Apsarasen im Mahābhārata

Apsarasen sind eine Gruppe weiblicher, halbgöttlicher Wesen der indischen Mythologie. Das Ziel der vorliegenden Diplomarbeit ist es, Apsarasen im Text der kritischen Edition des Mahābhārata zu untersuchen. Dafür wurden alle 242 Belegstellen für apsaras- gesichtet und nach inhaltlichen Kriterien systematisch verschiedenen Kapiteln zugeordnet.Innerhalb der Kapitel werden jeweils alle relevanten Mahābhārata Belege angeführt und paraphrasiert. Übernehmen die Apsarasen einen wichtigen Part in einem Mythologem, werden die entsprechenden Stellen im Kontext übersetzt. Nach einem Kapitel, das sich den verschiedenen Theorien über die bis heute ungeklärte Etymologie des Wortes widmet, werden die Stellen, die über ihre Herkunft informieren, bearbeitet. Danach folgt ein Kapitel, welches die Apsarasen in ihrer wichtigsten Rolle im Mahābhārata behandelt, nämlich als attraktive Verführerinnen, die sehr oft eine Versuchung für enthaltsam lebende Asketen darstellen. Von ihren Tätigkeiten ist in einem weiteren Abschnitt die Rede. Ihre sehr wichtige Rolle in paradiesischen Jenseitsvorstellungen wird im nächsten Kapitel beschrieben: Die Apsarasen sind sehr schöne himmlische Frauen, die im Jenseits auf diejenigen warten, die Zeit ihres Lebens ihre Pflichten erfüllt haben. Das sind vor allem in der Schlacht gefallene Krieger und Männer, die im Diesseits gespendet oder ausgiebig, den Regeln entsprechend gefastet haben. Die kriegerische Auseinandersetzung zwischen zwei Linien des Bharata-Geschlechts bildet das Zentrum der Erzählungen des Mahābhārata, deshalb wurde den Apsarasen in Hinblick auf die Schlacht ein eigenes Kapitel gewidmet. In Schilderungen vom Kampf treten sie fast immer zusammen mit anderen himmlischen Wesen auf, wobei sie meist Zuseherinnen sind, die gleichzeitig für eine erhabene Atmosphäre sorgen. Stirbt ein Held, heben sie ihn in ein Vimāna, eine Art fliegender Palast, und gehen mit ihm davon, oder sie erwarten die Gefallenen im Himmel, um ihn zum Gemahl zu nehmen. Ihre Aufenthaltsorte werden im nächsten Abschnitt der Arbeit behandelt: Ihr Zuhause sind die himmlischen Sphären, die meisten Belege verorten sie dort. Danach sind ihre liebsten Aufenthaltsorte die Berge. Die Untersuchung der Stellen hinsichtlich ihrer Beziehung zu einzelnen Göttern des epischen Pantheons ergab, dass sie in erster Linie mit dem Götterkönig Indra assoziiert werden, der sich auch öfter ihrer Verführungskünste bedient, wenn er danach strebt die Macht eines Asketen zu mindern. Eine ganz besondere Beziehung besteht zwischen den Apsarasen und den Gandharvas, ebenfalls eine Klasse halbgöttlicher Wesen. Mit diesen teilen die schönen himmlischen Frauen nahezu die Hälfte aller Belegstellen. Die Eigenschaften der Apsarasen werden unterteilt in die, die auf die Apsarasen als Gruppe Bezug nehmen und die, die individuelle Apsarasen beschreiben. Auf eine jeweilige alphabetische Auflistung folgt eine Unterteilung nach inhaltlichen Gesichtspunkten. Die zehn Namenslisten des Textus Constitutus werden gemeinsam mit den fünf Namenslisten des Apparatus Criticus im 14. Kapitel besprochen. Am Ende der Arbeit findet sich ein Kapitel, in dem Kontext und Übersetzung von drei Stellen angegeben werden, die keinem der oben genannten Kapitel zugeordnet werden konnten und außerdem die Zusammenfassung

Influence of RNA structural stability on the RNA chaperone activity of the Escherichia coli protein StpA

Proteins with RNA chaperone activity are able to promote folding of RNA molecules by loosening their structure. This RNA unfolding activity is beneficial when resolving misfolded RNA conformations, but could be detrimental to RNAs with low thermodynamic stability. In order to test this idea, we constructed various RNAs with different structural stabilities derived from the thymidylate synthase (td) group I intron and measured the effect of StpA, an Escherichia coli protein with RNA chaperone activity, on their splicing activity in vivo and in vitro. While StpA promotes splicing of the wild-type td intron and of mutants with wild-type-like stability, splicing of mutants with a lower structural stability is reduced in the presence of StpA. In contrast, splicing of an intron mutant, which is not destabilized but which displays a reduced population of correctly folded RNAs, is promoted by StpA. The sensitivity of an RNA towards StpA correlates with its structural stability. By lowering the temperature to 25°C, a temperature at which the structure of these mutants becomes more stable, StpA is again able to stimulate splicing. These observations clearly suggest that the structural stability of an RNA determines whether the RNA chaperone activity of StpA is beneficial to folding

