Undergraduate honors paper--Mount Holyoke College, 2007. Program in Biochemistry. / Includes bibliographical references (leaves 54-58).

This study aims to functionally characterize two enzymes, HGPRT and XPRT, of an essential purine salvage pathway in the infection stage of Trypanosoma brucei. Localization, in vivo function and in vitro activity of these enzymes were characterized. Effect of acyclic nucleoside phosphonates, putative inhibitors of HGXPRT, on the viability of bloodstream form of T. brucei was evaluated.

The variant surface glycoprotein (VSG) of African trypanosomes plays an essential role in protecting the parasites from host immune factors. These trypanosomes undergo antigenic variation resulting in the expression of a single VSG isoform out of a repertoire of around 2000 genes. The molecular mechanism central to the expression and regulation of the VSG is however not fully understood. Gene expression in trypanosomes is unusual due to the absence of typical RNA polymerase II promoters and the polycistronic transcription of genes. The regulation of gene expression is therefore mainly post-transcriptional. Regulatory sequences, mostly present in the 3´ UTRs, often serve as key elements in the modulation of the levels of individual mRNAs. In T. brucei VSG genes, a 100 % conserved 16mer motif within the 3´ UTR has been shown to modulate the stability of VSG transcripts and hence their expression. As a stability-associated sequence element, the absence of nucleotide substitutions in the motif is however unusual. It was therefore hypothesised that the motif is involved in other essential roles/processes besides stability of the VSG transcripts. In this study, it was demonstrated that the 100 % conservation of the 16mer motif is not essential for cell viability or for the maintenance of functional VSG protein levels. It was further shown that the intact motif in the active VSG 3´ UTR is neither required to promote VSG silencing during switching nor is it needed during differentiation from bloodstream forms to procyclic forms. Crosstalk between the VSG and procyclin genes during differentiation to the insect vector stage is also unaffected in cells with a mutated 16mer motif. Ectopic overexpression of a second VSG however requires the intact motif to trigger silencing and exchange of the active VSG, suggesting a role for the motif in transcriptional VSG switching. The 16mer motif therefore plays a dual role in VSG in situ switching and stability of VSG transcripts. The additional role of the 16mer in the essential process of antigenic variation appears to be the driving force for the 100 % conservation of this RNA motif. A screen aimed at identifying candidate RNA-binding proteins interacting with the 16mer motif, led to the identification of a DExD/H box protein, Hel66. Although the protein did not appear to have a direct link to the 16mer regulation of VSG expression, the DExD/H family of proteins are important players in the process of ribosome biogenesis. This process is relatively understudied in trypanosomes and so this candidate was singled out for detailed characterisation, given that the 16mer story had reached a natural end point. Ribosome biogenesis is a major cellular process in eukaryotes involving ribosomal RNA, ribosomal proteins and several non-ribosomal trans-acting protein factors. The DExD/H box proteins are the most important trans-acting protein factors involved in the biosynthesis of ribosomes. Several DExD/H box proteins have been directly implicated in this process in yeast. In trypanosomes, very few of this family of proteins have been characterised and therefore little is known about the specific roles they play in RNA metabolism. Here, it was shown that Hel66 is involved in rRNA processing during ribosome biogenesis. Hel66 localises to the nucleolus and depleting the protein led to a severe growth defect. Loss of the protein also resulted in a reduced rate of global translation and accumulation of rRNA processing intermediates of both the small and large ribosomal subunits. Hel66 is therefore an essential nucleolar DExD/H protein involved in rRNA processing during ribosome biogenesis. As very few protein factors involved in the processing of rRNAs have been described in trypanosomes, this finding represents an important