HelF, a suppressor of RNAi mediated gene silencing in Dictyostelium discoideum

RNA interference (RNAi) is a recently discovered process, in which double stranded RNA (dsRNA) triggers the homology-dependant degradation of cognate messenger RNA (mRNA). In a search for new components of the RNAi machinery in Dictyostelium, a new gene was identified, which was called helF. HelF is a putative RNA helicase, which shows a high homology to the helicase domain of Dicer, to the helicase domain of Dictyostelium RdRP and to the C. elegans gene drh-1, that codes for a dicer related DExH-box RNA helicase, which is required for RNAi. The aim of the present Ph.D. work was to investigate the role of HelF in PTGS, either induced by RNAi or asRNA. A genomic disruption of the helF gene was performed, which resulted in a distinct mutant morphology in late development. The cellular localization of the protein was elucidated by creating a HelF-GFP fusion protein, which was found to be localized in speckles in the nucleus. The involvement of HelF in the RNAi mechanism was studied. For this purpose, RNAi was induced by transformation of RNAi hairpin constructs against four endogenous genes in wild type and HelF- cells. The silencing efficiency was strongly enhanced in the HelF K.O. strain in comparison with the wild type. One gene, which could not be silenced in the wild type background, was successfully silenced in HelF-. When the helF gene was disrupted in a secondary transformation in a non-silenced strain, the silencing efficiency was strongly improved, a phenomenon named here “retrosilencing”. Transcriptional run-on experiments revealed that the enhanced gene silencing in HelF- was a posttranscriptional event, and that the silencing efficiency depended on the transcription levels of hairpin RNAs. In HelF-, the threshold level of hairpin transcription required for efficient silencing was dramatically lowered. The RNAi-mediated silencing was accompanied by the production of siRNAs; however, their amount did not depend on the level of hairpin transcription. These results indicated that HelF is a natural suppressor of RNAi in Dictyostelium. In contrast, asRNA mediated gene silencing was not enhanced in the HelF K.O, as shown for three tested genes. These results confirmed previous observations (H. Martens and W. Nellen, unpublished) that although similar, RNAi and asRNA mediated gene silencing mechanisms differ in their requirements for specific proteins. In order to characterize the function of the HelF protein on a molecular level and to study its interactions with other RNAi components, in vitro experiments were performed. Besides the DEAH-helicase domain, HelF contains a double-stranded RNA binding domain (dsRBD) at its N-terminus, which showed high similarity to the dsRBD domain of Dicer A from Dictyostelium. The ability of the recombinant dsRBDs from HelF and Dicer A to bind dsRNA was examined and compared. It was shown by gel-shift assays that both HelF-dsRBD and Dicer-dsRBD could bind directly to long dsRNAs. However, HelF-dsRBD bound more efficiently to dsRNA with imperfect matches than to perfect dsRNA. Both dsRBDs bound specifically to a pre-miRNA substrate (pre-let-7). The results suggested that most probably there were two binding sites for the proteins on the pre-miRNA substrate. Moreover, it was shown that HelF-dsRBD and Dicer-dsRBD have siRNA-binding activity. The affinities of the two dsRBDs to the pre-let-7 substrate were also examined by plasmon surface resonance analyses, which revealed a 9-fold higher binding affinity of the Dicer-dsRBD to pre-let-7 compared to that of the HelF-dsRBD. The binding of HelF-dsRBD to the pre-let-7 was impaired in the presence of Mg2+, while the Dicer-dsRBD interaction with pre-let-7 was not influenced by the presence of Mg2+. The results obtained in this thesis can be used to postulate a model for HelF function. In this, HelF acts as a nuclear suppressor of RNAi in wild type cells by recognition and binding of dsRNA substrates. The protein might act as a surveillance system to avoid RNAi initiation by fortuitous dsRNA formation or low abundance of dsRNA trigger. If the protein acts as an RNA helicase, it could unwind fold-back structures in the nucleus and thus lead to decreased RNAi efficiency. A knock-out of HelF would result in initiation of the RNAi pathway even by low levels of dsRNA. The exact molecular function of the protein in the RNAi mechanism still has to be elucidated. RNA interferenz (RNAi) ist ein in jüngster Zeit entdeckter Mechanismus, bei dem doppelsträngige RNA Moleküle (dsRNA) eine Homologie-abhängige Degradation einer verwandten messenger-RNA (mRNA) auslösen. Auf der Suche nach neuen Komponenten der RNAi-Maschinerie in Dictyostelium konnte ein neues Gen (helF) identifiziert werden. HelF ist eine putative RNA-Helikase mit