studied because expression of this gene is a sensitive reporter of intracellular iron levels. It was found to be downregulated in bacteria in sputum compared to laboratory grown bacteria. This result suggests the bacteria are inhabiting a more iron-replete environment within the lung. This finding advances our understanding of the CF lung environment and the impact it has on P. aeruginosa infection. This knowledge has medical implications for the development of novel therapies to combat P. aeruginosa infection.

Biodegradation of poorly water soluble hydrocarbons, such as n-alkanes and polycyclic aromatic hydrocarbons (PAHs) is often limited by the low availability of the pollutant to microbes. Adhesion of microorganisms to the oil-water interface can influence this availability. Our approach was to study a range of compounds and mechanisms to promote the adhesion of a hydrophilic PAH degrading bacterium, Pseudomonas fluorescens LP6a, to an oil-water interface and examine the effect on biodegradation of phenanthrene by the bacteria. The cationic surfactants cetylpyridinium chloride (CPC), poly-L-lysine and chlorhexidine gluconate (CHX) and the long chain alcohols 1-dodecanol, 2-dodecanol and farnesol increased the adhesion of P. fluorescens LP6a to n-hexadecane from ca. 30% to ca. 90% of suspended cells adhering. The alcohols also caused a dramatic change in the oil-water contact angle of the cell surface, increasing it from 24° to 104°, whereas the cationic compounds had little effect. In contrast, cationic compounds changed the electrophoretic mobility of the bacteria, reducing the mean zeta potential from –23 to –7 mV in 0.01M potassium phosphate buffer, but the alcohols had no effect on zeta potential. This results illustrate that alcohols acted through altering the cell surface hydrophobicity, whereas cationic surfactants changed the surface charge density. Phenanthrene was dissolved in heptamethylnonane and introduced to the aqueous growth medium, hence forming a two phase system. Introducing 1-dodecanol at concentrations of 217, 820 or 4100 mg/L resulted in comparable increases in phenanthrene biodegradation of about 30% after 120 h incubation with non-induced cultures. After 100 h of incubation with LP6a cultures induced with 2-aminobenzoate, 4.5% of the phenanthrene was mineralized by cultures versus more than 10% by the cultures containing initial 1-dodecanol or 2-dodecanol concentrations of 120 or 160 mg/L. The production and accumulation of metabolites in the aqueous phase responded similarly to the addition of 1-dodecanol. Further experiments showed that the positive influence of the alcohols could not be attributed to the changes in surface and interfacial tension or increase in biomass concentration. The results suggest that enhanced adhesion of bacterial cells to the oil-water interface was the main factor responsible for the observed increase in phenanthrene biodegradation by P. fluorescens LP6a. / Chemical Engineering

Butane-grown Pseudomonas butanovora oxidized butane by a soluble butane monooxygenase through the terminal pathway yielding 1 -butanol as the predominant product. Alcohol dehydrogenases (ADHs) involved in butane oxidation in P. butanovora were purified and characterized at the biochemical, genetic and physiological levels. Butane-grown P. butanovora expressed a type I soluble quinoprotein 1 -butanol dehydrogenase (BOH), a soluble type II quinohemoprotein 1 -butanol dehydrogenase (BDH) and an NAD���-dependent secondary ADH. Two additional NAD���-dependent secondary ADHs were also detected in cells grown on 2-butanol and lactate. BDH was purified to near homogeneity and characterized. BDH is a monomer of 66 kDa consisting of one mole of pyrroloquinoline quinone (PQQ) and 0.25 mole of heme c as the prosthetic groups. BOH was partially purified and its deduced amino acid sequence suggests a 67-kDa ADH containing a PQQ as a cofactor. BOH and BDH exhibited high activities and preference towards I -butanol and fair preference towards butyraldehyde. While BDH could not oxidize 2-butanol, BOH is capable of 2-butanol oxidation and has a broader substrate range than that of BDH. Genes encoding BOH and BDH and their deduced amino acid sequences were identified. BOH and BDH mRNAs and 1-butanol oxidation activity were induced when cells were exposed to butane. Primary C��� and C��� alcohols were the most effective inducers for boh and bdh. Some secondary alcohols, such as 2-butanol, were also inducers for BOH mRNA, but not for BDH mRNA. Insertional inactivation of boh or bdh affected unfavorably, but did not eliminate, butane utilization in P. butanovora. The P. butanovora mutant strain with both boh and bdh genes disrupted was unable to grow on butane and 1-butanol. This result confirmed the involvement of BOH and BDH in butane and 1-butanol metabolism in P. butanovora. Roles of B011 and BDH in butane and 1-butanol metabolism were further studied at the physiological level. There are no substantial differences between BOH and BDH in the mRNA expressions in response to three different 1- butanol levels tested and in their abilities to respond to 1-butanol toxicity. Different bioenergetic roles of BOH and BDH in butane and 1-butanol metabolism were suggested. A model of 1 -butanol- dependent respiratory systems was proposed where the electrons from 1 -butanol oxidation follow a branched electron transport chain. The role of BOH was suggested to function primarily in energy generation because B011 may couple to ubiquinone with the electrons being transported to a cyanide-sensitive terminal oxidase. BDH may be more important in the detoxification of 1 -butanol because the electrons from BDH may be transferred to a terminal oxidase system that is less sensitive to cyanide, which is not capable of energy generation. / Graduation date: 2003

I have investigated the evolutionary response of Pseudomonas aeruginosa to salt (NaCl) stress, and the physiological mechanisms responsible for this adaptation. Populations of P. aeruginosa founded from the same ancestral genotype were selected at three different concentrations of NaCl, low, moderate and high for about 660 generations with four independent replicates for each concentration. Adaptation was measured as the fitness of the evolved populations relative to the ancestor assessed in direct, head-to-head competition experiments conducted in the same environment in which they were selected (direct response) as well as in all alternative environments (correlated response). Results suggest that selection in each salt environment led to adaptation to that environment and a modest degree of specialization that evolved because correlated responses to selection were smaller than direct responses. In order to identify the physiological mechanisms contributing to the populations' adaptation in high NaCl concentration, I chose a sample of evolved lines that showed the strongest evidence for specialization to salt and competed them against the common ancestor in KCl and sucrose. Results suggested that increased Na+ /H+ antiporter activity is probably the primary mechanism behind adaptation to high NaCl concentration, however alternative mechanisms cannot be excluded. Tolerance curves, which measure the performance of a genotype across a gradient of salt concentrations, suggested no change in the high salt group’s ability to tolerate extreme concentrations of NaCl. We conclude that high salt evolved population showed improvements to its ionic/osmotic stress resistance strategies mainly to Na+ efflux strategies but with no changes to salt niche.