platform for future investigation of this topic. / Das variable Oberflächen-Glykoprotein (“varaint surface glycoprotein“, VSG) der Afrikanischen Trypanosomen schützt den Parasiten vor Immunfaktoren des Wirtes. Trypanosomen beherrschen die antigene Variation und expremieren nur eine einzige VSG Isoform aus einem Repertoire von ungefähr 2000 Genen. Der molekulare Mechanismus der die Expression dieser VSG Gene reguliert ist nicht komplett bekannt. Die Genexpression ist in Trypanosomen sehr ungewöhnlich. Es gibt keine typischen Promotoren für RNA Polymerase II und Gene werden polycistronisch transkribiert. Daher ist die Regulation der Genexpression hauptsächlich posttranskriptional. Die Expression individueller mRNAs wird durch regulatorische Sequenzen reguliert, die sich häufig in den 3´ UTRs befinden. In den VSG Genen von T. brucei moduliert ein zu 100% konserviertes 16mer Motiv in der 3´ UTR die Stabilität der VSG Transkripte und damit deren Expression. Für eine Sequenz, die die Stabilität der mRNA reguliert, ist das Fehlen von Nukleotid Substitutionen sehr ungewöhnlich. Es wurde deshalb spekuliert, dass das 16mer Motiv neben der Stabilisierung des VSG Transkriptes noch an anderen essentiellen Prozessen beteiligt ist. In dieser Arbeit wurde gezeigt, dass die 100%ige Konservierung des 16mer Motives weder für das Überleben der Zellen, noch für den Erhalt der Expression des VSG Protein in funktioneller Menge notwendig ist. Außerdem wurde gezeigt dass das intakte Motiv in der 3´UTR des aktiven VSGs weder für das „VSG silencing“ während des VSG Austausches („switching“) noch für die Differenzierung von Blutbahnformen zu prozyklischen Formen benötigt wird. Auch die Interaktionen („crosstalk“), die während der Differenzierung zum Insekten Stadium zwischen den VSG und Prozyklin Genen stattfinden, sind in Zellen mit mutiertem 16mer Motiv noch funktionell. Die ektopische Überexpression eines zweiten VSGs benötigt allerdings das intakte Motiv, um das aktive VSG zu inaktivieren und auszutauschen: dies suggeriert eine Rolle des Motivs im transkriptionalen „VSG switching“. Das 16mer Motif spielt daher eine Doppelrolle bei der Regulation der Stabilität der VSG Transkripte und im VSG in situ „switching“. Letzteres, die Rolle im essentiellen Prozess der antigenen Variation, ist dabei offensichtlich die treibende Kraft hinter der 100%igen Konservierung des RNA Motives. Eine Suche nach möglichen RNA bindenden Proteinen, die mit dem 16mer interagieren, führte zur Identifikation des DExD/H box Proteins Hel66. Obwohl das Protein wohl nicht direkt an der Regulation der VSG Expression über das 16mer beteiligt ist, spielen Mitglieder der DexD/H Proteinfamilie eine wichtige Rolle in der Biogenese von Ribosomen. Dieser Prozess ist in Trypanosomen noch nicht komplett verstanden und daher wurde das Protein für eine nähere Analyse ausgewählt, auch weil die 16mer Story ohne weitere Kandidaten zu einem Ende gekommen war. Die Biogenese von Ribosomen ist ein wichtiger zellulärer Prozess in Eukaryoten und benötigt ribosomale RNA, ribosomale Proteine sowie einige nicht-ribosomale, trans-agierende Protein Faktoren. Proteine der DExD/H box Familie sind die wichtigsten trans- agierenden Proteinfaktoren, die an der Biogenese der Ribosomen beteiligt sind. In der Hefe sind mehrere DExD/H box Proteine bekannt, die eine direkte Rolle in diesem Prozess spielen. In Trypanosomen sind erst sehr wenige Proteine aus dieser Familie untersucht worden und es ist daher kaum bekannt, welche spezifische Rollen sie im RNA Metabolismus spielen. In dieser Arbeit wurde gezeigt, dass Hel66 an der rRNA Prozessierung während der Biogenese der Ribosomen beteiligt ist. Hel66 ist im Nukleolus lokalisiert und die Reduktion des Proteins durch RNAi führte zu einem schweren Wachstumsphänotyp. Reduktion von Hel66 führte auch zu einer globalen Reduktion der Translation sowie zur Akkumulation von Synthese- Zwischenstadien der rRNAs sowohl der kleinen und als auch der großen ribosomalen Untereinheit. Hel66 ist daher ein essentielles nukleoläres DExD/H Protein dass an der Prozessierung der rRNA während der Biogenese der Ribosomen beteiligt ist. Da bisher erst wenige Proteine bekannt sind, die in Trypanosomen an diesem Prozess beteiligt sind, sind diese Ergebnisse ein sehr wichtiger Ausgangspunkt für weitere Untersuchungen in der Zukunft.

