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1 something about srna in archaea or: Processed Small RNAs in Archaea and BHB Elements Sarah Berkemer Bioinformatics Vienzig
2 Archaea? Sarah Berkemer (Bioinformatics Vienzig) BHB elements in Archaea 2 / 23
3 Sarah Berkemer (Bioinformatics Vienzig) BHB elements in Archaea 3 / 23
4 Archaea I Figure: Phylogenetic Tree (commons.wikimedia.org) Sarah Berkemer (Bioinformatics Vienzig) BHB elements in Archaea 4 / 23
5 Archaea II Definition [Woese et al., 1990] Domain Archaea [Greek adjective for ancient, primitive]: Cells prokaryotic Membrane lipids unique Ribosomes containing an archaeal type of rrna Figure: Archaeal species Sulfolobus ( Sarah Berkemer (Bioinformatics Vienzig) BHB elements in Archaea 5 / 23
6 Figure: Phylogenetic Tree (commons.wikimedia.org) Sarah Berkemer (Bioinformatics Vienzig) BHB elements in Archaea 6 / 23
7 Sarah Berkemer (Bioinformatics Vienzig) BHB elements in Archaea 6 / 23
8 3 domains vs. 2 domains of life Figure: Possible Tree of life [Williams et al., 2013] Sarah Berkemer (Bioinformatics Vienzig) BHB elements in Archaea 7 / 23
9 Archaea III Sarah Berkemer (Bioinformatics Vienzig) BHB elements in Archaea 8 / 23
10 Archaea III Sarah Berkemer (Bioinformatics Vienzig) BHB elements in Archaea 8 / 23
11 Archaea III Sarah Berkemer (Bioinformatics Vienzig) BHB elements in Archaea 8 / 23
12 Archaea III Sarah Berkemer (Bioinformatics Vienzig) BHB elements in Archaea 8 / 23
13 Archaea III Sarah Berkemer (Bioinformatics Vienzig) BHB elements in Archaea 8 / 23
14 Splicing mechanism Splicing Eukarya: splicing with spliceosome Bacteria: no splicing Archaea: splicing with at least two protein enzymes (specific endonuclease and ligase) - BHB (bulge-helix-bulge) element as recognition Sarah Berkemer (Bioinformatics Vienzig) BHB elements in Archaea 9 / 23
15 Splicing mechanism Splicing Eukarya: splicing with spliceosome Bacteria: no splicing Archaea: splicing with at least two protein enzymes (specific endonuclease and ligase) - BHB (bulge-helix-bulge) element as recognition A B C Figure: Scheme for a BHB element Sarah Berkemer (Bioinformatics Vienzig) BHB elements in Archaea 9 / 23
16 BHB structural element GCGGGCTTTTAACCGCG...loop...TGCGGGAAGCAACCCGT hhhhhhhhhbbbggggg...loop...ggggghhhhbbbhhhhh (((((((((...(((((...loop...)))))))))...))))) Figure: BHB element, sequence and secondary structure in trna Lys of S.tokodaii [Marck & Grosjean, 2003] Sarah Berkemer (Bioinformatics Vienzig) BHB elements in Archaea 10 / 23
17 Workflow Sarah Berkemer (Bioinformatics Vienzig) BHB elements in Archaea 11 / 23
18 Candidate crnas Sarah Berkemer (Bioinformatics Vienzig) BHB elements in Archaea 12 / 23
![trna introns Figure: Splice sites in trnas [Yoshihisa, 2014]](/docs-images/94/121802822/images/19-0.jpg "Sarah Berkemer (Bioinformatics Vienzig) BHB elements in Archaea")
19 trna introns Figure: Splice sites in trnas [Yoshihisa, 2014] Sarah Berkemer (Bioinformatics Vienzig) BHB elements in Archaea 13 / 23
20 Candidate crnas Sarah Berkemer (Bioinformatics Vienzig) BHB elements in Archaea 14 / 23
21 Sarah Berkemer (Bioinformatics Vienzig) BHB elements in Archaea 15 / 23
22 MSA Sarah Berkemer (Bioinformatics Vienzig) BHB elements in Archaea 16 / 23
23 MSA Sarah Berkemer (Bioinformatics Vienzig) BHB elements in Archaea 16 / 23
24 Workflow Sarah Berkemer (Bioinformatics Vienzig) BHB elements in Archaea 17 / 23
25 Results Species C/D BHB no BHB M. kandleri (80) 14 (8) N. equitans 11 9 (6) 2 (1) S. solfataricus 20 7 (3) 13 (5) S. acidocaldarius (16) 2 (2) Sarah Berkemer (Bioinformatics Vienzig) BHB elements in Archaea 18 / 23
26 Results Species C/D BHB no BHB M. kandleri (80) 14 (8) N. equitans 11 9 (6) 2 (1) S. solfataricus 20 7 (3) 13 (5) S. acidocaldarius (16) 2 (2) Species splicesites MSA1 MSA2 M. kandleri N. equitans I. hospitalis S. acidocaldarius S. solfataricus Sarah Berkemer (Bioinformatics Vienzig) BHB elements in Archaea 18 / 23
27 trna Sarah Berkemer (Bioinformatics Vienzig) BHB elements in Archaea 19 / 23
28 C/D box Sarah Berkemer (Bioinformatics Vienzig) BHB elements in Archaea 20 / 23
29 Results combining forces and reducing search space helps most of known box C/D srnas flanked with BHB elements new candidates identified Outlook still circularized introns without BHB elements just known RNA classes can be tested: no generalized model Sarah Berkemer (Bioinformatics Vienzig) BHB elements in Archaea 21 / 23
30 Thanks to: Peter Stadler Christian Höner zu Siederdissen Ivo Hofacker Fabian Amman Sebastian Will Peter Kerpedjiev... and the TBI table soccer team Sarah Berkemer (Bioinformatics Vienzig) BHB elements in Archaea 22 / 23
31 References References Brochier-Armanet, C., Forterre, P., & Gribaldo, S. (2011). Phylogeny and evolution of the Archaea: one hundred genomes later. Current opinion in microbiology, 14(3), Höner zu Siederdissen, C., Berkemer, S., Amman, F., Wintsche, A., Will, S., Prohaska, S. J., & Stadler, P. F. (2014). Comparative Detection of Processed Small RNAs in Archaea. accepted: IWBBio, Granada. Marck, C. & Grosjean, H. (2003). Identification of BHB splicing motifs in intron-containing trnas from 18 archaea: evolutionary implications. RNA, 9. Williams, T. A., Foster, P. G., Cox, C. J., & Embley, T. M. (2013). An archaeal origin of eukaryotes supports only two primary domains of life. Nature, 504(7479), Woese, C. R., Kandler, O., & Wheelis, M. L. (1990). Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. PNAS, 87(12). Yoshihisa, T. (2014). Handling trna introns, archaeal way and eukaryotic way. Front Genet., 5, 213. Sarah Berkemer (Bioinformatics Vienzig) BHB elements in Archaea 23 / 23
Processed Small RNAs in Archaea and BHB Elements
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