einer hohen Homologie zur Helikasedomäne der bekannten Dicerproteine, der Helikasedomäne der Dictyostelium RdRP und zu dem C. elegans Gen drh-1, welches für eine Dicer-bezogene DExH-box RNA Helikase codiert, die am RNAi-Mechanismus beteiligt ist. Das Ziel dieser Arbeit war es, die Funktion von HelF im Zusammenhang des RNAi oder asRNA induzierten PTGS zu untersuchen. Es wurde eine Unterbrechung des helF-Gens auf genomischer Ebene (K.O.) vorgenommen, was bei den Mutanten zu einer veränderten Morphologie in der späten Entwicklung führte. Die Lokalisation des Proteins in der Zelle konnte mit Hilfe einer GFP-Fusion analysiert werden und kleinen Bereichen innerhalb des Nukleus zugewiesen werden. Im Weiteren wurde der Einfluss von HelF auf den RNAi-Mechanismus untersucht. Zu diesem Zweck wurde RNAi durch Einbringen von RNAi Hairpin-Konstrukten gegen vier endogene Gene im Wiltypstamm und der HelF--Mutante induziert. Im Vergleich zum Wildtypstamm konnte im HelF--Mutantenstamm eine stark erhöhte „Silencing“-Effizienz nachgewiesen werden. Ein Gen, welches nach RNAi Initiation im Wildtypstamm unverändert blieb, konnte im HelF--Mutantenstamm erfolgreich stillgelegt werden. Durch sekundäres Einführen einer Gendisruption im helF-Locus in einen Stamm, in welchem ein Gen nicht stillgelegt werden konnte, wurde die Effizienz des Stilllegens deutlich erhöht. Dieses Phänomen wurde hier erstmals als „Retrosilencing“ beschrieben. Mit Hilfe von transkriptionellen run-on Experimenten konnte belegt werden, dass es sich bei dieser erhöhten Stilllegungseffizienz um ein posttranskriptionelles Ereignis handelte, wobei die Stillegungseffizienz von der Transkriptionsstärke der Hairpin RNAs abhängt. Für die HelF--Mutanten konnte gezeigt werden, dass der Schwellenwert zum Auslösen eines effizienten Stillegens dramatisch abgesenkt war. Obwohl die RNAi-vermittelte Genstilllegung immer mit der Produktion von siRNAs einhergeht, war die Menge der siRNAs nicht abhängig von dem Expressionsniveau des Hairpin-Konstruktes. Diese Ergebnisse legen nahe, dass es sich bei der HelF um einen natürlichen Suppressor des RNAi-Mechanismus in Dictyostelium handelt. Im Gegensatz hierzu war die as-vermittelte Stilllegung von drei untersuchten Genen im HelF-K.O. im Vergleich zum Wildyp unverändert. Diese Ergebnisse bestätigten frühere Beobachtungen (H. Martens und W. Nellen, unveröffentlicht), wonach die Mechanismen für RNAi und asRNA-vermittelte Genstilllegung unterschiedliche spezifische Proteine benötigen. Um die Funktion des HelF-Proteins auf der molekularen Ebene genauer zu charakterisieren und die Interaktion mit anderen RNAi-Komponenten zu untersuchen, wurden in vitro Versuche durchgeführt. Das HelF-Protein enthält, neben der DEAH-Helikase-Domäne eine N-terminale Doppelstrang RNA bindende Domäne (dsRBD) mit einer hohen Ähnlichkeit zu der dsRBD des Dicer A aus Dictyostelium. Die dsRNA-Bindungsaktivität der beiden dsRBDs aus HelF und Dicer A wurde analysiert und verglichen. Es konnte mithilfe von Gel-Retardationsanalysen gezeigt werden, dass sowohl HelF-dsRBD als auch Dicer-dsRBD direkt an lange dsRNAs binden können. Hierbei zeigte sich, dass die HelF-dsRBD eine höhere Affinität zu einem imperfekten RNA-Doppelstrang besitzt, als zu einer perfekt gepaarten dsRNA. Für beide dsRBDs konnte eine spezifische Bindung an ein pre-miRNA Substrat nachgewiesen werden (pre-let-7). Dieses Ergebnis legt nah, dass es zwei Bindestellen für die Proteine auf dem pre-miRNA Substrat gibt. Überdies hinaus konnte gezeigt werden, dass die dsRBDs beider Proteine eine siRNA bindende Aktivität besitzen. Die Affinität beider dsRBDs an das pre-let-7 Substrat wurde weiterhin mit Hilfe der Plasmon Oberflächen Resonanz untersucht. Hierbei konnte eine 9-fach höhere Bindeaffinität der Dicer-dsRBD im Vergleich zur HelF-dsRBD nachgewiesen werden. Während die Bindung der HelF-dsRBD an das pre-let-7 durch die Anwesenheit von Mg2+ beeinträchtigt war, zeigte sich kein Einfluß von Mg2+ auf das Bindeverhalten der Dicer-dsRBD. Mit Hilfe der in dieser Arbeit gewonnen Ergebnisse lässt sich ein Model für die Funktion von HelF postulieren. In diesem Model wirkt HelF durch Erkennen und Binden von dsRNA Substraten als Suppressor von der RNAi im Kern. Das Protein kann als Überwachungsystem gegen eine irrtümliche Auslösung von RNAi wirken, die durch zufällige dsRNA Faltungen oder eine zu geringe Häufigkeit der siRNAs hervorgerufen sein könnte. Falls das Protein eine Helikase-Aktivität besitzt, könnte es rückgefaltete RNA Strukturen im Kern auflösen, was sich in einer verringerten RNAi-Effizienz wiederspiegelt. Durch Ausschalten des helF-Gens würde nach diesem Modell eine erfolgreiche Auslösung von RNAi schon bei sehr geringer Mengen an dsRNA möglich werden. Das Modell erlaubt, die exakte molekulare Funktion des HelF-Proteins im RNAi-Mechanismus weiter zu untersuchen.

