Parasites of phylum Apicomplexa cause devastating diseases on a global scale. Toxoplasma gondii, the etiological agent of toxoplasmosis, and Plasmodium falciparum, the most virulent agent of human malaria, have the most substantial effects on human health and are the most widely studied. The success of these parasites is due in part to a sophisticated molecular arsenal that supports a variety of novel biological processes including a unique form of host cell invasion. Accessing the protective environment of the host cell is paramount to parasite survival and is mediated through an active invasion process: the parasite propels itself through a circumferential ring known as the moving junction (MJ) formed between its apical tip and the host cell membrane. The MJ ring is comprised of a parasite surface protein (AMA1) that engages a protein secreted by the parasite into the host cell and presented on the host cell surface (RON2). Thus, through an intriguing mechanism the parasite provides both receptor and ligand to enable host cell invasion. Prior to the studies described herein, the characterization of the AMA1-RON2 association was limited to low-resolution experiments that provided little insight into the functional and architectural details of this crucial binary complex. Towards elucidating the mechanism of AMA1-RON2 dependent invasion, I first structurally characterized T. gondii AMA1 bound to the corresponding binding region of RON2; analysis of the AMA1-RON2 interface along with biophysical data revealed an intimate association likely capable of withstanding the shearing forces generated as the parasite dives through the constricted MJ ring. To investigate the role of the AMA1-RON2 complex across genera, species and life-cycle stages, I next characterized the AMA1-RON2 complex from a distantly related genus within Apicomplexa (Plasmodium) and from a divergent pairing within T. gondii. By combining structural, biophysical and biological data, I was able to generate a detailed model describing the role of AMA1 and RON2 in MJ dependent invasion, which is currently supporting efforts to develop novel vaccines and cross-reactive small molecule therapeutics. / Graduate / 0487 / tonkin.ml@gmail.com

Post-translational modification is an intracellular process that modifies the properties of proteins to extend the range of protein function without spending energy in de novo peptide synthesis. There are many post-translational modifications, for example, phosphorylation, ubiquitination, and S-nitrosylation. S-Nitrosylation is a post-translational modification which adds nitric oxide (NO) to sulfhydryl groups at cysteine residues to form S-nitrosothiol (SNO), and is required for plant immunity and fertility. Cellular NO changes between a pool of free NO and bound SNO. During pathogen infection, nitrosative stress in plants is mainly controlled by Snitrosothiolglutathione reductase (GSNOR) via the decomposition of GSNO. GSNOR is an alcohol dehydrogenase type 3 (ADH3) which has both GSNOR and formaldehyde dehydrogenase (FDH) activities. The roles of S-nitrosylation in mammals overlap with those in plants. This conservation led us to explore the relationship between S-nitrosylation, immune response, and fertility in Drosophila melanogaster as it might prove to be a good genetic model for further analysis of the role of S-nitrosylation in animals. I have identified fdh as the likely gsnor in D. melanogaster and have knocked this out using an overlapping deficiency technique in order to observe the effect on immunity and fertility. There are two main pathways in the Drosophila innate immune response, the Toll pathway for protecting against gram-positive bacteria and fungi, and the Imd pathway against gram-negative bacteria. I have investigated the effect of removing GSNOR on sensitivity to gramnegative bacteria (Escherichia coli and Erwinia carotovora) by septic and oral infection, and to fungi (Beauveria bassiana). Susceptibility to infection by the gram negative bacteria was similar to wild-type but susceptibility to B. bassiana was increased. This increase in susceptibility correlated with reduced anti-fungal antimicrobial peptide (AMP) production after B. bassiana infection. This suggests that GSNOR might be required for the normal activity of the Toll pathway or novel Toll-independent processes. We also observed that gsnor knockout impairs fertility and development of embryos.