The transmission of Trypanosoma brucei, the causative agent of human African trypanosomiasis, depends upon the development in the bloodstream of 'stumpy forms' from non-transmissible 'slender forms'. In stumpy forms many mRNAs are downregulated and translation is generally repressed. However, a small subset of genes escape this repression and are upregulated, presumably as an adaptation for transmission. To understand the basic of this, regulatory sequences within the 3'UTR of a major stumpy-enriched transcript (an ESAG9 gene) have been characterised. This identified a signal responsible for gene silencing in slender forms and gene activation when cells develop to stumpy forms. An investigation was made of upstream open reading frames (uORFs) as a mechanism for the control of stumpy form gene expression. No evidence was found of uORF control, but one gene investigated was found to produce two transcripts through trans-splicing at different sites. These transcripts, which were found to exhibit some differential abundance between life-cycle stages, would generate a long and short form (from an internal ATG) of the encoded protein. Both are predicted to contain a UBA/TS-N (ubiquitin associated) domain, however, the longer form of the protein is also predicted to contain a transmembrane helix and cleavable signal peptide, suggesting a different localisation. However, ectopic expression of either protein form with a Ty epitope tag resulted in the same protein localisation. Additionally, the transcripts of two translational protein homologues, TbeIF4E4 and TbeIF6, were identified as upregulated in stumpy forms. Radiolabelled-methionine experiments and polysome analysis showed that overexpression or RNAi-mediated ablation of TbeIF6 resulted in a decrease in protein synthesis and decrease in translation. Unlike its archaeal homologue, TbeIF6 protein was not induced by coldshock treatment. Finally, to identify which transcripts escape translational repression in stumpy forms an analysis was made of polysome-associated transcripts by RNA-sequencing. This identified potentially interesting genes for further investigation, and showed that many procyclic-enriched transcripts were also enriched in stumpy form polysomeassociated RNA, confirming these cells as preadapted for transmission. Together, this work has characterised a 3’UTR regulatory element in a stumpy-enriched transcript, examined alternative trans-splicing of another transcript, investigated two translational protein homologues and identified transcripts that escape translational repression in the transmissible life-cycle stage of T. brucei.

Le trypanosome est le parasite responsable de la maladie du sommeil chez l’homme et de la Nagana chez le bétail. Afin d’échapper au système immunitaire de son hôte mammifère, il remplace périodiquement la protéine VSG (Variant Surface Glycoprotein) présente en 10 millions d’exemplaires à sa surface. Ce mécanisme a pour nom la variation antigénique. Pour être exprimé, le gène de VSG (VSG) doit se trouver en fin d’un site d’expression (ES) particulier. Cet ES est polycistronique, télomérique et transcrit par une ARN polymérase de type ribosomique (Pol I). 20 à 40 ESs similaires et un millier de VSGs sont recensés dans le génome du trypanosome. Cependant, un seul ES est totalement transcrit (actif) et un seul VSG est exprimé. La variation antigénique est donc possible par deux mécanismes: soit l’activation d’un autre ES, soit le remplacement du VSG dans l’ES actif. La base de ce système est l’activation d’un seul ES à la fois (contrôle monoallélique). Au laboratoire, un modèle a été proposé où la transcription s’initie au niveau de tous les ESs mais n’aboutit au VSG que dans le cas de l’ES actif (Vanhamme et al., 2000). Dans ce cas uniquement, le transcrit primaire subit une maturation correcte (épissage et polyadénylation) et est exporté dans le cytoplasme. Etant donné que des transcrits Pol I subissent une maturation identique à des transcrits Pol II, la régulation s’effectuerait par recrutement d’une machinerie d’élongation/maturation de l’ARN de type Pol II (Pol II « RNA factory »). Cette dernière serait