The role of Ken&Barbie in JAK/STAT signalling during development of Drosophila melanogaster

Cell-cell interactions during embryonic development are crucial in the co-ordination of growth, differentiation and maintenance of many different cell types. To achieve this co-ordination each cell must properly translate signals received from neighbouring cells, into spatially and temporally appropriate developmental responses. A surprisingly limited number of signal pathways are responsible for the differentiation of enormous variety of cell types. As a result, pathways are frequently 'reused' during development. Thus, in mammals the JAK/STAT pathway is required during early embryogenesis, mammary gland formation, hematopoiesis and, finally, plays a pivotal role in immune response. In the canonical way, the JAK/STAT pathway is represented by a transmembrane receptor associated with a Janus kinase (JAK), which upon stimulation by an extra-cellular ligand, phosphorylates itself, the receptor and, finally, the signal transducer and activator of transcription (STAT) molecules. Phosphorylated STATs dimerise and translocate to the nucleus where they activate transcription of target genes. The JAK/STAT pathway has been conserved throughout evolution, and all known components are present in the genome of Drosophila melanogaster. Besides hematopoietic and immunity functions, the pathway is also required during development for processes including embryonic segmentation, tracheal morphogenesis, posterior spiracle formation etc. This study describes Drosophila Ken&Barbie (Ken) as a selective regulator of JAK/STAT signalling. ken mutations identified in a screen for modulators of an eye overgrowth phenotype, caused by over-expression of the pathway ligand unpaired, also interact genetically with the pathway receptor domeless (dome) and the transcription factor stat92E. Over-expression of Ken can phenocopy developmental defects known to be caused by the loss of JAK/STAT signalling. These genetic interactions suggest that Ken may function as a negative regulator of the pathway. Ken has C-terminal Zn-finger domain, presumably for DNA binding, and N-terminal BTB/POZ domain, often found in transcriptional repressors. Using EGFP-fused construct expressed in vivo revealed nuclear accumulation of Ken. Therefore, it is proposed that Ken may act as a suppresser of STAT92E target genes. An in vitro assay, termed SELEX, determined that Ken specifically binds to a DNA sequence, with the essential for DNA recognition core overlapping that of STAT92E. This interesting observation suggests that not all STAT92E sites may also allow Ken binding. Strikingly, when effects of ectopic Ken on the expression of putative JAK/STAT pathway target genes were examined, only a subset of the genes tested, namely vvl, trh and kni, were down-regulated by Ken, whereas some others, such as eve and fj, appeared to be unresponsive. Further analysis of vvl, one of the genes susceptible to ectopic Ken, was undertaken. In the developing hindgut, expression of vvl is JAK/STAT pathway dependent, but remains repressed in the posterior spiracles, despite the stimulation of STAT92E by Upd in their primordia. Importantly, ken is also expressed in the developing posterior spiracles. Strikingly, up-regulation of vvl is observed in these tissues in ken mutant embryos. These imply that while ectopic Ken is sufficient to repress the expression of vvl in the hindgut, endogenous Ken is also necessary to prevent its activation in the posterior spiracles. It is therefore conceivable that ectopic vvl expression in the posterior spiracles of the ken mutants may be the result of de-repression of endogenous STAT92E activity. Another consequence of these observations is a fine balance that must exist between STAT92E and Ken activities. Apparently, endogenous level of Ken is sufficient to repress vvl, but not other, as yet unidentified, JAK/STAT pathway targets, whose presumable activation by STAT92E is required for posterior spiracle development as the embryos mutant for dome, the receptor of the pathway, show severe spiracle defects. These defects are also observed in the embryos mis-expressing Ken. Though it is possible that the posterior spiracle phenotype caused by higher levels of Ken results from a JAK/STAT pathway independent activity, it seems to be more likely that Ken acts in a dosage dependent manner, and extra Ken is able to further antagonise JAK/STAT pathway target genes. While STAT92E binding sites required for target gene expression have been poorly characterised, the existence of genome data allows the prediction of candidate STAT92E sites present in target genes promoters to be attempted. When a 6kb region containing the putative regulatory domains flanking the vvl locus are examined, only a single potential STAT92E binding site located 825bp upstream of the translational start can be detected. Strikingly, this site also includes a perfect Ken binding sequence. Such an in silico observation, though consistent with both Ken DNA binding assay in vitro and regulation of STAT92E target genes in vivo, however, requires further analysis. The JAK/STAT pathway is implicated in a variety of processes during embryonic and larval development as well as in imago. In each case, stimulation of the same transcription factor results in different developmental outcomes. While many potential mechanisms have been proposed and demonstrated to explain such pleiotropy, the present study indicates that Ken may represent another mechanism, with which signal transduction pathways are controlled. Ken selectively down-regulates a subset of potential target genes and so modifies the transcriptional profile generated by activated STAT92E - a mechanism, which may be partially responsible for differences in the morphogenetic processes elicited by JAK/STAT signalling during development.

