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In the mammalian host, the Trypanosoma brucei cell surface is covered with a densely packed protein coat of a single protein, the variant surface glycoprotein (VSG). The VSG is believed to shield invariant surface proteins from host antibodies but there is limited information on how far antibodies can penetrate into the VSG monolayer. Here, the VSG surface coat was probed to determine whether it acts as a barrier to binding of antibodies to the membrane proximal VSG C-terminal domain. The binding of C-terminal domain antibodies to VSG221 or VSG118 was compared with antibodies recognising the cognate whole VSGs. The C-terminal VSG domain was inaccessible to antibodies on live cells but not on fixed cells. This provides further evidence that the VSG coat acts as a barrier and protects the cell from antibodies that would otherwise bind to some of the other externally disposed proteins.
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.
Die Schlafkrankheit hat ihren Schrecken seit den Zeiten Robert Kochs und Paul Ehrlichs nicht verloren. Die zielgerichtete Entwicklung neuer Medikamente ist für die Menschen in den Endemiegebieten damals wie heute von elementarer Bedeutung. Die Naphtylisochinolin-Alkaloide stellen eine neue chemische Substanzklasse dar, die gute Kandidaten für die Entwicklung neuer Medikamente enthält. Mit GBAP 94 im speziellen liegt eine Substanz vor, die gute Startvorrausetzungen hierfür mitbringt. Diese sind eine sehr gute Wirksamkeit gegen Trypanosomen, gepaart mit einer hohen Selektivität durch einen sehr wahrscheinlich relativ spezifisch anti-trypanosomalen Wirkmechanismus. Die verwendeten Naphtylisochinolin-Alkaloide GBAP 94 und GBAP 146 wurden nach unterschiedlichen Gesichtspunkten ausgewählt. GBAP 94 wurde aufgrund seiner guten antitrypanosomalen Wirkung und seiner hohen Selektivität für Trypanosomen ausgewählt. Die IC50 liegt mit 0,383 µmol/l im Vergleich zu den aktuell verwendeten Medikamenten sehr niedrig. Die Selektivitätsindices (IC50 Trypanosoma brucei brucei / IC50 Makrophagen J774.1) mit 85,6 und (IC50 Try-panosoma brucei brucei / IC50 Leishmania major) mit 15,1 liegen in einem sehr günstigen Bereich. GBAP 146 wurde hauptsächlich wegen seiner guten Fluoreszenz-Eigenschaften ausgewählt. Die antitrypanosomale Aktivität ist mit einer IC50 von 0,289 µmol/l zwar sehr gut, eine große Selektivität ist aber nicht gegeben. Die beiden Alkaloide waren aufgrund ihrer Eigenfluoreszenz gut fluoreszenz-mikroskopisch in den Parasiten zu detektieren. Nach 10 min war in den ersten Trypanosomen die Anreicherung der Wirkstoffe erkennbar. Nach 30 min war bei fast allen Parasiten eine Färbung erkennbar. Die Wirkstoffe reicherten sich zunächst in mehreren kleinen Vakuolen an. Bei längeren Inkubationszeiten zeigte sich eine fast homogene Verteilung innerhalb des kompletten Parasiten. Durch-gängig ausgespart blieb eine vakuolische Struktur. Diese entwickelte oder vergrößerte sich im Verlauf der Inkubationszeit im vorderen Drittel des Parasiten, etwa im Bereich des Kinetoplasten. Diese Vakuole konnte auch lichtmikroskopisch in der Giemsa-Färbung nachgewiesen werden. Der Anteil der veränderten Trypanosomen lag bei diesen Untersuchungen nach 1 h bei 25,4%, stieg bis zum Zeitpunkt 2 h auf 46,6% und stabilisierte sich nach 4 h bei 44,8%. Die vakuolische Struktur führte durch ihre Vergrößerung zur zunehmenden Verplumpung der Trypanosomen bis zu einer kugelförmigen Zellform mit geisselartig-wirkender Flagelle. Aufgrund der veränderten Form wurden die Zellorganellen verdrängt. Dies konnte durch die Fluoreszenzmarkierung des Mitochondriums mit Rodamine B Hexylester und der sauren Kompartimente, besonders des Lysosoms, mit LysoTracker® gezeigt werden. Die Vakuolisierung von Trypanosomen im Zusammenhang mit Apoptose ist bekannt. Die neu entstehende Vakuole konnte weder mit LysoTracker® green, noch mit dem endosomalen Farbstoff FM 4-64 angefärbt werden. Damit können eine lysosomale und eine endosomale Herkunft der Vakuole ausgeschlossen werden. Eine genaue Klärung der Genese der Vakuole steht noch aus. In den Untersuchungen mit Annexin V und Propidium-Jodid im FACS® konnte gezeigt werden, dass die Wirkung der NIQs sehr wahrscheinlich Apoptose induziert. Annexin V ist auch bei Trypanosomen als Marker für Apoptose etabliert. Zudem zeigte sich ein Anstieg der Anzahl apoptotischer Trypanosomen mit Periode von 6 h – 8 h. Diese Dauer entspricht ungefähr der Dauer des trypanosomalen Zellzyklus. Ein Eingriff der NIQs in den Zellzyklus ist somit sehr wahrscheinlich. Eine Hemmung von Teilen des Zellzyklus ist als Auslöser für Apoptose bekannt. Über die genaue Zielstruktur der NIQs kann allerdings nur spekuliert werden. Die apotose-induzierende Wirkung anderer Alkaloide auf Trypanosomen ist inzwischen nachgewiesen. Ein weiteres Indiz ist, dass die Ergebnisse von Ponte-Sucre mit den NIQs bei Leishmanien ebenfalls in Richtung Apoptose weisen.