uniquement localisée au niveau de l’ES actif dans le compartiment nucléaire appelé ES body (Navarro and Gull, 2001). Durant cette thèse, diverses stratégies ont été élaborées pour tester la validité du modèle. La première visait à comparer l’état de maturation d’un ES en fonction de son activité. Nos résultats ont appuyé l’idée que les transcrits d’ESs ayant subi une maturation correcte provenaient préférentiellement de l’ES actif mais le(s) facteur(s) en quantité limitante ne permettant cette maturation qu’au niveau de l’ES actif doivent encore être identifiés. Le seconde stratégie analysait l’acétylation des histones ainsi qu’un éventuel attachement différentiel à la matrice nucléaire de l’ES suivant son activité. Le niveau d’acétylation d’un ES lorsqu’il est actif n’a pu être étudié. Des résultats préliminaires en faveur d’une association préférentielle de l’ES à la matrice nucléaire lorsqu’il est actif ont été obtenus. Enfin, nous avons cloné deux homologues d’un facteur général de la transcription appelé TFIIS. Ce dernier permet à la Pol de redémarrer lorsqu’elle est bloquée par un site de pause. Individuellement chacun de ces facteurs ne semble pas être essentiel au trypanosome. Cependant, un retard de croissance a été observé lorsque les deux facteurs sont invalidés dans la même lignée cellulaire. Ce phénotype particulier doit être caractérisé. En parallèle, nous avons envisagé de caractériser le complexe de la Pol I du trypanosome. Cette stratégie constituait la manière la plus simple de mettre en évidence un éventuel contact physique et/ou fonctionnel entre la Pol I transcrivant l’ES et la machinerie d’élongation/maturation de l’ARN de type Pol II « RNA factory ». 5 sous-unités du complexe ont été identifiées, associées à une protéine de fonction inconnue ainsi qu’à des histones. L’identification d’autres protéines associées au complexe constitue notre perspective principale. La phosphorylation de la plus grande sous-unité du complexe a été démontrée mais son rôle doit encore être élucidé.

Trypanosomen sind Protozoen, die Krankheiten bei Mensch und Tier verursachen, die unbehandelt infaust verlaufen. Die Zellen sind hoch motil, angetrieben von einem einzelständigen Flagellum, welches entlang des Zellkörpers angeheftet ist. Selbst in Zellkultur hören Trypanosomen niemals auf sich zu bewegen und eine Ablation funktioneller Bestandteile des Flagellarapparates ist letal für Blutstromformen. Es wurde gezeigt, dass Motilität notwendig ist für die Zellteilung, Organellenpositionierung und Infektiosität. Dies macht Trypanosomen zu besonders geeigneten Modellorganismen für die Untersuchung der Motilität. Dennoch ist erstaunlich wenig über die Motilität bei Trypanosomen bekannt. Dies gilt auch noch genereller für die Protozoen. Unlängst ist dieses Gebiet allerdings in den Fokus vieler Arbeiten gerückt, was bereits erstaunliche, neue Erkenntnisse hervorgebracht hat. Doch Vieles ist noch nicht abschliessend geklärt, so z.B. wie der Flagellarschlag genau reguliert wird, oder wie sich der Schlag des Flagellums entlang des Zellkörpers ausbreitet. Die vorliegende Arbeit befasst sich besonders mit den Einflüssen, die die Mikroumgebung auf die Motilität von Blutstromform-Trypanosomen ausübt. In ihrem natürlichen Lebensraum finden sich Trypanosomen in einer hoch komplexen Umgebung wieder. Dies gilt sowohl für den Blutkreislauf, als auch für den Gewebezwischenraum in ihrem Säugerwirt. Die hohe Konzentration von Zellen, Gewebeverbänden und extrazellulären Netzwerken könnte man als Ansammlung von Hindernissen für die Fortbewegung auffassen. Diese Arbeit zeigt dagegen, dass der Mechanismus der Bewegung eine Adaptation an genau diese Umweltbedingungen darstellt, so z.B. an die Viskosität von Blut. Es wird auch ein Bewegungsmodell vorgestellt, das erläutert, worin diese Adaption besteht. Dies erklärt auch, warum die Mehrheit der Zellen einer Trypanosomenkultur eine ungerichtete Taumel-Bewegung aufweist in nieder-viskosem Medium, das keine solchen “Hindernisse” enthält. Die Zugabe von Methylcellulose in einer Konzentration von ca. 0,5% (w/v) erwies sich als geeigneter Ersatz von Blut, um optimale Bedingungen für