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Developmental Cell, 20, 148-61. kleine RNAs https://doi.org/10.17192/z2014.0482 2014-12-12 Fachbereich Biologie Von kleinen RNAs geleitete Prozesse im hyperthermophilen Methanogen Mathanopyrus kandleri ppn:352394595 doctoralThesis 2014 ths Dr. Randau Lennart Randau, Lennart (Dr.) In this thesis, a combination of RNAseq, computational and biochemical methods was applied to analyze processes that use small RNAs (sRNAs) as guide molecules at extreme temperatures. Here, the hyperthermophilic archaeon Methanopyrus kandleri, which grows at temperatures of up to 110°C, was used as a model organism. The genome of M. kandleri harbors two CRISPR-Cas systems that use CRISPR RNA (crRNA) as guide molecules to target foreign nucleic acids. RNAseq analysis revealed a high abundance and processing of crRNAs in M. kandleri that indicated that CRISPR-Cas systems are highly active at extreme temperatures. Furthermore, the crystal structure of the CRISPR-associated protein Csm3 was solved in collaboration with Prof. Dr. Elena Conti (MPI Martinsried). Csm3 was found to bind crRNAs and was shown to function as the crRNA-binding backbone protein in type III-A CRISPR-Cas interference complexes. A recently discovered nucleic acid-guided mechanism uses prokaryotic Argonaute (pAgo) proteins. In M. kandleri, a pAgo protein was found to be encoded within a potential operon of CRISPR-associated genes and the analysis of recombinant pAgo protein production revealed a high toxicity in Escherichia coli that might correlate with its potential defense function against plasmid DNA. Methylation of rRNA is regulated by a different sRNA-guided mechanism that utilizes C/D box sRNAs to target a ribonucleoprotein complex to the rRNA methylation site. In M. kandleri, a record number of 126 C/D box sRNAs were detected by RNAseq analysis and indicate an increased potential for rRNA methylation reactions. Furthermore, most of the C/D box sRNAs were detected as circular molecules. Taken together, the circularization of C/D box sRNAs and the high requirement for rRNA methylation are suggested to be adaptations to the hyperthermophilic lifestyle of M. kandleri. Finally, RNAseq analyses were used to identify tRNA precursors in M. kandleri that feature a unique C-to-U editing reaction of base 8. The occurrence of this editing event was used to deduce the order of tRNA processing steps in a non-compartmentalized cell, indicating that termini truncation precedes intron removal and editing. kleine RNAs urn:nbn:de:hebis:04-z2014-04826 2015-01-05 application/pdf CRISPR-Cas English In der vorliegenden Arbeit wurden RNAseq, sowie bioinformatische und biochemische Methoden angewandt um zelluläre Prozesse zu analysieren die von kleinen RNAs (sRNA) gesteuert werden. Um zu untersuchen, wie diese Prozesse bei extremen Temperaturen funktionieren, wurde das hyperthermophile Archaeon Methanopyrus kandleri, welches bei Temperaturen von bis zu 110°C lebt, als Modellorganismus verwendet. Das Genom von M. kandleri enthält zwei CRISPR-Cas Systeme, welche crRNAs (CRISPR RNAs) als Zielerkennungsmoleküle verwenden, um sich gegen Viren zur Wehr zu setzen. Durch RNAseq Analysen wurden große Mengen an prozessierten crRNAs detektiert. Dies deutet darauf hin, dass CRISPR-Cas Systeme bei extremer Temperatur sehr aktiv sind. Zudem wurde die Kristallstruktur des CRISPR-assoziierten Proteins Csm3 in Zusammenarbeit mit Prof. Dr. Elena Conti (MPI Martinsried) aufgeklärt. Anhand von RNA Bindestudien wurde Csm3 als crRNA-bindendes Protein identifiziert, welches als Gerüstprotein des Typ III-A CRISPR-Cas Interferenzkomplexes fungiert. Erst kürzlich konnte gezeigt werden, dass pAgo (prokaryotic Argonaute) Proteine kurze Nukleinsäuresequenzen verwenden, um Zielmoleküle zu erkennen. In M. kandleri, ist ein solches pAgo Protein in einem potentiellen Operon zusammen mit Proteinen des CRISPR-Cas Systems kodiert. Versuche pAgo rekombinant herzustellen wiesen auf eine hohe Toxizität des Proteins in Escherichia coli hin, was mit einer möglichen Abwehrfunktion gegen Plasmid DNA in Zusammenhang stehen könnte. Die Methylierung von RNA Molekülen wird durch einen anderen Prozess gesteuert, welcher C/D Box sRNAs als Zielerkennungssequenzen verwendet, um Ribonukleoproteinkomplexe an Methylierungsstellen ribosomaler RNAs zu führen. In M. kandleri wurde eine Rekordzahl von 126 C/D Box sRNAs durch RNAseq Analysen detektiert, welche auf eine erhöhte Methylierung von rRNAs hinweist. Zudem wurde ein Großteil der C/D box sRNAs als zirkuläre Moleküle detektiert. Zusammenfassend können die Zirkularisierung von C/D Box sRNAs und der erhöhte Bedarf an RNA Methylierungen als Adaptionen an die hyperthermophile Lebensweise von M. kandleri angesehen werden. Abschließend wurden durch RNAseq Analysen tRNA-Vorläufer Moleküle identifiziert, welche die nur in M. kandleri vorkommende C-zu-U Modifikation der Base 8 aufwiesen. Das Auftreten dieser Modifikation wurde genutzt, um daraus Rückschlüsse auf die Reihenfolge von tRNA Prozessierungsschritten in nicht kompartimentierten Zellen zu schließen. Unsere Analysen ergaben, dass das Beschneiden der Enden dem Entfernen von Introns, sowie der Editierungsreaktion vorrausgeht. https://archiv.ub.uni-marburg.de/diss/z2014/0482/cover.png Life sciences Biowissenschaften, Biologie Su, Andreas A. H. Su Andreas A. H. CRISPR-Cas Philipps-Universität Marburg opus:5883