Switches in trypanosome differentiation: ALBA proteins acting on post-transcriptional mRNA control
(2011)
Trypanosoma brucei is a digenetic eukaryotic parasite that develops in different tissues of a mammalian host and a tsetse fly. It is responsible for sleeping sickness in sub-saharan Africa. The parasite cycle involves more than nine developmental stages that can be clearly distinguished by their general morphology, their metabolism and the relative positioning of their DNA-containing organelles. During their development, trypanosomes remain exclusively extracellular and encounter changing environments with different physico-chemical properties (nutritional availability, viscosity, temperature, etc.). It has been proposed that trypanosomes use their flagellum as a sensing organelle, in agreement with the established role of structurally-related cilia in metazoa and ciliates. Recognition of environmental triggers is presumed to be at the initiation of differentiation events, leading to the parasite stage that is the best suited to the new environment. These changes are achieved by the modification of gene expression programmes, mostly underlying post-transcriptional control of mRNA transcripts. We first demonstrate that the RNA-binding proteins ALBA3/4 are involved in specific differentiation processes during the parasite development in the fly. They are cytosolic and expressed throughout the parasite cycle with the exception of the stages found in the tsetse fly proventriculus, as shown by both immunofluorescence and live cell analysis upon endogenous tagging with YFP. Knock-down of both proteins in the developmental stage preceding these forms leads to striking modifications: cell elongation, cell cycle arrest and relocalization of the nucleus in a posterior position, all typical of processes acting in parasites found in the proventriculus region. When ALBA3 is over-expressed from an exogenous copy during infection, it interferes with the relocalization of the nucleus in proventricular parasites. This is not observed for ALBA4 over-expression that does not visibly impede differentiation. Both ALBA3/4 proteins react to starvation conditions by accumulating in cytoplasmic stress granules together with DHH1, a recognized RNA-binding protein. ALBA3/4 proteins also partially colocalize with granules formed by polyA+ RNA in these conditions. We propose that ALBA are involved in trypanosome differentiation processes where they control a subset of developmentally regulated transcripts. These processes involving ALBA3/4 are likely to result from the specific activation of sensing pathways. In the second part of the thesis, we identify novel flagellar proteins that could act in sensing mechanisms. Several protein candidates were selected from a proteomic analysis of intact flagella performed in the host laboratory. This work validates their flagellar localization with high success (85% of the proteins examined) and defines multiple different patterns of protein distribution in the flagellum. Two proteins are analyzed during development, one of them showing down-regulation in proventricular stages. The functional analysis of one novel flagellar membrane protein reveals its rapid dynamics within the flagellum but does not yield a visible phenotype in culture. This is coherent with sensory function that might not be needed in stable culture conditions, but could be required in natural conditions during development. In conclusion, this work adds new pieces to the puzzle of identifying molecular switches involved in developmental mRNA control and environmental sensing in trypanosome stages in the tsetse fly.
Die Kontrolle der monoallelen Expression, antigenen Variation und Entwicklung in Trypanosoma brucei
(2013)
Die ausschließliche Expression von nur einem Gen aus einer großen Genfamilie ist ein weit verbreitetes Phänomen, das als monoallele Expression bezeichnet wird. In dem Blutparasiten Trypanosoma brucei stellt die Expression eines einzigen variablen Oberflächenglykoproteins (VSG) aus einem Repertoire von über 1000 verschiedenen Genen die Grundlage für die Immunevasion dar. Durch einen periodischen Wechsel der VSG Expression (Antigene Variation) bleibt der Parasit vom Immunsystem des Wirtes unerkannt. Die VSG Gene werden aus telomerischen Blutstromform Expressionsstellen (BES) transkribiert, von denen nur eine zu einem bestimmten Zeitpunkt aktiv ist. Die Kontrolle der monoallelen VSG Expression ist somit einer der wichtigsten Virulenzfaktoren von T. brucei.