gerichtetes Schwimmen von Blutstromform Trypanosomen zu erreichen. Zusätzlich wurden in dieser Arbeit unterschiedliche Arten von Hindernissen, wie Mikroperlen (Beads) oder molekulare Netzwerke, sowie artifizielle, geordnete Mikrostrukturen verwendet, um die Interaktion mit einer festen Matrix zu untersuchen. In deren Anwesenheit war sowohl die Schwimmgeschwindigkeit, als auch der Anteil an persistent schwimmenden Trypanosomen erhöht. Zellen, die frei schwimmend in Flüssigkeiten vorkommen (wie Euglena oder Chlamydomonas), werden effizient durch einen planaren Schlag des Flagellums angetrieben. Trypanosomen hingegen mussten sich evolutionär an eine komplexe Umgebung anpassen, die mit einer zu raumgreifenden Welle interferieren würde. Der dreidimensionale Flagellarschlag des, an die Zelloberfläche angehefteten, Flagellums erlaubt den Trypanosomen eine effiziente Fortbewegung durch die Interaktion mit Objekten in jedweder Richtung gleichermassen. Trypanosomen erreichen dies durch eine hydrodynamisch verursachte Rotation ihres Zellkörpers entlang ihrer Längsachse, entgegen dem Uhrzeigersinn. Der Einfluss der Mikroumgebung wurde in früheren Untersuchungen bisher vernachlässigt, ist zum Verständnis der Motilität von T. brucei jedoch unerlässlich. Ein weiterer, bisher nicht untersuchter Aspekt der Beeinflussung der Motilität durch die Umwelt sind hydrodynamische Strömungseffekte, denen Trypanosomen im kardiovaskulären System ausgesetzt sind. Diese wurden in dieser Arbeit mittels Mikrofluidik untersucht. Um unser Verständnis der Motilität von Trypanosomen von 2D, wie üblich in der Motilitätsanalyse mittels Lebend-Zell-Mikroskopie, auf drei Dimensionen auszudehnen, wurde als bildgebendes Verfahren auch die Holographie eingesetzt. Mikrofluidik und Holographie sind beides aufkommende Techniken mit großem Anwendungspotential in der Biologie, die zuvor noch nie für die Motilitätsanalyse von Trypanosomen eingesetzt worden waren. Dies erforderte daher interdisziplinäre Kooperationen. Zusätzlich wurde in dieser Arbeit auch ein vollständig automatisiertes und Software-gesteuertes Fluoreszenzmikroskopiesystem entwickelt, das in der Lage ist, einzelne Zellen durch entsprechende Steuerung des Mikroskoptisches autonom zu verfolgen und somit eine Bewegungsanalyse in Echtzeit ermöglicht, ohne weitere Benutzerinteraktion. Letztendlich konnte dadurch auch die Bewegung der schlagenden Flagelle und des gesamten Zellkörpers mit hoher zeitlicher und räumlicher Auflösung mittels Hochgeschwindigkeits-Fluoreszenzmikroskopie aufgeklärt werden. / Trypanosomes are protozoa causing fatal diseases in livestock and man. The cells show vivid motility, driven by a single flagellum that runs along the cell body, attached to the cell surface. Even in cell culture, trypanosomes never stop moving and ablation of functional components of the flagellum is lethal for bloodstream-forms. Motility has been shown to be essential for cell division, organelle positioning and infectivity. This renders trypanosomes valuable model organisms for studying motility. But, surprisingly little is known about motility in trypanosomes, as well as in protozoa, in general. Recently, motility of trypanosomes therefore has gotten into the spotlight of interest which brought some new insights, but many essential points are still a matter of debate, for example how the flagellar beat is regulated or how it is propagated along the cell body. In this work, the effects of the micro-environment of blood-stream form trypanosomes on motility were investigated. In their natural habitat, trypanosomes find themselves in a crowded environment. This is not only the case in the blood circulatory system, but also in extra-tissue space. The high concentration of cells and extra-cellular networks might be regarded as a kind of obstacle to cellular motion. This work shows that the mode of motility of bloodstream form trypanosomes instead is adapted to the viscosity of blood. Also a mechanistic model is presented which elucidates how this adaptation works. This also explains why most trypanosomes are tumbling in low-viscous cell culture medium, lacking other cellular components. Addition