Genomic SELEX for Hfq-binding RNAs identifies genomic aptamers predominantly in antisense transcripts

An unexpectedly high number of regulatory RNAs have been recently discovered that fine-tune the function of genes at all levels of expression. We employed Genomic SELEX, a method to identify protein-binding RNAs encoded in the genome, to search for further regulatory RNAs in Escherichia coli. We used the global regulator protein Hfq as bait, because it can interact with a large number of RNAs, promoting their interaction. The enriched SELEX pool was subjected to deep sequencing, and 8865 sequences were mapped to the E. coli genome. These short sequences represent genomic Hfq-aptamers and are part of potential regulatory elements within RNA molecules. The motif 5′-AAYAAYAA-3′ was enriched in the selected RNAs and confers low-nanomolar affinity to Hfq. The motif was confirmed to bind Hfq by DMS footprinting. The Hfq aptamers are 4-fold more frequent on the antisense strand of protein coding genes than on the sense strand. They were enriched opposite to translation start sites or opposite to intervening sequences between ORFs in operons. These results expand the repertoire of Hfq targets and also suggest that Hfq might regulate the expression of a large number of genes via interaction with cis-antisense RNAs

A structural determinant required for RNA editing

RNA editing by adenosine deaminases acting on RNAs (ADARs) can be both specific and non-specific, depending on the substrate. Specific editing of particular adenosines may depend on the overall sequence and structural context. However, the detailed mechanisms underlying these preferences are not fully understood. Here, we show that duplex structures mimicking an editing site in the Gabra3 pre-mRNA unexpectedly fail to support RNA editing at the Gabra3 I/M site, although phylogenetic analysis suggest an evolutionarily conserved duplex structure essential for efficient RNA editing. These unusual results led us to revisit the structural requirement for this editing by mutagenesis analysis. In vivo nuclear injection experiments of mutated editing substrates demonstrate that a non-conserved structure is a determinant for editing. This structure contains bulges either on the same or the strand opposing the edited adenosine. The position of these bulges and the distance to the edited base regulate editing. Moreover, elevated folding temperature can lead to a switch in RNA editing suggesting an RNA structural change. Our results indicate the importance of RNA tertiary structure in determining RNA editing

A conserved 3′ extension in unusual group II introns is important for efficient second-step splicing

The B.c.I4 group II intron from Bacillus cereus ATCC 10987 harbors an unusual 3′ extension. Here, we report the discovery of four additional group II introns with a similar 3′ extension in Bacillus thuringiensis kurstaki 4D1 that splice at analogous positions 53/56 nt downstream of domain VI in vivo. Phylogenetic analyses revealed that the introns are only 47–61% identical to each other. Strikingly, they do not form a single evolutionary lineage even though they belong to the same Bacterial B class. The extension of these introns is predicted to form a conserved two-stem–loop structure. Mutational analysis in vitro showed that the smaller stem S1 is not critical for self-splicing, whereas the larger stem S2 is important for efficient exon ligation and lariat release in presence of the extension. This study clearly demonstrates that previously reported B.c.I4 is not a single example of a specialized intron, but forms a new functional class with an unusual mode that ensures proper positioning of the 3′ splice site

Preparation of Group I Introns for Biochemical Studies and Crystallization Assays by Native Affinity Purification

The study of functional RNAs of various sizes and structures requires efficient methods for their synthesis and purification. Here, 23 group I intron variants ranging in length from 246 to 341 nucleotides—some containing exons—were subjected to a native purification technique previously applied only to shorter RNAs (<160 nucleotides). For the RNAs containing both exons, we adjusted the original purification protocol to allow for purification of radiolabeled molecules. The resulting RNAs were used in folding assays on native gel electrophoresis and in self-splicing assays. The intron-only RNAs were subjected to the regular native purification scheme, assayed for folding and employed in crystallization screens. All RNAs that contained a 3′ overhang of one nucleotide were efficiently cleaved off from the support and were at least 90% pure after the non-denaturing purification. A representative subset of these RNAs was shown to be folded and self-splicing after purification. Additionally, crystals were grown for a 286 nucleotide long variant of the Clostridium botulinum intron. These results demonstrate the suitability of the native affinity purification method for the preparation of group I introns. We hope these findings will stimulate a broader application of this strategy to the preparation of other large RNA molecules