Fcγ receptors (FcγR) which recognize the Fc fraction of IgG play key roles in the modulation of a range of cellular responses as part of the host defense against foreign microbes and antigens. An important function of FcγR is to mediate internalization of soluble IgG-containing immune complexes via endocytosis. The mechanisms of internalization and intracellular transport of FcγR after internalization are less clear. In this thesis, I investigated the trafficking behaviours of human FcγRIIA and FcγRIIB2 upon clustering with immune complexes. In Chapter 3, I demonstrate FcγRIIA, when engaged with multivalent heat aggregated IgG (agIgG), is delivered along with its ligand to lysosomal compartments for degradation, whereas FcγRIIB2 becomes dissociated from the ligand and routed separately into a recycling pathway. FcγRIIA sorting to lysosomes requires receptor multimerization, but does not require either Src family kinase (SFK) activity or receptor ubiquitylation. Upon co-engagement, these two receptors are sorted independently to distinct final fates after dissociating from their co-clustering ligand. In Chapter 4, I show that while the ubiquitin-conjugating system is required for FcγRIIA-mediated endocytosis, it is not required for FcγRIIB2 endocytosis. FcγRIIB2 internalizes immune complexes at a faster rate than FcγRIIA and accelerates the endocytosis of FcγRIIA upon receptor co-engagement. Taken together, these results reveal fundamental differences in the trafficking behaviour of FcγRIIA and FcγRIIB2 both during the initial induction of endocytosis as well as during subsequent intracellular sorting.

Fcγ receptors (FcγR) which recognize the Fc fraction of IgG play key roles in the modulation of a range of cellular responses as part of the host defense against foreign microbes and antigens. An important function of FcγR is to mediate internalization of soluble IgG-containing immune complexes via endocytosis. The mechanisms of internalization and intracellular transport of FcγR after internalization are less clear. In this thesis, I investigated the trafficking behaviours of human FcγRIIA and FcγRIIB2 upon clustering with immune complexes. In Chapter 3, I demonstrate FcγRIIA, when engaged with multivalent heat aggregated IgG (agIgG), is delivered along with its ligand to lysosomal compartments for degradation, whereas FcγRIIB2 becomes dissociated from the ligand and routed separately into a recycling pathway. FcγRIIA sorting to lysosomes requires receptor multimerization, but does not require either Src family kinase (SFK) activity or receptor ubiquitylation. Upon co-engagement, these two receptors are sorted independently to distinct final fates after dissociating from their co-clustering ligand. In Chapter 4, I show that while the ubiquitin-conjugating system is required for FcγRIIA-mediated endocytosis, it is not required for FcγRIIB2 endocytosis. FcγRIIB2 internalizes immune complexes at a faster rate than FcγRIIA and accelerates the endocytosis of FcγRIIA upon receptor co-engagement. Taken together, these results reveal fundamental differences in the trafficking behaviour of FcγRIIA and FcγRIIB2 both during the initial induction of endocytosis as well as during subsequent intracellular sorting.

Much of our current mechanistic understanding of the innate immune response in animals has grown out of empirical work in insect models, especially the fruit fly Drosophila melanogaster. The mainstream understanding of the fly immune response to bacteria has been that it exists in two parts; a cellular and a humoral response. Drosophila also harbor substantial genetic variation for antibacterial defense and investment in immunity is thought to involve a costly trade-off with life history traits, including development, life-span and reproduction. My first study (chapter 2) aimed to understand the way in which insects invest in fighting bacterial infection. We selected for survival following systemic infection with the opportunistic pathogen, Pseudomonas aeruginosa in wild-caught D. melanogaster over 10 generations. We then examined genome wide changes in expression in the selected flies relative to unselected controls, both of which had been infected with the pathogen to specifically identify the genetic basis of the evolved immune response. In response to selection, population level survivorship to infection increased from 15% to 70%. The evolved capacity for defense was costly as evidenced by reduced longevity and larval viability and a rapid loss of the trait once selection pressure was removed. Counter to expectation, we observed more rapid developmental rates in the selected flies. Selection associated changes in expression of genes with dual involvement in developmental and immune pathways suggest pleiotropy as a possible mechanism for the positive correlation. We also found that both the Toll and Imd pathways work synergistically to limit infectivity and that cellular immunity plays a more critical role in overcoming P. aeruginosa infection than previously reported. Females usually produce a more robust immune response and are often less susceptible to infection. This female bias has been documented in humans, mice and some birds and reptiles. The most common explanation is that males increase their mating success at the cost of immune investment whilst females invest in immunity