of Methylcellulose at a concentration of about 0.5% (w/v) was found to be a potent substitute for blood, providing optimal conditions for trypanosome motility. Also different types of obstacles like beads and molecular networks, as well as arranged pillar microstructures were used as a tool to mimic interaction with a solid matrix. In presence of these, the swimming speed as well as the percentage of persistent swimming cells was increased. Cells inhabiting an open-ranged environment (like Euglena or Chlamydomonas) are efficiently propelled by a planar flagellar wave. Trypanosomes in contrast, had to evolutionary adapt to a crowded environment, which would infer with any extensive planar wave. The three-dimensional flagellar beat of the attached flagellum allows trypanosomes to harness any rigid matrix for effective propulsion, in all directions equally. Trypanosomes achieve this by a rotational counter-clockwise motion of their whole cell body. Another environmental aspect for trypanosome motility that had not been studied before is the influence of hydrodynamic flow, which trypanosomes are subjected to, when swimming in the blood circulatory system. For studying this, in this work, the motilty of trypanosomes was analyzed in microfluidic devices. To extend our understanding of trypanosomal motility from 2D, like in standard microscopy based live-cell imaging analysis, to 3D, a imaging technique known as holography was used, in addition. Microfluidics as well as Holography both are emerging, high-potential techniques in biology, which had not been used for the motility analysis of trypanosomes before and establishing this therefore only got possible due to interdisciplinary collaborations. In addition, a custom fully automated, software-controlled, fluorescence microscopic system was developed in this work, which is able to track and follow single cells for motility analysis in real-time without the need for user input. The motion of the flagellar beat and the cell itself was investigated at high spatio-temporal resolution using highspeed fluorescence microscopy.

Genomes are constantly challenged by agents that promote DNA damage, with interstrand crosslinks (ICLs) representing a particularly dangerous lesion. Ongoing work in the Wilkinson laboratory aimed at identifying novel agents that target Trypanosoma brucei, the causative agent of African trypanosomiasis, identified several prodrugs that once activated form ICLs in this protozoan parasite. To understand the complexity of ICL repair systems that T. brucei employs to resolve such damage, a variety of null mutant lines were generated that lack activities postulated to fix such lesions. Phenotypic screens using various DNA damaging agents revealed that TbMRE11, TbEXO1, TbCSB, TbCHL1, TbFAN1, TbBRCA2 and TbRAD51 all help to resolve ICLs, implicating components of the homologous recombination, nucleotide excision repair and mismatch repair pathways in resolving this form of damage: This approach demonstrated that components of the translesion synthesis pathway (TbREV2 and TbREV3) do not play a significant role in ICL repair. In many organisms, nucleases belonging to the SNM1/PSO2 family play a key and specific role in the repair of ICLs with this property extending to the T. brucei homologue, TbSNM1. To assess whether there is a functional linkage between the DNA repair factors noted above and TbSNM1, a series of double null mutants were constructed and the susceptibility of these lines to ICL inducing agents determined. Identification of their epistatic/non-epistatic interactions revealed that T. brucei expresses at least two ICL repair systems with one pathway involving the concerted activities of TbSNM1/TbCSB/TbEXO1, that we postulate functions to repair ICLs encountered by the transcriptional machinery, while the other is centred upon TbMRE11/TbFAN1/TbEXO1 that may help resolve lesions which cause stalling of DNA replication forks. By unravelling how T. brucei repairs ICLs, specific inhibitors against key components of these pathways could be developed and used in combination with DNA damaging agents to target trypanosomal infections.