Ziel dieser Arbeit war es, die Vorgänge eines transkriptionellen Wechsels zwischen zwei BESs zu beschreiben. Das Ausschalten des aktiven VSGs durch RNA-Interferenz hatte zuvor gezeigt, dass dies nicht zu einer erhöhten Wechselrate führt. Es wurde daher untersucht, welche Auswirkungen das Anschalten einer zweiten BES auf die monoallele Expression hat. Da es bisher keine Möglichkeit gibt, eine inaktive BES gezielt zu aktivieren, wurde ein artifizielles System gewählt, das die gezielte induzierbare Expression eines Gens ermöglicht. Die BESs unterscheiden sich in der Anzahl und Zusammensetzung der Expressionsstellen-assoziierte-Gene (ESAGs), jedoch besitzt jede BES ein telomernahes VSG. Somit wird, bei einer BES Aktivierung, in jedem Fall ein neues VSG exprimiert. Durch die induzierbare Expression eines zweiten VSGs wurde so das Anschalten einer neuen BES simuliert. Mithilfe dieses Systems konnte gezeigt werden, dass das VSG selbst für die Kontrolle der monoallelen Expression verantwortlich ist. Die ektopische Überexpression eines zweiten VSGs führte zu einer graduellen Inaktivierung der BES. Infolge dessen verlangsamte sich der Zellzyklus und die Zellen verblieben bis zu fünf Tage in einem ruhenden Zustand. Genauere Analysen dieses Zustandes zeigten, dass es sich hierbei um ein bisher unbekanntes, reversibles Zwischenstadium zwischen proliferierenden sogenannten Long Slender und arretierten sogenannten Short Stumpy Formen handelt. Die Ergebnisse dieser Arbeit führten zu einem neuen Modell, das die Kontrolle der monoallelen VSG Expression mit der Entwicklung der Trypanosomen mechanistisch verbindet.
We have discovered a new mechanism of monoallelic gene expression that links antigenic variation, cell cycle, and development in the model parasite Trypanosoma brucei. African trypanosomes possess hundreds of variant surface glycoprotein (VSG) genes, but only one is expressed from a telomeric expression site (ES) at any given time. We found that the expression of a second VSG alone is sufficient to silence the active VSG gene and directionally attenuate the ES by disruptor of telomeric silencing-1B (DOT1B)-mediated histone methylation. Three conserved expression-site-associated genes (ESAGs) appear to serve as signal for ES attenuation. Their depletion causes G1-phase dormancy and reversible initiation of the slender-to-stumpy differentiation pathway. ES-attenuated slender bloodstream trypanosomes gain full developmental competence for transformation to the tsetse fly stage. This surprising connection between antigenic variation and developmental progression provides an unexpected point of attack against the deadly sleeping sickness.
While gene expression is a fundamental and tightly controlled cellular process that is regulated at multiple steps, the exact contribution of each step remains unknown in any organism. The absence of transcription initiation regulation for RNA polymerase II in the protozoan parasite Trypanosoma brucei greatly simplifies the task of elucidating the contribution of translation to global gene expression. Therefore, we have sequenced ribosome-protected mRNA fragments in T. brucei, permitting the genome-wide analysis of RNA translation and translational efficiency. We find that the latter varies greatly between life cycle stages of the parasite and ∼100-fold between genes, thus contributing to gene expression to a similar extent as RNA stability. The ability to map ribosome positions at sub-codon resolution revealed extensive translation from upstream open reading frames located within 5' UTRs and enabled the identification of hundreds of previously un-annotated putative coding sequences (CDSs). Evaluation of existing proteomics and genome-wide RNAi data confirmed the translation of previously un-annotated CDSs and suggested an important role for >200 of those CDSs in parasite survival, especially in the form that is infective to mammals. Overall our data show that translational control plays a prevalent and important role in different parasite life cycle stages of T. brucei.
Post-translational histone modifications (PTMs) such as methylation of lysine residues influence chromatin structure and function. PTMs are involved in different cellular processes such as DNA replication, transcription and cell differentiation. Deregulations of PTM patterns are responsible for a variety of human diseases including acute leukemia. DOT1 enzymes are highly conserved histone methyltransferases that are responsible for methylation of lysine 79 on histone H3 (H3K79). Most eukaryotes contain one single DOT1 enzyme, whereas African trypanosomes have two homologues, DOT1A and DOT1B, which methylate H3K76 (H3K76 is homologous to H3K79 in other organisms). DOT1A is essential and mediates mono- and di-methylations, whereas DOT1B additionally catalyzes tri-methylation of H3K76. However, a mechanistic understanding how these different enzymatic activities are achieved is lacking. This thesis exploits the fact that trypanosomes possess two DOT1 enzymes with different catalytic properties to understand the molecular basis for the differential product-specificity of DOT1 enzymes. A trypanosomal nucleosome reconstitution system was established to analyze methyltransferase activity under defined in vitro conditions. Homology modeling allowed the identification of critical residues within and outside the catalytic center that modulate product-specificity. Exchange of these residues transferred the product-specificity from one enzyme to the other and revealed regulatory domains adjacent to the catalytic center. This work provides the first evidence that few specific residues in DOT1 enzymes are crucial to catalyze methyl-state-specific reactions. These results have also consequences for the functional understanding of homologous enzymes in other eukaryotes.