Studies of cap-independent mRNA translation in Drosophila melanogaster

Control of protein synthesis is a key step in the regulation of gene expression during apoptosis and the heat shock response. Under such conditions, cap-dependent translation is impaired and Internal Ribosome Entry Site (IRES)-dependent translation plays a major role in mammalian cells. Although the role of IRES-dependent translation during apoptosis has been mainly studied in mammals, its role in the translation of Drosophila apoptotic genes has not been yet studied. The observation that the Drosophila mutant embryos for the cap-binding protein, the eukaryotic initiation factor eIF4E, exhibits increased apoptosis in correlation with up-regulated proapoptotic gene reaper (rpr) transcription constitutes the first evidence for the existence of a cap-independent mechanism for the translation of Drosophila proapoptotic genes. The mechanism of translation of rpr and other proapoptotic genes was investigated in this work. We found that the 5 UTR of rpr mRNA drives translation in an IRES-dependent manner. It promotes the translation of reporter RNAs in vitro either in the absence of cap, in the presence of cap competitors, or in extracts derived from heat shocked and eIF4E mutant embryos and in vivo in cells transfected with reporters bearing a non functional cap structure, indicating that cap recognition is not required in rpr mRNA for translation. We also show that rpr mRNA 5 UTR exhibits a high degree of similarity with that of Drosophila heat shock protein 70 mRNA (hsp70), an antagonist of apoptosis, and that both are able to conduct IRES-mediated translation. The proapoptotic genes head involution defective (hid) and grim, but not sickle, also display IRES activity. Studies of mRNA association to polysomes in embryos indicate that both rpr, hsp70, hid and grim endogenous mRNAs are recruited to polysomes in embryos in which apoptosis or thermal stress was induced. We conclude that hsp70 and, on the other hand, rpr, hid and grim which are antagonizing factors during apoptosis, use a similar mechanism for protein synthesis. The outcome for the cell would thus depend on which protein is translated under a given stress condition. Factors involved in the differential translation driven by these IRES could play an important role. For this purpose, we undertook the identification of the ribonucleoprotein (RNP) complexes assembled onto the 5 UTR of rpr mRNA. We established a tobramycin-affinity-selection protocol that allows the purification of specific RNP that can be further analyzed by mass spectrometry. Several RNA binding proteins were identified as part of the rpr 5 UTR RNP complex, some of which have been related to IRES activity. The involvement of one of them, the La antigen, in the translation of rpr mRNA, was established by RNA-crosslinking experiments using recombinant protein and rpr 5 UTR and by the analysis of the translation efficiency of reporter mRNAs in Drosophila cells after knock down of the endogenous La by RNAi experiments. Several uncharacterized proteins were also identified, suggesting that they might play a role during translation, during the assembly of the translational machinery or in the priming of the mRNA before ribosome recognition. Our data provide evidence for the involvement of La antigen in the translation of rpr mRNA and set a protocol for purification of tagged-RNA-protein complexes from cytoplasmic extracts. To further understand the mechanisms of translation initiation in Drosophila, we analyzed the role of eIF4B on cap-dependent and cap-independent translation. We showed that eIF4B is mostly involved in cap-, but not IRES-dependent translation as it happens in mammals.

Characterization of the role of Drosophila JAK/STAT signalling in cellular proliferation