The breakdown of glucose to pyruvate, known as glycolysis, is a central biochemical pathway, critically important for energy production and biosynthesis. Phosphofructokinase (PFK), the third enzyme in the pathway, is a crucial regulator of glycolytic flux, being the first committed step of glycolysis and modulating entry into the pentose-phosphate-pathway. Alterations in PFK activity have been implicated in many neurological conditions, including Tarui's disease, epilepsy, Alzheimer's disease, Down's syndrome, and cancers. There are three isoforms of human PFK; it is assumed that these evolved to fulfil specific metabolic niches both within cells and between tissue types. However, the differences between isoforms have never been systematically compared. Understanding these differences is an essential prerequisite for developing novel therapeutic agents targeting human PFK. Trypanosomatid parasites are a major global cause of neurological morbidity and mortality. Neglected tropical diseases caused by trypanosomatid parasites include African Sleeping Sickness (Trypanosoma brucei), Chagas disease (Trypanosoma cruzi), and leishmaniasis (Leishmania spp.). There is increasing interest in targeting the metabolic enzymes of these parasites, including PFK, which greatly differ from mammalian counterparts. This thesis describes biochemical, bio-physical, and bio-informatic studies on the three human PFK isoforms (PFK-M, PFK-L, and PFK-P), expressed in S. cerevisiae. Biophysical studies showed that the active conformation was tetrameric, with activity regulated by time and concentration dependent dissociation into smaller inactive species. The propensity to dissociate differed between isoforms, with PFK-M being most stable and PFK-P least stable. Dissociation was synergistically slowed by the addition of substrates and reducing agents, indicating different mechanisms of action. Kinetic studies were performed with respect to both substrates (ATP and F6P) in the presence of natural metabolites hypothesised to act as modulators of enzyme activity. Each isoform conformed to an allosteric sigmoidal kinetic model and had differing kinetic properties, with PFK-M being the most active and PFK-P the least active. ATP was found to act as both substrate and allosteric inhibitor, with activity showing a biphasic response to ATP concentration. Each isoform showed different susceptibilities to both ATP inhibition and regulation by allosteric modulators. The reverse reaction was shown to be possible under certain conditions. Bio-informatic data on intra-cellular and inter-cellular locations were determined using the Human Protein Atlas and the FANTOM5 datasets. PFK-M localises to the cytosol and may co-localise with endoplasmic reticulum; PFK-L associates with nucleoli and mitochondria; and PFK-P is cytosolic. Splice variants were not shown to be physiologically significant. Each isoform had different tissue expression levels, with overall PFK expression varying by tissue type. PFK-P was the principal isoform in cancers, whereas PFK-L was dominantly expressed in immune cells. Activated macrophages switched rapidly from PFK-L to PFK-P. PFK-M and PFK-P were the dominant isoforms in the brain, although there were differences between brain areas. Neurons expressed less PFK than astrocytes, in keeping with the lactate shuttle theory. PFK from each of the three main pathological trypanosomatid species were compared (T. brucei, TbPFK; T. cruzi, TcPFK; L. infantum, LmPFK); expressed in E. coli. Biophysical analysis showed each PFK to be tetrameric; no evidence of time or concentration dependent dissociation or inactivation was found. Kinetic properties differed between isoforms, with TcPFK being most active and LmPFK being least active. LmPFK was very poorly active with regard to F6P titrations unless AMP was present. No other modulators were shown to affect activity, although GTP was an alternate substrate. The reverse reaction was shown to be possible and may be compatible with physiological concentrations of ADP and F16BP in the trypanosomatid glycosome.