Trypanosoma brucei is a uniflagellated protist and the causative agent of African trypanosomiasis, a neglected tropical disease. The single flagellum of T. brucei is essential to a number of cellular processes such as motility, and has been a longstanding focus of scientific enquiry. A number of cytoskeletal structures are associated with the flagellum in T. brucei, and one such structure—a multiprotein complex containing the repeat motif protein TbMORN1—is the focus of this review. The TbMORN1-containing complex, which was discovered less than ten years ago, is essential for the viability of the mammalian-infective form of T. brucei. The complex has an unusual asymmetric morphology, and is coiled around the flagellum to form a hook shape. Proteomic analysis using the proximity-dependent biotin identification (BioID) technique has elucidated a number of its components. Recent work has uncovered a role for TbMORN1 in facilitating protein entry into the cell, thus providing a link between the cytoskeleton and the endomembrane system. This review summarises the extant data on the complex, highlights the outstanding questions for future enquiry, and provides speculation as to its possible role in a size-exclusion mechanism for regulating protein entry. The review additionally clarifies the nomenclature associated with this topic, and proposes the adoption of the term “hook complex” to replace the former name “bilobe” to describe the complex.
Characterization of a novel putative factor involved in host adaptation in Trypanosoma brucei
(2016)
Trypanosomes are masters of adaptation to different host environments
during their complex life cycle. Large-scale proteomic approaches provide information on changes at
the cellular level in a systematic way. However, a detailed work on single components is necessary
to understand the adaptation mechanisms on a molecular level. Here we have performed a detailed
characterization of a bloodstream form (BSF) stage-specific putative flagellar host adaptation
factor (Tb927.11.2400) identified previously in a SILAC-based comparative proteome study.
Tb927.11.2400 shares 38% amino acid identity with TbFlabarin (Tb927.11.2410), a procyclic form
(PCF) stage specific flagellar BAR domain protein. We named Tb927.11.2400 TbFlabarin like
(TbFlabarinL) and demonstrate that it is a result of a gene duplication event, which occurred in
African trypanosomes. TbFlabarinL is not essential for growth of the parasites under cell culture
conditions and it is dispensable for developmental differentiation from BSF to the PCF in vitro. We
generated a TbFlabarinL-specific antibody and showed that it localizes in the flagellum. The
co-immunoprecipitation experiment together with a biochemical cell fractionation indicated a dual
association of TbFlabarinL with the flagellar
membrane and the components of the paraflagellar rod.
The protozoan parasite Trypanosoma brucei is the causal agent of sleeping sickness and besides its epidemiological importance it has been used as model organism for the study of many aspects of cellular and molecular biology especially the post-transcriptional control of gene expression.
Several studies in the last 30 years have shown the importance of mRNA processing and stability for gene regulation. In T. brucei genes are unusually arranged in polycistronic transcription units (PTUs) and a coupled process of trans-splicing and polyadenylation produces the mature mRNAs. Both processes, mRNA processing and stability, cannot completely explain the control of gene expression in the different life cycle stages analyzed in T. brucei so far.
In recent years, the relevance of expression regulation at the level of translation has become evident in other eukaryotes. Therefore, in the first part of my thesis I studied the impact of translational regulation by means of a genome-wide ribosome profiling approach. My data suggest that translational efficiencies vary between life cycle stages of the parasite as well as between genes within one life cycle stage. Furthermore, using ribosome profiling I was able to identify many new putative un-annotated coding sequences and to evaluate the coding potential of upstream open reading frames (uORF). Comparing my results with previously published proteomic and RNA interference (RNAi) target sequencing (RIT-seq) datasets allowed me to validate some of the new coding sequences and to evaluate their relevance for the fitness of the parasite.
In the second part of my thesis I used the transcriptomic and translatomic profiles obtained from the ribosome profiling analysis for the identification of putative non-coding RNAs (ncRNAs). These results led to the analysis of the coding potential in the regions upstream and downstream of the expressed variant surface glycoprotein (VSG), which is outlined in the third part of the results section. The region upstream of the VSG, the co-transposed region (CTR), has been implicated in an increase of the in situ switching rate upon its deletion. The ribosome profiling results indicated moderate transcription but not translation in this region. These results raised the possibility that the CTR may be transcribed into ncRNA. Therefore, in the third part of my thesis, I performed a primary characterization of the CTR-derived transcripts based on northern blotting and RACE. The results suggested the presence of a unique transcript species of about 1,200 nucleotides (nt) and polyadenylated at the 3’-end of the sequence.
The deletion of the CTR sequence promoting and increase of the in situ switching rates was performed around 20 years ago by means of inserting reporter genes. With the recent development of endonuclease-based tools for genome editing, it is now possible to delete sequences in a marker-free way. In the fourth part of my thesis, I show the results on the implementation of the highly efficient genome-editing CRISPR-Cas9 system in T. brucei using episomes. As a proof of principle, I inserted the sequence coding for the enhanced green fluorescent protein (eGFP) at the end of the SCD6 coding sequence (CDS). Fluorescent cells were observed as early as two days after transfection. Therefore, after the successful set up of the CRISPR-Cas9 system it will be possible to modify genomic regions with more relevance for the biology of the parasite, such as the substitution of codons present in gene tandem arrays.