to maximize life-time egg production. In insects, however, there is growing evidence of male-biased immune performance. Using fly survival data from my first study, I found that males exhibited higher post-infection survival than females. In my second study (chapter 3), I related these differences in survival rate to changes in gene transcription. Firstly, we examined the expression of a set of immunity genes in both sexes in the presence and absence of infection. We found that male-biased survival may be partially attributable to a higher baseline expression of immune genes in males. Contrary to previous published work, we found that immune gene expression was readily induced in flies upon exposure to P. aeruginosa and that the two sexes responded in a similar manner. Lastly, we found that selection altered the expression of genes in males alone and only in the presence of infection. Together our findings suggest a superior immune response in male Drosophila. Wolbachia pipientis is an obligate intracellular bacterium capable of spreading itself through populations by manipulating the reproduction of its hosts. The Wolbachia strain wMelPop, which reduces longevity in D. melanogaster, has been introduced into the Dengue virus mosquito vector, Aedes aegypti, as a strategy to reduce disease transmission. The infecting Wolbachia halve the lifespan of the mosquito and induce numerous behavioral and physiological abnormalities including heightened locomotor activity and an age dependent reduction in blood feeding success. In my third study (chapter 4), we aimed to understand the mechanism underpinning these changes and hence chose to explore how Wolbachia may be interacting with the insect’s nervous and muscle tissue. Because wMelPop over-replicates in Drosophila, first we measured the bacterial density in A. aegypti. We found that there was a relationship between some of the feeding associated defects in the mosquito and the density of Wolbachia in the nervous and muscle tissue. Next, we carried out a series whole genome profiling experiments based on the head and muscle tissues to identify mosquito pathways affected by the microbe. Key findings that may relate to the phenotypes of interest include increased expression of genes relating to muscle contraction and synthesis of the neurotransmitter dopamine. Other novel findings that may not relate directly to the phenotypes of interest include evidence of a strong local tissue based immune response and widespread changes in expression of mosquito methylation and acetylation associated genes. We then used then amplification of inter-methylated sites (AIMS test) to obtain DNA fingerprints representative of the methylome of A. aegypti infected and uninfected with wMelPop. The presence of wMelPop caused hypermethylation in loci where they were not methylated in uninfected mosquitoes.

Diss. (sammanfattning) Uppsala : Sveriges lantbruksuniv. / Härtill 4 uppsatser.

Ebola virus (EBOV) causes severe disease in humans characterized by high case fatality rates and significant immune dysfunction. A hallmark of EBOV infection is the formation of viral inclusions in the cytoplasm of infected cells. These inclusions contain the EBOV nucleocapsids and are sites of viral replication and nucleocapsid maturation. Although there is growing evidence that viral inclusions create a protected environment that fosters EBOV gene expression and genome replication, little is known about their role in the host response to infection. The cellular stress response is an antiviral strategy that leads to stress granule (SG) formation and translational arrest mediated by the phosphorylation of the alpha subunit of eukaryotic translation initiation factor 2 (eIF2α). Related to this response is the post-transcriptional regulation of RNA mediated by stability elements called AU-rich elements (AREs) and their associated binding proteins (ARE-BPs), many of which are found in SGs. Because these processes have antiviral implications, many viruses have evolved strategies to interfere with SG formation, or appropriate ARE-BPs to benefit viral replication. However, it is unknown if EBOV interacts with these cellular systems. Here, we show that SG proteins were sequestered within EBOV inclusions where they formed distinct granules that colocalized with viral RNA. The inclusion-bound aggregates were not canonical SGs, and did not lead to translational arrest in infected cells. EBOV did not induce cytoplasmic SGs at any time post infection, but was unable to overcome SG formation induced by additional stressors. Despite the sequestration of SG proteins, canonical SGs did not form within inclusions. At high levels of expression, viral protein 35 (VP35), the viral polymerase co-factor that also mediates various immune evasion functions, disrupted SGs formation independently of eIF2α phosphorylation. Finally, we found that the cellular ARE-BP tristetraprolin (TTP) specifically targeted the 3’untranslated region (UTR) of the viral nucleoprotein (NP) mRNA and promoted its degradation. Interestingly, TTP was not found within viral inclusions, leading us to speculate that inclusions might serve to prevent viral RNA from encountering TTP. These results indicate that EBOV interacts with the cellular stress response and associated RNA regulatory proteins in ways that promote viral replication.