Der Janus Kinase / signal transducer and activator of transcription (JAK/STAT) Signal- transduktionsweg wird für viele Entwicklungsvorgänge benötigt und spielt eine zentrale Rolle bei der Hämatopoese und bei der Immunantwort. Obwohl der JAK/STAT-Signalweg in den vergangenen Jahren Gegenstand intensiver Forschung war, erschwert die Redundanz des Signalwegs bei Wirbeltieren genetische Untersuchungen zur Identifizierung derjenigen Mechanismen, die den JAK/STAT-Signalweg regulieren. Der JAK/STAT-Signaltransduktionsweg ist evolutionär konserviert und ebenfalls bei der Taufliege Drosophila melanogaster vorhanden. Im Gegensatz zu Wirbeltieren ist der Signaltransduktionsweg von Drosophila weniger redundant und beinhaltet folgende Hauptkomponenten: den Liganden Unpaired (Upd), den Transmembranrezeptor Domeless (Dome), die einzige JAK-Tyrosinkinase Hopscotch (hop), sowie den Transkriptionsfaktor STAT92E. In der vorliegenden Arbeit wird die Rolle des JAK/STAT-Signalwegs bei der zellulären Proliferation mithilfe der Modellsysteme der Flügel- und der Augen-Imaginalscheiben von Drosophila charakterisiert. "Loss-of-function"- und "Gain-of-function"-Experimente zur Verminderung beziehungs-weise Erhöhung der Signalaktivität zeigten, dass der JAK/STAT-Signalweg eine Rolle bei der zellulären Proliferation der Flügel-Imaginalscheiben spielte, ohne die Zellgröße oder Apoptose zu verändern. Bei der Flügelentwicklung während des zweiten und des frühen dritten Larvalstadiums war die Aktivität des JAK/STAT-Signalwegs sowohl notwendig für die zelluläre Proliferation als auch hinreichend, um Überproliferation anzutreiben. Allerdings änderte sich während der späten dritten Larvalstadien die JAK/STAT-Signalaktivität, sodass endogene STAT92E-Mengen einen anti-proliferativen Effekt im gleichen Gewebe aufwiesen. Weiterhin reichte die ektopische Aktivierung des JAK/STAT-Signalwegs zu diesem späten Entwicklungszeitpunkt aus, um die Mitose zu inhibieren und die Zellen in der Phase G2 des Zellzyklus zu arretieren. Diese Ergebnisse legen den Schluss nahe, dass der JAK/STAT-Signalweg sowohl pro-proliferativ in frühen Flügelscheiben als auch anti-proliferativ zu späten Stadien der Flügelscheiben-Entwicklung wirken kann. Dieser späte anti-proliferative Effekt wurde durch einen nicht-kanonischen Mechanismus der STAT92E-Aktivierung vermittelt, da späte hop defiziente Zellverbände im Vergleich zu Wildtyp-Zellen keine Veränderungen im Ausmaß der zellulären Proliferation aufwiesen. Ferner konnte gezeigt werden, dass eine während der Larvalstadien exprimierte dominant-negative und im N-Terminus deletierte Form von STAT92E (?NSTAT92E) nicht für den anti-proliferativen Effekt verantwortlich ist. Diese Tatsache ist ein weiteres Indiz dafür, dass das vollständige STAT92E den späten anti-proliferativen Effekt verursacht. Um Modulatoren für die von JAK/STAT vermittelte zelluläre Proliferation zu identifieren, wurde ein P-Element-basierter genetischer Interaktions-Screen in einem sensibilisierten genetischen Hintergrund durchgeführt. Insgesamt wurden dazu 2267 unabhängige P-Element-Insertionen auf ihre Wechselwirkung mit der JAK/STAT-Signalaktivität untersucht und 24 interagierende Loci identifiziert. Diese Kandidaten können in folgende Gruppen eingeordnet werden: Zellzyklusproteine, Transkriptionsfaktoren, DNA und RNA bindende Proteine, ein Mikro-RNA-Gen, Komponenten anderer Signaltransduktionswege und Zelladhäsionsproteine. In den meisten Fällen wurden mehrere Allele der interagierenden Kandidatengene getestet. 18 Kandidatengene mit übereinstimmend interagierenden Allelen wurden dann zur weiteren Analyse ausgewählt. Von diesen 18 Kandidaten-Loci wurden 7 mögliche JAK/STAT-Signalwegskomponenten und 6 neue Zielgene des Signalwegs gefunden. Zusammenfassend wurde das Verständnis um STAT92E verbessert. Dieses Protein hat die gleiche Funktion wie das STAT3-Protein der Wirbeltiere und treibt die zelluläre Proliferation voran. Analog zu STAT1 hat STAT92E aber auch einen anti-proliferativen Effekt. Ferner wurden 24 mögliche Modulatoren der JAK/STAT-Signalaktivität identifiziert. Die Charakterisierung dieser Wechselwirkungen eröffnet vielversprechende Wege zu dem Verständnis, wie JAK/STAT die zelluläre Proliferation reguliert und könnte bei der Entwicklung von neuartigen therapeutischen Targets zur Behandlung von Krebskrankheiten und Entwicklungsstörungen beitragen.

Mechanisms of residue mulch-induced cereal growth increases in West Africa

The use of crop residues (CR) has been widely reported as a means of increasing crop yields across West Africa. However, little has been done to compare the magnitude and mechanisms of CR effects systematically in the different agro-ecological zones of the region. To this end, a series of field trials with millet (Pennisetum glaucum L.), sorghum [Sorghum bicolor (L.) Moench], and maize (Zea mays L.) was conducted over a 4-yr period in the Sahelian, Sudanian, and Guinean zones of West Africa. Soils ranged in pH from 4.1 to 5.4 along a rainfall gradient from 510 to 1300 mm. Treatments in the factorial experiments were three CR rates (0,500, and 2000 kg ha^-1)and several levels of phosphorus and nitrogen. The results showed CR-induced total dry matter (TDM) increases in cereals up to 73% for the Sahel compared with a maximum of 16% in the wetter Sudanian and Guinean zones. Residue effects on weakly buffered Sahelian soils were due to improved P availability and to a protection of seedlings against wind erosion. Additional effects of CR mulching on topsoil properties in the Sahel were a decrease in peak temperatures by 4°C and increased water availability. These mulch effects on soil chemical and physical properties strongly decreased from North to South. Likely explanations for this decrease are the decline of dust deposition and wind erosion hazards, the higher soil clay content, lower air temperature, and a faster decomposition rate of mulch material with increasing rainfall from the Sahel to the Sudanian and Guinean zones.