The implementation of ribosome profiling in T. brucei opens the opportunity for the study of translational regulation in a genome-wide scale, the re-annotation of the currently available genome, the search for new putative coding sequences, the detection of putative ncRNAs, the evaluation of the coding potential in uORFs and the role of unstranslated regions (UTRs) in the regulation of translation. In turn, the implementation of the CRISPR-Cas9 system offers the possibility to manipulate the genome of the parasite at a nucleotide resolution and without the need of including resistant makers. The CRISPR-Cas9 system is a powerful tool for editing ncRNAs, UTRs, multicopy gene families and CDSs keeping their endogenous UTRs. Moreover, the system can be used for the modification of both alleles after just one round of transfection and of codons coding for amino acids carrying post-translational modifications (PTMs) among other possibilities.
Eukaryotic cells have several mRNA quality control checkpoints to avoid the production of aberrant proteins. Intron-containing mRNAs are actively degraded by the nuclear exosome, prevented from nuclear exit and, if these systems fail, degraded by the cytoplasmic NMD machinery. Trypanosomes have only two introns. However, they process mRNA5 from long polycistronic precursors by trans-splicing and polycistronic mRNA molecules frequently arise from any missed splice site. Here, we show that RNAi depletion of the trypanosome exosome, but not of the cytoplasmic 5'-3' exoribonuclease XRNA or the NMD helicase UPF1, causes accumulation of oligocistronic mRNA5. We have also revisited the localization of the trypanosome exosome by expressing eYFP-fusion proteins of the exosome subunits RRP44 and RRP6. Both proteins are significantly enriched in the nucleus. Together with published data, our data suggest a major nuclear function of the trypanosome exosome in rRNA, snoRNA and mRNA quality control.
Trypanosomes are masters of adaptation to different host environments during their complex life cycle. Large-scale proteomic approaches provide information on changes at the cellular level, and in a systematic way. However, detailed work on single components is necessary to understand the adaptation mechanisms on a molecular level. Here, we have performed a detailed characterization of a bloodstream form (BSF) stage-specific putative flagellar host adaptation factor Tb927.11.2400, identified previously in a SILAC-based comparative proteome study. Tb927.11.2400 shares 38% amino acid identity with TbFlabarin (Tb927.11.2410), a procyclic form (PCF) stage-specific flagellar BAR domain protein. We named Tb927.11.2400 TbFlabarin-like (TbFlabarinL), and demonstrate that it originates from a gene duplication event, which occurred in the African trypanosomes. TbFlabarinL is not essential for the growth of the parasites under cell culture conditions and it is dispensable for developmental differentiation from BSF to the PCF in vitro. We generated TbFlabarinL-specific antibodies, and showed that it localizes in the flagellum. Co-immunoprecipitation experiments together with a biochemical cell fractionation suggest a dual association of TbFlabarinL with the flagellar membrane and the components of the paraflagellar rod.
Base J, β-D-glucosyl-hydroxymethyluracil, is a chromatin modification of thymine in the nuclear DNA of flagellated protozoa of the order Kinetoplastida. In Trypanosoma brucei, J is enriched, along with histone H3 variant (H3.V), at sites involved in RNA Polymerase (RNAP) II termination and telomeric sites involved in regulating variant surface glycoprotein gene (VSG) transcription by RNAP I. Reduction of J in T. brucei indicated a role of J in the regulation of RNAP II termination, where the loss of J at specific sites within polycistronic gene clusters led to read-through transcription and increased expression of downstream genes. We now demonstrate that the loss of H3.V leads to similar defects in RNAP II termination within gene clusters and increased expression of downstream genes. Gene derepression is intensified upon the subsequent loss of J in the H3.V knockout. mRNA-seq indicates gene derepression includes VSG genes within the silent RNAP I transcribed telomeric gene clusters, suggesting an important role for H3.V in telomeric gene repression and antigenic variation. Furthermore, the loss of H3.V at regions of overlapping transcription at the end of convergent gene clusters leads to increased nascent RNA and siRNA production. Our results suggest base J and H3.V can act independently as well as synergistically to regulate transcription termination and expression of coding and non-coding RNAs in T. brucei, depending on chromatin context (and transcribing polymerase). As such these studies provide the first direct evidence for histone H3.V negatively influencing transcription elongation to promote termination.