A host can adopt two strategies when facing infection: resistance, where host immune responses prevent or reduce pathogen replication; or tolerance, which refers to all mechanisms that reduce the impact of the infection on host health or performance. Both strategies may be under host genetic control, and could thus be targeted for genetic improvement. Although there is ample evidence of genetic variation in resistance to infection, there is limited evidence to suggest that individuals also differ genetically in tolerance. Furthermore, although resistance and tolerance are typically considered as alternative host defense mechanisms, relatively little is known about the genetic relationship between them and how they change together over time and jointly determine infection outcome. In this thesis, two datasets from experimental challenge infection experiments were considered for investigating tolerance genetics: Porcine Reproductive & Respiratory Syndrome (PRRS), an endemic viral disease which causes loss of growth and mortality in growing pigs; and Listeria monoctyogenes (Lm), a bacterium which causes food-borne infections in mammals. The two datasets differed substantially in size and genetic structure; the PRRS dataset consists of thousands of records from outbred commercial pig populations, whereas the Listeria dataset comprises much fewer records from genetically diverse highly inbred strains of a mice as a model species. The aims of this thesis were to: 1) Identify if genetic variation in host tolerance to infection exists, with case studies in PRRS and listeria, using conventional reaction-norm methodology; 2) Identify if host tolerance, along with resistance, changes longitudinally as infection progresses; 3) Identify whether the WUR genotype is associated with tolerance slope; 4) Analyse the dynamic relationship between host performance and pathogen load over the time-course of infection by examining the relationship at different stages of infection using GWAS; 5) Develop novel trajectory methodology to offer insight into health-infection dynamics, and identify whether there is genetic variation in trajectories; 6) Develop novel trajectory-derived phenotypes that analyse changes in host performance with respect to changes in pathogen load, as an alternative to tolerance, and identify whether genetic variation exists. This study found that conventional reaction-norm methodology is limited to capture genetic variation in tolerance in outbred populations without measures of performance in the absence of infection. However, by utilising repeated longitudinal data on the same dataset, stages of infection (early, mid and late) were defined for each individual, based on host pathogen load. Using these stages of infection, genetic variation in tolerance was identified over all stages of infection and at mid to late stage of infection. Genetic correlation between resistance and tolerance was strong and positive over all stages of infection, and evidence suggested that resistance and tolerance may be under pleiotropic control. Furthermore, this research found that genetic correlations between resistance and growth changed considerably over time, and that individuals who expressed high genetic resistance early in infection tended to grow slower during that time-period, but were more likely to clear the virus by late stage, and thus recover in growth. However, at mid-late stage of infection, those with high virus load also had high growth, indicating potential epidemiological problems with genetic selection of host resilience to infection. Furthermore, genome wide association studies for pathogen load and growth associated with different stages of infection did not identify novel genetic loci associated with these traits than those previously reported for the whole infection period. By adopting conventional methodology, this study found genetic variation in tolerance of genetically diverse mouse strains to Lm and pigs to PRRS, despite statistical problems. The relationship between resistance and tolerance indicated that both traits should be considered in genetic selection programs. By adopting novel trajectory analysis, this study demonstrated that level of expression of resistance and tolerance changed throughout the experimental infection period and, furthermore, that expression of resistance, followed by tolerance, determined survival of infection. Survivors and non-survivors followed different infection trajectories, which were partially determined by genetics. By deriving novel phenotypes from trajectories that explained changes in growth in relation to change in pathogen load at specific time points, and applying these to the PRRS data, this study did not identify genetic variation in these phenotypes. The genetic signal in these phenotypes may have been masked by the fact that individuals were likely at different stages of infection. In summary, this study has shown that genetic improvement of tolerance, in addition to resistance may be desirable, but could be difficult to achieve in practice due to shortcomings in obtaining accurate and unbiased tolerance estimates based on conventional reaction-norms. Infection trajectories have proven to be a promising tool for achieving an optimally timed balance between resistance and tolerance, but further work is needed to incorporate them in genetic improvement programs.