Heterochromatin und epigenetische Kontrolle der Centromere in Dictyostelium discoideum

Heterochromatin Protein 1 (HP1) is an evolutionarily conserved protein required for formation of a higher-order chromatin structures and epigenetic gene silencing. The objective of the present work was to functionally characterise HP1-like proteins in Dictyostelium discoideum, and to investigate their function in heterochromatin formation and transcriptional gene silencing. The Dictyostelium genome encodes three HP1-like proteins (hcpA, hcpB, hcpC), from which only two, hcpA and hcpB, but not hcpC were found to be expressed during vegetative growth and under developmental conditions. Therefore, hcpC, albeit no obvious pseudogene, was excluded from this study. Both HcpA and HcpB show the characteristic conserved domain structure of HP1 proteins, consisting of an N-terminal chromo domain and a C-terminal chromo shadow domain, which are separated by a hinge. Both proteins show all biochemical activities characteristic for HP1 proteins, such as homo- and heterodimerisation in vitro and in vivo, and DNA binding activtity. HcpA furthermore seems to bind to K9-methylated histone H3 in vitro. The proteins thus appear to be structurally and functionally conserved in Dictyostelium. The proteins display largely identical subnuclear distribution in several minor foci and concentration in one major cluster at the nuclear periphery. The localisation of this cluster adjacent to the nucleus-associated centrosome and its mitotic behaviour strongly suggest that it represents centromeric heterochromatin. Furthermore, it is characterised by histone H3 lysine-9 dimethylation (H3K9me2), which is another hallmark of Dictyostelium heterochromatin. Therefore, one important aspect of the work was to characterise the so-far largely unknown structural organisation of centromeric heterochromatin. The Dictyostelium homologue of inner centromere protein INCENP (DdINCENP), co-localized with both HcpA and H3K9me2 during metaphase, providing further evidence that H3K9me2 and HcpA/B localisation represent centromeric heterochromatin. Chromatin immunoprecipitation (ChIP) showed that two types of high-copy number retrotransposons (DIRS-1 and skipper), which form large irregular arrays at the chromosome ends, which are thought to contain the Dictyostelium centromeres, are characterised by H3K9me2. Neither overexpression of full-length HcpA or HcpB, nor deletion of single Hcp isoforms resulted in changes in retrotransposon transcript levels. However, overexpression of a C-terminally truncated HcpA protein, assumed to display a dominant negative effect, lead to an increase in skipper retrotransposon transcript levels. Furthermore, overexpression of this protein lead to severe growth defects in axenic suspension culture and reduced cell viability. In order to elucidate the proteins functions in centromeric heterochromatin formation, gene knock-outs for both hcpA and hcpB were generated. Both genes could be successfully targeted and disrupted by homologous recombination. Surprisingly, the degree of functional redundancy of the two isoforms was, although not unexpected, very high. Both single knock-out mutants did not show any obvious phenotypes under standard laboratory conditions and only deletion of hcpA resulted in subtle growth phenotypes when grown at low temperature. All attempts to generate a double null mutant failed. However, both endogenous genes could be disrupted in cells in which a rescue construct that ectopically expressed one of the isoforms either with N-terminal 6xHis- or GFP-tag had been introduced. The data imply that the presence of at least one Hcp isoform is essential in Dictyostelium. The lethality of the hcpA/hcpB double mutant thus greatly hampered functional analysis of the two genes. However, the experiment provided genetic evidence that the GFP-HcpA fusion protein, because of its ability to compensate the loss of the endogenous HcpA protein, was a functional protein. The proteins displayed quantitative differences in dimerisation behaviour, which are conferred by the slightly different hinge and chromo shadow domains at the C-termini. Dimerisation preferences in increasing order were HcpA-HcpA << HcpA-HcpB << HcpB-HcpB. Overexpression of GFP-HcpA or a chimeric protein containing the HcpA C-terminus (GFP-HcpBNAC), but not overexpression of GFP-HcpB or GFP-HcpANBC, lead to increased frequencies of anaphase bridges in late mitotic cells, which are thought to be caused by telomere-telomere fusions. Chromatin targeting of the two proteins is achieved by at least two distinct mechanisms. The N-terminal chromo domain and hinge of the proteins are required for targeting to centromeric heterochromatin, while the C-terminal portion encoding the CSD is required for targeting to several other chromatin regions at the nuclear periphery that are characterised by H3K9me2. Targeting to centromeric heterochromatin likely involves direct binding to DNA. The Dictyostelium genome encodes for all subunits of the origin recognition complex (ORC), which is a possible upstream component of HP1 targeting to chromatin. Overexpression of GFP-tagged OrcB, the Dictyostelium Orc2 homologue, showed a distinct nuclear localisation that partially overlapped with the HcpA distribution. Furthermore, GFP-OrcB localized to the centrosome during the entire cell cycle, indicating an involvement in centrosome function. DnmA is the sole DNA methyltransferase in Dictyostelium required for all DNA(cytosine-)methylation. To test for its in vivo activity, two different cell lines were established that ectopically expressed DnmA-myc or DnmA-GFP. It was assumed that overexpression of these proteins might cause an increase in the 5-methyl-cytosine(5-mC)-levels in the genomic DNA due to genomic hypermethylation. Although DnmA-GFP showed preferential localisation in the nucleus, no changes in the 5-mC-levels in the genomic DNA could be detected by capillary electrophoresis.

