Düsseldorf, University, Diss., 2004.

University, Diss., 2004--Düsseldorf.

Background: The colonial ascidian Didemnum vexillum, sea carpet squirt, is not only a key marine organism to study morphological ancestral patterns of chordates evolution but it is also of great ecological importance due to its status as a major invasive species. Non-coding RNAs, in particular microRNAs (miRNAs), are important regulatory genes that impact development and environmental adaptation. Beyond miRNAs, not much in known about tunicate ncRNAs. Results: We provide here a comprehensive homology-based annotation of non-coding RNAs in the recently sequenced genome of D. vexillum. To this end we employed a combination of several computational approaches, including blast searches with a wide range of parameters, and secondary structured centered survey with infernal. The resulting candidate set was curated extensively to produce a high-quality ncRNA annotation of the first draft of the D. vexillum genome. It comprises 57 miRNA families, 4 families of ribosomal RNAs, 22 isoacceptor classes of tRNAs (of which more than 72% of loci are pseudogenes), 13 snRNAs, 12 snoRNAs, and 1 other RNA family. Additionally, 21 families of mitochondrial tRNAs and 2 of mitochondrial ribosomal RNAs and 1 long non-coding RNA. Conclusions: The comprehensive annotation of the D. vexillum non-coding RNAs provides a starting point towards a better understanding of the restructuring of the small RNA system in ascidians. Furthermore it provides a valuable research for efforts to establish detailed non-coding RNA annotations for other recently published and recently sequences in tunicate genomes.

Die Pseudodistomine gehören zu den ersten Piperidinalkaloiden marinen Ursprungs, die 1987 von Ishibashi et al. aus der Tunikate (Ascidie) Pseudodistoma kanoko isoliert wurden. Aus der gleichen Tunikate wurde 1995 das Pseudodistomin C isoliert. Die amphiphilen Piperidinalkaloide zeigen eine Antitumor-Aktivität gegen bestimmte Mäuseleukämiezellen, wobei Pseudodistomin C auch eine Cytotoxizität gegen menschliche HeLa-abgeleitete Krebszellen KB aufweist. In der Einleitung wird ausführlich auf Vorkommen, Struktur, Biogenese, pharmakologische Perspektiven und literaturbekannten Synthesen dieser amphiphilen Piperidin-Alkaloide eingegangen. Im Hauptteil wird zunächst eine gescheiterte Synthese ausgehend von D-Ribose über das Konzept einer Tandem Wittig-[3+2]-Cycloaddition beschrieben. Daraufhin wird ein völlig neuer Syntheseweg vorgestellt, welcher den formalen Aufbau des Pseudodistomin C über einen bekannten Piperidin-Grundkörper ermöglich. Des weiteren konnte das vollständig geschützte Pseudodistomin E synthetisiert werden. / Pseudodistomines belong to the first known piperidine alkaloids of marine origin, isolated by Ishibashi et al. from the tunicate (ascidie) pseudodistoma kanoko in 1987. From the same tunicate Pseudodistomin C was isolated in 1995. The amphiphilic piperidin alkaloids show an antitumor activity against certain leukemic cells derived from mice, whereas Pseudodistomin C also exhibits an antitumor activity against human HeLa-derived cancer cells KB. The introduction goes into details about occurrence, structure, biogenesis, pharmacological perspectives and literature known synthesis of these amphiphilic piperidine alkaloids. The main part starts with a failed synthesis based on D-ribose by the concept of a tandem wittig-[3+2]-cycloaddition. Consequently an entirely new synthesis pathway is presented, which enables the formal buildup of Pseudodistomin C by a known piperidine compound. Furthermore I was able to synthesize the fully protected Pseudodistomin E.

Background: The colonial ascidian Didemnum vexillum, sea carpet squirt, is not only a key marine organism to study morphological ancestral patterns of chordates evolution but it is also of great ecological importance due to its status as a major invasive species. Non-coding RNAs, in particular microRNAs (miRNAs), are important regulatory genes that impact development and environmental adaptation. Beyond miRNAs, not much in known about tunicate ncRNAs. Results: We provide here a comprehensive homology-based annotation of non-coding RNAs in the recently sequenced genome of D. vexillum. To this end we employed a combination of several computational approaches, including blast searches with a wide range of parameters, and secondary structured centered survey with infernal. The resulting candidate set was curated extensively to produce a high-quality ncRNA annotation of the first draft of the D. vexillum genome. It comprises 57 miRNA families, 4 families of ribosomal RNAs, 22 isoacceptor classes of tRNAs (of which more than 72% of loci are pseudogenes), 13 snRNAs, 12 snoRNAs, and 1 other RNA family. Additionally, 21 families of mitochondrial tRNAs and 2 of mitochondrial ribosomal RNAs and 1 long non-coding RNA. Conclusions: The comprehensive annotation of the D. vexillum non-coding RNAs provides a starting point towards a better understanding of the restructuring of the small RNA system in ascidians. Furthermore it provides a valuable research for efforts to establish detailed non-coding RNA annotations for other recently published and recently sequences in tunicate genomes.