Escherichia coli patogênicas aviárias (APEC) causam infecções extraintestinais em frangos conhecidas como colibacilose. A APEC MT78, ao contrário de outras linhagens APEC, foi capaz de invadir células não-fagocitárias no modelo de fibroblastos aviários (CEC-32). Considerando que as interações patógeno-hospedeiro envolvem modificações na abundância de proteínas e padrões de expressão, principalmente nas proteínas de superfície, nosso objetivo foi comparar o proteoma da MT78 crescida em meio de cultura celular com o proteoma de MT78 isolada de fibroblastos aviários infectados (condição de co-cultura). Desenvolvemos aqui a padronização das etapas de extração de proteínas totais, isolamento de células bacterianas do co-cultivo e análise proteômica de modo a obtermos uma análise proteômica global reprodutível e de qualidade. A análise da interação APEC MT78 e células CEC-32 por microscopia óptica e eletrônica de varredura revelou que essa cepa se associa à célula-alvo em um padrão de adesão localizada. A internalização de APEC MT78 pareceu ocorrer como resultado de uma interação entre bactéria-célula que dispara rearranjos do citoesqueleto de actina da célula-alvo, formando estruturas filo e lamelipodiais que são dependentes da viabilidade bacteriana. O reisolamento de células bacterianas intactas, observadas por microscopia eletrônica de transmissão, após o co-cultivo com CEC-32 foi obtido através da técnica de solubilização diferencial de membranas. As células bacterianas foram sonicadas e as proteínas digeridas em solução seguida de uma etapa de purificação. Nós identificamos 69 proteínas, distribuídas em 9 classes funcionais, incluindo as proteínas de membrana FimA, OmpA and OmpC. A proteína OmpA já foi associada a invasão do patógeno humano NMEC (neonatal meningitis-associated E. coli) à células HBMEC. Esses experimentos representam a primeira investigação proteômica global em E. coli patogênica aviária. As proteínas identificadas representaram diferentes rotas metabólicas, funções fisiológicas e diferentes localizações subcelulares. / In poultry, Avian Pathogenic Escherichia coli (APEC) cause localized extra- intestinal infections that often become systemic. APEC strain MT78 was able to invade non-phagocytic avian fibroblasts in vitro, raising the possibility that some APEC strains may invade epithelial cells and gain systemic access. Using light microscopy and scanning electron microscopy, we observed that viable MT78 strain associated with CEC-32 fibroblasts cells in clusters, and following association, MT78 internalization appeared to result from cytoskeleton rearrangements, such as filopodia and lamellipodia, in the eukaryotic membrane. Considering that host-pathogen interactions involve modifications of protein abundance and expression, mainly in surface proteins, we compared the proteome of MT78 harvested from culture medium with the proteome of MT78 isolated from infected avian fibroblasts (co-culture condition). For this purpose, we developed standard analytical procedures for global protein extraction and isolation of bacterial cells from infected CEC-32. Judged by transmission electron microscopy, we successfully reisolated intact APEC MT78 cells from CEC-32 fibroblasts using the differential membrane solubilization method. Bacterial cells were then sonicated and proteins digested in solution following a clean up procedure. We identified 69 proteins, distributed in 9 functional classes, including the membrane proteins FimA, OmpA and OmpC. The OmpA protein was already associated to invasion of the human pathogen called NMEC (neonatal meningitis-associated E. coli) to endothelial cell line HBMEC. Our results represent the first global proteomic investigation in APEC. The proteome of MT78 infecting avian fibroblasts may allow us to identify key proteins linked to the successful adhesion and/or invasion of host cells by APEC and thus throw light into the pathogenesis of avian colibacillosis.