Molecular mechanisms controlling the precision of chemokine guided cell migration

By the end of the first day of embryonic development, zebrafish primordial germ cells (PGCs) arrive at the site where the gonad develops. In our study we investigated the mechanisms controlling the precision of primordial germ cell arrival at their target. We found that in contrast with our expectations which were based on findings in Drosophila and mouse, the endoderm does not constitute a preferred migration substrate for the PGCs. Rather, endoderm derivatives are important for later stages of organogenesis keeping the PGC clusters separated. It would be interesting to investigate the precise mechanism by which endoderm controls germ cell position in the gonad. In their migration towards the gonad, zebrafish germ cells follow the gradient of chemokine SDF-1a, which they detect using the receptor CXCR4b that is expressed on their membrane. Here we show that the C-terminal region of CXCR4b is responsible for down-regulation of receptor activity as well as for receptor internalization. We demonstrate that receptor molecules unable to internalize are less potent in guiding germ cells to the site where the gonad develops, thereby implicating chemokine receptor internalization in facilitating precision of migration during chemotaxis in vivo. We demonstrate that while CXCR4b activity positively regulates the duration of the active migration phases, the down-regulation of CXCR4b signalling by internalization limits the duration of this phase. This way, receptor signalling contributes to the persistence of germ cell migration, whereas receptor down-regulation enables the cells to stop and correct their migration path close to the target where germ cells encounter the highest chemokine signal. Chemokine receptors are involved in directing cell migration in different processes such as lymphocyte trafficking, cancer and in the development of the vascular system. The C-terminal domain of many chemokine receptors was shown to be essential for controlling receptor signalling and internalization. It would therefore be important to determine whether the role for receptor internalization in vivo as described here (allowing periodical corrections to the migration route) and the mechanisms involved (reducing the level of signalling) apply for those other events, too.

Artificial micro RNA system in Dictyostelium discoideum

Dictyostelium discoideum is a social amoeba that serves as a model system for RNA interference and related mechanisms. Its position between plants and animals enables evolutionary snapshot of mechanisms and protein machinery involved in investigated subjects. MiRNAs are small regulatory RNAs that are evolutionary conserved and present in animals, plants, viruses and some prokaryotes. They have roles in development, cell growth and differentiation, apoptosis and their miss-regulation is associated with many diseases such as cancer, neurodegenerative disorders and diabetes. Recently, through sequencing of DNA libraries miRNAs have been discovered in D. discoideum. In this work, it has been shown that heterologues miRNA let-7 can be expressed and processed in D. discoideum. Expression of let-7 miRNA in social amoeba resulted in a strong developmental phenotype suggesting an overload of the processing/silencing system or/and endogenous targets. The various effects on prel-7 strain have been observed and characterized, serving as a background for postulation of miRNA roles. An artificial miRNA system has been established and imposed to D. discoideum, showing that miRNAs in Dictyostelium could mediate gene expression on the level of mRNA stability and on the posttranscriptional level. Furthermore, presence of translational inhibition as a type of gene control was shown for the first time in this organism. Due to it new structures representing co-localities of miRNA and target mRNA have been detected. Taken together, this work shows functional artificial miRNA system and postulates roles of endogenous small RNA in social amoeba.