Molecular modelling of the GIR1 branching ribozyme gives new insight into evolution of structurally related ribozymes

Twin-ribozyme introns contain a branching ribozyme (GIR1) followed by a homing endonuclease (HE) encoding sequence embedded in a peripheral domain of a group I splicing ribozyme (GIR2). GIR1 catalyses the formation of a lariat with 3 nt in the loop, which caps the HE mRNA. GIR1 is structurally related to group I ribozymes raising the question about how two closely related ribozymes can carry out very different reactions. Modelling of GIR1 based on new biochemical and mutational data shows an extended substrate domain containing a GoU pair distinct from the nucleophilic residue that dock onto a catalytic core showing a different topology from that of group I ribozymes. The differences include a core J8/7 region that has been reduced and is complemented by residues from the pre-lariat fold. These findings provide the basis for an evolutionary mechanism that accounts for the change from group I splicing ribozyme to the branching GIR1 architecture. Such an evolutionary mechanism can be applied to other large RNAs such as the ribonuclease P

Transient RNA–protein interactions in RNA folding

The RNA folding trajectory features numerous off-pathway folding traps, which represent conformations that are often equally as stable as the native functional ones. Therefore, the conversion between these off-pathway structures and the native correctly folded ones is the critical step in RNA folding. This process, referred to as RNA refolding, is slow, and is represented by a transition state that has a characteristic high free energy. Because this kinetically limiting process occurs in vivo, proteins (called RNA chaperones) have evolved that facilitate the (re)folding of RNA molecules. Here, we present an overview of how proteins interact with RNA molecules in order to achieve properly folded states. In this respect, the discrimination between static and transient interactions is crucial, as different proteins have evolved a multitude of mechanisms for RNA remodeling. For RNA chaperones that act in a sequence-unspecific manner and without the use of external sources of energy, such as ATP, transient RNA–protein interactions represent the basis of the mode of action. By presenting stretches of positively charged amino acids that are positioned in defined spatial configurations, RNA chaperones enable the RNA backbone, via transient electrostatic interactions, to sample a wider conformational space that opens the route for efficient refolding reactions

RNA chaperoning and intrinsic disorder in the core proteins of Flaviviridae

RNA chaperone proteins are essential partners of RNA in living organisms and viruses. They are thought to assist in the correct folding and structural rearrangements of RNA molecules by resolving misfolded RNA species in an ATP-independent manner. RNA chaperoning is probably an entropy-driven process, mediated by the coupled binding and folding of intrinsically disordered protein regions and the kinetically trapped RNA. Previously, we have shown that the core protein of hepatitis C virus (HCV) is a potent RNA chaperone that can drive profound structural modifications of HCV RNA in vitro. We now examined the RNA chaperone activity and the disordered nature of core proteins from different Flaviviridae genera, namely that of HCV, GBV-B (GB virus B), WNV (West Nile virus) and BVDV (bovine viral diarrhoea virus). Despite low-sequence similarities, all four proteins demonstrated general nucleic acid annealing and RNA chaperone activities. Furthermore, heat resistance of core proteins, as well as far-UV circular dichroism spectroscopy suggested that a well-defined 3D protein structure is not necessary for core-induced RNA structural rearrangements. These data provide evidence that RNA chaperoning—possibly mediated by intrinsically disordered protein segments—is conserved in Flaviviridae core proteins. Thus, besides nucleocapsid formation, core proteins may function in RNA structural rearrangements taking place during virus replication

Survey of group I and group II introns in 29 sequenced genomes of the Bacillus cereus group: insights into their spread and evolution

Group I and group II introns are different catalytic self-splicing and mobile RNA elements that contribute to genome dynamics. In this study, we have analyzed their distribution and evolution in 29 sequenced genomes from the Bacillus cereus group of bacteria. Introns were of different structural classes and evolutionary origins, and a large number of nearly identical elements are shared between multiple strains of different sources, suggesting recent lateral transfers and/or that introns are under a strong selection pressure. Altogether, 73 group I introns were identified, inserted in essential genes from the chromosome or newly described prophages, including the first elements found within phages in bacterial plasmids. Notably, bacteriophages are an important source for spreading group I introns between strains. Furthermore, 77 group II introns were found within a diverse set of chromosomal and plasmidic genes. Unusual findings include elements located within conserved DNA metabolism and repair genes and one intron inserted within a novel retroelement. Group II introns are mainly disseminated via plasmids and can subsequently invade the host genome, in particular by coupling mobility with host cell replication. This study reveals a very high diversity and variability of mobile introns in B. cereus group strains