African trypanosomiasis is a disease endemic to sub-Saharan Africa. It affects humans as well as wild and domestic animals. The human form of the disease is known as sleeping sickness and the animal form as nagana, which are usually fatal if left untreated. The cause of African trypanosomiasis is the unicellular parasite Trypanosoma brucei. During its life cycle, Trypanosoma brucei shuttles between a mammalian host and the tsetse fly vector. In the mammalian host the parasite multiplies as bloodstream form (BSF) extracellularly in the bloodstream or the lymphatic system. Survival of BSF parasites relies on immune evasion by antigenic variation of surface proteins because its extracellular lifestyle leads to direct exposure to immune responses. At any given time each BSF cell expresses a single type of variant surface glycoprotein (VSG) on its surface from a large repertoire. The active VSG is transcribed from one of 15 specialized subtelomeric domains, termed bloodstream expression sites (BESs). The remaining 14 BESs are silenced. This monoallelic expression and periodic switching of the expressed VSG enables to escape the immune response and to establish a persistent infection in the mammalian host. During developmental differentiation from BSF to the insect vector-resident procyclic form (PCF), the active BES is transcriptionally silenced to stop VSG transcription. Thus, all 15 BESs are inactive in the PCF cells as surface protein expression is developmentally regulated.
Previous reports have shown that the telomere complex components TbTRF, TbRAP1 and TbTIF2 are involved in VSG transcriptional regulation. However, the precise nature of their contribution remains unclear. In addition, no information is available about the role of telomeres in the initiation and regulation of developmental BES silencing. To gain insights into the regulatory mechanisms of telomeres on VSG transcription and developmental repression it is therefore essential to identify the complete composition of the trypanosome telomere complex.
To this end, we used two complementary biochemical approaches and quantitative label-free interactomics to determine the composition of telomere protein complexes in T. brucei. Firstly, using a telomeric pull-down assay we found 17 potential telomere-binding proteins including the known telomere-binding proteins TbTRF and TbTIF2. Secondly, by performing a co-immunoprecipitation experiment to elucidate TbTRF interactions we co-purified five proteins. All of these five proteins were also enriched with telomeric DNA in the pull-down assay.
To validate these data, I characterized one of the proteins found in both experiments (TelBP1). In BSF cells, TelBP1 co-localizes with TbTRF and interacts with already described telomere-binding proteins such as TbTRF, TbTIF2 and TbRAP1 indicating that TelBP1 is a novel component of the telomere complex in trypanosomes. Interestingly, protein interaction studies in PCF cells suggested a different telomere complex composition compared to BSF cells. In contrast to known members of the telomere complex, TelBP1 is dispensable for cell viability indicating that its function might be uncoupled from the known telomere-binding proteins. Overexpression of TelBP1 had also no effect on cell viability, but led to the discovery of two additional shorter isoforms of TelBP1. However, their source and function remained elusive.
Although TelBP1 is not essential for cell viability, western blot analysis revealed a 4-fold upregulation of TelBP1 in the BSF stage compared to the PCF stage supporting the concept of a dynamic telomere complex composition. We observed that TelBP1 influences the kinetics of transcriptional BES silencing during developmental transition from BSF to PCF. Deletion of TelBP1 caused faster BES silencing compared to wild-type parasites.
Taken together, TelBP1 function illustrates that developmental BES silencing is a fine-tuned process, which involves stage-specific changes in telomere complex formation.
Trypanosoma brucei is a protozoan flagellate that is transmitted by tsetse flies into the mammalian bloodstream. The parasite has a huge impact on human health both directly by causing African sleeping sickness and indirectly, by infecting domestic cattle. The biology of trypanosomes involves some highly unusual, nuclear-localised processes. These include polycistronic transcription without classical promoters initiated from regions defined by histone variants, trans-splicing of all transcripts to the exon of a spliced leader RNA, transcription of some very abundant proteins by RNA polymerase I and antigenic variation, a switch in expression of the cell surface protein variants that allows the parasite to resist the immune system of its mammalian host. Here, we provide the nuclear proteome of procyclic Trypanosoma brucei, the stage that resides within the tsetse fly midgut. We have performed quantitative label-free mass spectrometry to score 764 significantly nuclear enriched proteins in comparison to whole cell lysates. A comparison with proteomes of several experimentally characterised nuclear and non-nuclear structures and pathways confirmed the high quality of the dataset: the proteome contains about 80% of all nuclear proteins and less than 2% false positives. Using motif enrichment, we found the amino acid sequence KRxR present in a large number of nuclear proteins. KRxR is a sub-motif of a classical eukaryotic monopartite nuclear localisation signal and could be responsible for nuclear localization of proteins in Kinetoplastida species. As a proof of principle, we have confirmed the nuclear localisation of six proteins with previously unknown localisation by expressing eYFP fusion proteins. While proteome data of several T. brucei organelles have been published, our nuclear proteome closes an important gap in knowledge to study trypanosome biology, in particular nuclear-related processes.
Single-molecule fluorescence microscopy in live \(Trypanosoma\) \(brucei\) and model membranes
(2018)
The eukaryotic parasite Trypanosoma brucei has evolved sophisticated strategies to escape
the host immune response and maintain a persistent infection inside a host. One central
feature of the parasite’s defense mechanism relies on the shielding function of their surface
protein coat. This coat is composed of a dense arrangement of one type of glycosylphosphatidylinositol
(GPI)-anchored variant surface glycoproteins (VSGs) which impair the
identification of epitopes of invariant surface proteins by the immune system. In addition
to the importance of understanding the function of the VSG coat and use it as a potential
target to efficiently fight the parasite, it is also crucial to study its biophysical properties as it is not yet understood sufficiently. This is due to the fact that microscopic investigations
on living trypanosomes are limited to a great extent by the intrinsic motility of the parasite.