Characterization of the molecular clockwork in the cockroach Rhyparobia maderae

Der Wechsel von Tag und Nacht erzeugt einen regelmäßigen Rhythmus von verschiedenen Umweltreizen, allen voran Licht und Temperatur. Fast jedes bis zum heutigen Tage untersuchte Lebewesen besitzt einen endogenen Mechanismus zur Zeitwahrnehmung, und diese "innere Uhr" befähigt Lebewesen dazu, sich vorausschauend an rhythmische Umwelt-Änderungen anzupassen. Circadiane Rhythmen bestehen auch ohne jegliche äußere Reize und basieren auf einem molekularen Rückkopplungs-Mechanismus, der Rhythmen in Genexpression und Proteinkonzentration von etwa 24 Stunden erzeugt. Obwohl sich die grundsätzlichen Mechanismen und Komponenten dieses molekularen Uhrwerks in allen Insekten ähneln, zeigte sich jedoch immer mehr, dass es im Detail doch wesentliche Unterschiede zwischen verschiedenen Insektengruppen gibt. Während das molekulare Uhrwerk der Fruchtfliege Drosophila melanogaster inzwischen sehr gut untersucht ist, fehlen bei den meisten Insektengruppen immernoch eingehende Untersuchungen. Fast nichts ist über die molekulare Basis von circadianen Rhythmen bei der Schabe Rhyparobia maderae bekannt, obwohl diese Art bereits seit Langem als Modellorganismus in der Chronobiologie dient. Um mit der Forschung am molekularen, circadianen System von R. maderae zu beginnen, wurde die Struktur und das Expressionsprofil der core feedback loop Gene per, tim1 und cry2 analysiert. Mittels degenerierten Primern und RACE konnte das vollständige offene Leseraster (OLR) von rmPer und rmCry2, und ein Teil des rmTim1 OLR kloniert werden. Eine phylogenetische Analyse gruppierte rmPER und rmCRY2 gemeinsam mit den Orthologa hemimetaboler Insekten. Viele bei D. melanogaster funktionell charakterisierte Domänen sind bei diesen Proteinen konserviert, was auf eine ähnliche Funktion in der inneren Uhr von R. maderae hinweist. Mittels quantitativer PCR konnte gezeigt werden, dass die mRNA von rmPer, rmTim1 und rmCry2 in verschiedenen Lichtregimen in der gleichen Phasenlage Tageszeit-abhängig schwankt. Die Phasenlage stellte sich bei unterschiedlichen Photoperioden jeweils relativ zum Beginn der Skotophase ein, mit Maxima in der ersten Hälfte der Nacht. Auch im Dauerdunkel zeigen sich Rhythmen in der rmTim1 und rmCry2 Expression. Die Amplitude der rmPer Expressionsrhythmen war jedoch so gering, dass keine signifikanten Unterschiede zwischen den einzelnen Zeitgeberzeiten (ZT) festgestellt werden konnten. Mittels Laufrad-Assays wurde untersucht wie Kurz- und Langtag Lichtregime die Verhaltensrhythmen beeinflussen. Es konnten nur Unterschiede in der Periodenlänge unter freilaufenden Bedingungen festgestellt werden, wenn höhere Lichtintensitäten (1000lx) zur Synchronisation (entrainment) genutzt wurden. Die Periode des freilaufenden Rhythmus war bei Tieren aus dem Kurztag länger. Die photoperiodische Plastizität zeigte sich also auch auf Verhaltensebene, obwohl höhere Lichtintensitäten notwendig waren um einen Effekt zu beobachten. Basierend auf den Sequenzen der zuvor klonierten OLR wurden gegen rmPER, rmTIM1 und rmCRY2 gerichtete Antikörper hergestellt. Die Antikörper gegen rmPER und rmTIM1 erkannten in western blots sehr wahrscheinlich spezifisch das jeweilige Protein. Zeitreihen von Gehirngewebe-Homogenisaten zeigten keinen offensichtlichen circadianen Rhythmus in der Proteinkonzentration, wahrscheinlich auf Grund einer Oszillation mit niedriger Amplitude. In Immunhistochemischen Färbungen konnte nur mit dem gegen rmPER gerichteten Antikörper aus Kaninchen ein Signal beobachtet werden. Beinahe jede Zelle des Zentralnervensystems war rmPER-immunreaktiv im Zellkern. Es konnten keine Unterschiede zwischen den untersuchten ZTs festgestellt werden, ähnlich wie bei den western blot Zeitreihen. In dieser Studie konnten erstmals molekulare Daten der circadianen Uhr von R. maderae erfasst und dargestellt werden. Die Uhrgene per, tim1 und cry2 werden in dieser Schabenart exprimiert und ihre Domänenstruktur sowie das circadiane Expressionsmuster ähneln dem hypothetischen ursprünglichen Insektenuhrwerk, welches der circadianen Uhr von Vertebraten nahesteht. Das molekulare Uhrwerk von R. maderae kann sich an unterschiedliche Photoperioden anpassen, und diese Anpassungen manifestieren sich im Expressionsprofil der untersuchten Uhrgene ebenso wie im Verhalten.

A simple retroelement based knock-down system in Dictyostelium

Characteristics of DIRS-1 Mediated Knock-Downs __ We have previously shown that the most abundant Dictyostelium discoideum retroelement DIRS-1 is suppressed by RNAi mechanisms. Here we provide evidence that both inverted terminal repeats have strong promoter activity and that bidirectional expression apparently generates a substrate for Dicer. A cassette containing the inverted terminal repeats and a fragment of a gene of interest was sufficient to activate the RNAi response, resulting in the generation of ~21 nt siRNAs, a reduction of mRNA and protein expression of the respective endogene. Surprisingly, no transitivity was observed on the endogene. This was in contrast to previous observations, where endogenous siRNAs caused spreading on an artificial transgene. Knock-down was successful on seven target genes that we examined. In three cases a phenotypic analysis proved the efficiency of the approach. One of the target genes was apparently essential because no knock-out could be obtained; the RNAi mediated knock-down, however, resulted in a very slow growing culture indicating a still viable reduction of gene expression.