Escherichia coli patogênicas aviárias (APEC) causam infecções extraintestinais em frangos conhecidas como colibacilose. A APEC MT78, ao contrário de outras linhagens APEC, foi capaz de invadir células não-fagocitárias no modelo de fibroblastos aviários (CEC-32). Considerando que as interações patógeno-hospedeiro envolvem modificações na abundância de proteínas e padrões de expressão, principalmente nas proteínas de superfície, nosso objetivo foi comparar o proteoma da MT78 crescida em meio de cultura celular com o proteoma de MT78 isolada de fibroblastos aviários infectados (condição de co-cultura). Desenvolvemos aqui a padronização das etapas de extração de proteínas totais, isolamento de células bacterianas do co-cultivo e análise proteômica de modo a obtermos uma análise proteômica global reprodutível e de qualidade. A análise da interação APEC MT78 e células CEC-32 por microscopia óptica e eletrônica de varredura revelou que essa cepa se associa à célula-alvo em um padrão de adesão localizada. A internalização de APEC MT78 pareceu ocorrer como resultado de uma interação entre bactéria-célula que dispara rearranjos do citoesqueleto de actina da célula-alvo, formando estruturas filo e lamelipodiais que são dependentes da viabilidade bacteriana. O reisolamento de células bacterianas intactas, observadas por microscopia eletrônica de transmissão, após o co-cultivo com CEC-32 foi obtido através da técnica de solubilização diferencial de membranas. As células bacterianas foram sonicadas e as proteínas digeridas em solução seguida de uma etapa de purificação. Nós identificamos 69 proteínas, distribuídas em 9 classes funcionais, incluindo as proteínas de membrana FimA, OmpA and OmpC. A proteína OmpA já foi associada a invasão do patógeno humano NMEC (neonatal meningitis-associated E. coli) à células HBMEC. Esses experimentos representam a primeira investigação proteômica global em E. coli patogênica aviária. As proteínas identificadas representaram diferentes rotas metabólicas, funções fisiológicas e diferentes localizações subcelulares. / In poultry, Avian Pathogenic Escherichia coli (APEC) cause localized extra- intestinal infections that often become systemic. APEC strain MT78 was able to invade non-phagocytic avian fibroblasts in vitro, raising the possibility that some APEC strains may invade epithelial cells and gain systemic access. Using light microscopy and scanning electron microscopy, we observed that viable MT78 strain associated with CEC-32 fibroblasts cells in clusters, and following association, MT78 internalization appeared to result from cytoskeleton rearrangements, such as filopodia and lamellipodia, in the eukaryotic membrane. Considering that host-pathogen interactions involve modifications of protein abundance and expression, mainly in surface proteins, we compared the proteome of MT78 harvested from culture medium with the proteome of MT78 isolated from infected avian fibroblasts (co-culture condition). For this purpose, we developed standard analytical procedures for global protein extraction and isolation of bacterial cells from infected CEC-32. Judged by transmission electron microscopy, we successfully reisolated intact APEC MT78 cells from CEC-32 fibroblasts using the differential membrane solubilization method. Bacterial cells were then sonicated and proteins digested in solution following a clean up procedure. We identified 69 proteins, distributed in 9 functional classes, including the membrane proteins FimA, OmpA and OmpC. The OmpA protein was already associated to invasion of the human pathogen called NMEC (neonatal meningitis-associated E. coli) to endothelial cell line HBMEC. Our results represent the first global proteomic investigation in APEC. The proteome of MT78 infecting avian fibroblasts may allow us to identify key proteins linked to the successful adhesion and/or invasion of host cells by APEC and thus throw light into the pathogenesis of avian colibacillosis.