In the present study, state-of-the-art single-molecule fluorescence microscopy (SMFM)
is introduced as a tool for biophysical investigations in the field of trypanosome research.
The work encompasses studies of VSG dynamics under the defined conditions of an
artificial supported lipid bilayer (SLB). First, the impact of the lateral protein density on
VSG diffusion was systematically studied in SLBs. Ensemble fluorescence after photobleaching
(FRAP) and complementary single-particle tracking experiments revealed that a
molecular crowding threshold (MCT) exists, above which a density dependent decrease
of the diffusion coefficient is measured. A relative quantification of reconstituted VSGs
illustrated that the VSG coat of living trypanosomes operates very close to its MCT and
is optimized for high density while maintaining fluidity. Second, the impact of VSG
N-glycosylation on VSG diffusion was quantitatively investigated. N-glycosylation was
shown to contribute to preserving protein mobility at high protein concentrations. Third,
a detailed analysis of VSG trajectories revealed that two distinct populations of freely
diffusing VSGs were present in a SLB, which is in agreement with the recent finding, that
VSGs are able to adopt two main structurally distinct conformations. The results from
SLBs were further complemented by single-particle tracking experiments of surface VSGs
on living trypanosomes. A high mobility and free diffusion were measured on the cell
surface, illustrating the overall dynamic nature of the VSG coat. It was concluded that
the VSG coat on living trypanosomes is a protective structure that combines density and
mobility, which is supported by the conformational flexibility of VSGs. These features are
elementary for the persistence of a stable infection in the host.
Different hydrogel embedding methods are presented, that facilitated SMFM in immobilized,
living trypanosomes. The hydrogels were found to be highly cytocompatible for one
hour after cross-linking. They exhibited low autofluorescence properties in the spectral
range of the investigations, making them suitable for super-resolution microscopy (SRM).
Exemplary SRM on living trypanosomes illustrated that the hydrogels efficiently immobilized
the cells on the nanometer lever. Furthermore, the plasma membrane organization was studied in living trypanosomes. A statistical analysis of a tracer molecule inside the
inner leaflet of the plasma membrane revealed that specific membrane domains exist, in
which the tracer appeared accumulated or diluted. It was suggested that this distribution
was caused by the interaction with proteins of the underlying cytoskeleton.
In conclusion, SMFM has been successfully introduced as a tool in the field of trypanosome
research. Measurements in model membranes facilitated systematic studies of VSG dynamics
on the single-molecule level. The implementation of hydrogel immobilization
allowed for the study of static structures and dynamic processes with high spatial and
temporal resolution in living, embedded trypanosomes for the first time.
For cellular viability, transcription is a fundamental process. Hereby, the DNA plays the most elemental and highly versatile role. It has long been known that promoters contain conserved and often well-defined motifs, which dictate the site of transcription initiation by providing binding sites for regulatory proteins. However, research within the last decade revealed that it is promoters lacking conserved promoter motifs and transcribing constitutively expressed genes that constitute the majority of promoters in eukaryotes. While the process of transcription initiation is well studied, whether defined DNA sequence motifs are required for the transcription of constitutively expressed genes in eukaryotes remains unknown. In the highly divergent protozoan parasite Trypanosoma brucei, most of the proteincoding genes are organized in large polycistronic transcription units. The genes within one polycistronic transcription unit are generally unrelated and transcribed by a common transcription start site for which no RNA polymerase II promoter motifs have been identified so far. Thus, it is assumed that transcription initiation is not regulated but how transcription is initiated in T. brucei is not known. This study aimed to investigate the requirement of DNA sequence motifs and chromatin structures for transcription initiation in an organism lacking transcriptional regulation. To this end, I performed a systematic analysis to investigate the dependence of transcription initiation on the DNA sequence. I was able to identify GT-rich promoter elements required for directional transcription initiation and targeted deposition of the histone variant H2A.Z, a conserved component during transcription initiation. Furthermore, nucleosome positioning data in this work provide evidence that sites of transcription initiation are rather characterized by broad regions of open and more accessible chromatin than narrow nucleosome depleted regions as it is the case in other eukaryotes. These findings highlight the importance of chromatin during transcription initiation. Polycistronic RNA in T. brucei is separated by adding an independently transcribed miniexon during trans-splicing. The data in this work suggest that nucleosome occupancy plays an important role during RNA maturation by slowing down the progressing polymerase and thereby facilitating the choice of the proper splice site during trans-splicing. Overall, this work investigated the role of the DNA sequence during transcription initiation and nucleosome positioning in a highly divergent eukaryote. Furthermore, the findings shed light on the conservation of the requirement of DNA motifs during transcription initiation and the regulatory potential of chromatin during RNA maturation. The findings improve the understanding of gene expression regulation in T. brucei, a eukaryotic parasite lacking transcriptional Regulation.