The parasitic protist Trypanosoma brucei is the causative agent of human African trypanosomiasis. The parasite undergoes a complex life cycle involving stages within the mammalian bloodstream and its tsetse fly vector. The fundamental differences between energy metabolism in the procyclic insect form (PCF) and long slender bloodstream form (BSF) T. brucei involve a switch in the directionality of the F1Fo- ATPase. In PCF, the need for oxidative phosphorylation in low glucose conditions requires the enzyme to generate ATP. In the slender BSF, the enzyme uses ATP from glycolysis to drive proton pumping to maintain the essential mitochondrial membrane potential. Fo-ATPase subunit 6 (A6) is critical for proton translocation in either direction and is encoded in the mitochondrial DNA (kDNA). The parasite’s kDNA is therefore essential in the slender BSF, and also in PCF where it encodes multiple subunits of the respiratory chain complexes that constitute the oxidative phosphorylation pathway. Specific point mutations in the nuclearly encoded γ subunit of the mitochondrial F1Fo-ATPase allow survival in the absence of kDNA in the slender BSF T. brucei (Dean et al., 2013). These mutations, even in the heterozygous genotype, cause an increase in resistance to multiple drugs in vitro (Gould and Schnaufer, 2014). This thesis investigates two questions: (1) What is the molecular mechanism of compensation for kDNA loss? (2) Are kDNA and a functional FoF1-ATPase required for life cycle progression? Slender BSF T. brucei were generated expressing ATPase L262Pγ. The effects of this γ mutation and kDNA loss, respectively, on structure/function of the F1Fo- ATPase were probed. Cells expressing L262Pγ show decreased sensitivity to Fo inhibitor oligomycin compared to WT cells, suggesting that the L262Pγ mutation functionally uncouples the enzyme. The impact of the L262Pγ mutation on the structure of the enzyme was probed by high resolution clear native electrophoresis. This shows there are dramatic consequences to F1Fo structure in the presence of the L262Pγ mutation. The apparent selection for cells that no longer express intact F1Fo suggests that L262Pγ uncouples the enzyme, resulting in a lethal proton leak. Pleomorphic T. brucei with and without kDNA were also generated by expressing mutant γ in strain AnTat1.1 90:13. Differentiation studies demonstrate kDNA0 cells can differentiate to insect-transmissible stumpy forms. These cells show a decreased lifespan, suggesting a critical role for a kDNA-encoded product in the stumpy form. Tsetse fly infections show kDNA is indispensable for progression to the PCF. Unexpectedly, parasites homozygous for L262Pγ can establish a midgut infection, while they do not infect the salivary glands. Heterozygous parasites, on the other hand, can form animal-transmissible metacyclics in the salivary glands, providing a potential mechanism for spreading decreased sensitivity to multiple drugs.

Contrasting physiological requirements for T. brucei survival between procyclic (vector) and bloodstream (mammal) forms necessitate different molecular processes and therefore changes in protein expression. Transcriptional regulation is unusual in T. brucei because the arrangement of genes is polycistronic; however, genes which are transcribed together are subsequently cleaved into separate mRNAs by trans-splicing and are individually regulated. During the process of trans-splicing, a 39-nucleotide splice-leader RNA is added to the 5´ end of mRNA. In this study, gene regulation in trypanosomes will be examined in the context of the 7-methylguanosine cap attached to the 5´ end of the splice-leader. Interestingly, in addition to the capping enzymes identified in other eukaryotes, trypanosomatids have an additional guanylyltransferase and methyltransferase in the form of a bifunctional enzyme (TbCGM1). TbCGM1 was found to be essential in bloodstream form T. brucei, although the purpose of this bifunctional capping enzyme remains unclear. Null mutants of a related enzyme, monomeric methyltransferase TbCMT1, did not show an effect on cell viability in culture, however, the enzyme proved to be important for virulence in vivo. Complementary to the study of T. brucei capping enzymes, we worked to develop a method to allow structural analysis of the 5´mRNA cap by mass spectrometry. Following pre-mRNA processing, regulation of the mature mRNAs is a tightly controlled cellular process. While multiple stage-specific transcripts have been identified, previous studies using RNA-seq found that the changes in overall transcript level do not necessarily reflect the abundance of the corresponding proteins. We hypothesized that in addition to mRNA stability, mRNA recruitment to ribosomes may play a significant role in the regulation of gene expression in T. brucei. To approach this question, we performed RNA-seq of total, subpolysomal, and polysomal mRNA. This transcriptomic data was then correlated with published proteomic studies to obtain a global picture of the relative translation efficiencies and their relationship to steady-state protein levels between bloodstream and procyclic form T. brucei.