The eukaryotic parasite Trypanosoma brucei has evolved sophisticated strategies to persist within its mammalian host. Trypanosomes evade the hosts' immune system by antigenic variation of their surface coat, consisting of variant surface glycoproteins (VSGs). Out of a repertoire of thousands of VSG genes, only one is expressed at any given time from one of the 15 telomeric expression sites (ES). The VSG is stochastically exchanged either by a transcriptional switch of the active ES (in situ switch) or by a recombinational exchange of the VSG within the active ES. However, for infections to persist, the parasite burden has to be limited. The slender (sl) bloodstream form secretes the stumpy induction factor (SIF), which accumulates with rising parasitemia. SIF induces the irreversible developmental transition from the proliferative sl to the cell cycle-arrested but fly-infective stumpy (st) stage once a concentration threshold is reached. Thus, antigenic variation and st development ensure persistent infections and transmissibility. A previous study in monomorphic cells indicated that the attenuation of the active ES could be relevant for the development of trypanosomes. The present thesis investigated this hypothesis using the inducible overexpression of an ectopic VSG in pleomorphic trypanosomes, which possess full developmental competence. These studies revealed a surprising phenotypic plasticity: while the endogenous VSG was always down-regulated upon induction, the ESactivity determined whether the VSG overexpressors arrested in growth or kept proliferating. Full ES-attenuation induced the differentiation of bona fide st parasites independent of the cell density and thus represents the sole natural SIF-independent differentiation trigger to date. A milder decrease of the ES-activity did not induce phenotypic changes, but appeared to prime the parasites for SIF-induced differentiation. These results demonstrate that antigenic variation and development are linked and indicated that the ES and the VSG are independently regulated. Therefore, I investigated in the second part of my thesis how ES-attenuation and VSG-silencing can be mediated. Integration of reporters with a functional or defective VSG 3'UTR into different genomic loci showed that the maintenance of the active state of the ES depends on a conserved motif within the VSG 3'UTR. In situ switching was only triggered when the telomere-proximal motif was partially deleted, suggesting that it serves as a DNA-binding motif for a telomere-associated protein. The VSG levels seem to be additionally regulated in trans based on the VSG 3'UTR independent of the genomic context, which was reinforced by the regulation of a constitutively expressed reporter with VSG 3' UTR upon ectopic VSG overexpression.
The nuclear envelope serves as important mRNA surveillance system. In yeast and humans, several control mechanisms act in parallel to prevent nuclear export of unprocessed mRNAs. However, trypanosomes lack homologues to most of the proteins involved. In addition, gene expression in trypanosomes relies almost completely on post-transcriptional regulation as they transcribe mRNAs as long polycistrons, which are subsequently processed into individual mRNA molecules by trans-splicing. As trans-splicing is not error-free, unspliced mRNAs may be recognized and prevented from reaching the cytoplasm by a yet unknown mechanism.
When trans-splicing is inhibited in trypanosomes, the formation of a novel RNA granule type at the cytoplasmic periphery of the nucleus, so called nuclear periphery granules (NPGs) was previously observed. To identify potential regulators of nuclear export control, changes in protein localization which occur when trans-splicing is inhibited, were globally analyzed during this work. For this, trypanosome nuclei were purified under conditions maintaining NPG attachment to the nucleus, in the absence and presence of trans-splicing. Mass spectrometry analyses identified 128 proteins which are specifically enriched in nuclear preparations of cells inhibited for trans-splicing. Amongst them are proteins, which change their localization to the nucleus or to the nuclear pores as well as many proteins that move into NPGs. Some of these proteins are promising candidates for nuclear export control proteins, as the changes in localization (to the nucleus or nuclear pores) were specific to the accumulation of unspliced mRNAs. The NPG proteome almost exclusively contains proteins involved in mRNA metabolism, mostly unique to trypanosomes, notably major translation initiation factors were absent. These data indicate that NPGs are RNP complexes which have started or completed nuclear export, but not yet entered translation. As a byproduct of these proteomic studies, a high-quality dataset of the yet unknown T. brucei nuclear proteome is provided, closing an important gap in knowledge to study trypanosome biology, in particular nuclear related processes.
NPGs were characterized in more detail by microscopy. The granules are cytoplasmic and present in at least two different trypanosome life cycle stages. There are at least two distinct granule subsets, with differences in protein composition. A closer analysis of NPGs by electron microscopy revealed that the granules are electron dense structures, which are connected to nuclear pores by string-like structures.
In order to approach the function of NPGs, on the one hand, the hypothesis that NPGs might be related to perinuclear germ granules of adult gonads of C. elegans was tested: we found no relation between the two granule types. On the other hand, initial single molecule mRNA FISH experiments performed in trypanosomes showed no accumulation of unspliced transcripts in NPGs, arguing against an involvement of the granules in mRNA quality control.