Ribosomal RNA sequencing

D. A. Stahl, D. J. Lane, G. J. Olsen, and N. R. Pace, Analysis of hydrothermal vent-associated symbionts by ribosomal RNA sequences. Science 224 409 (1984). 

Johnson, A.M. and Baverstock, B.P. (1989) Rapid ribosomal RNA sequencing and the phylogenetic analysis of protists. Parasitology Today 5, 102-105. 

Ginisty H, Serin G, Ghisolfi-Nieto L, Roger B, Libante V, Amalric F, Bouvet P (2000) Interaction of Nucleolin with an Evolutionarily Conserved Pre-ribosomal RNA Sequence Is Required for the Assembly of the Primary Processing Complex. J Biol Chem 275 18845-18850 Ginisty H, Sicard H, Roger B, Bouvet P (1999) Structure and functions of nucleolin. J Cell Sci 112 761-772... 

The knowledge of the primary structure was the basis for the construction of models of the secondary structure of the RNA molecules. Different approaches have been used in several laboratories to get experimental support for developing secondary structure models for example, chemic modification of the RNA, treatment with single- or double-strand-specihc nucleases, intramolecular RNA cross-linking, isolation and sequence analysis of double-stranded RNA, and, last but not least, comparison of ribosomal RNA sequences from different organisms (reviewed by Brimacombe et al., 1983). 

Cunningham, C.O., Mo, T.A., Collins, C.M., Buchmann, K., Thiery, R., Blanc, G. and Lautraite, A. (2001) Redescription of Gyrodactylus teuchis Lautraite, Blanc, Thiery, Daniel and Vigneulle, 1999 (Monogenea Gyrodactylidae), a species identified by ribosomal RNA sequence. Systematic Parasitology 48, 141-150. 

Kohring, L.L., Ringelberg, D.B., Devereux, R., Stahl, D.A., Mittelmann, M.M., and White, D.C. (1994) Comparison of phylogenetic relationships based on phospholipids fatty acid profiles and ribosomal RNA sequence similarities among dissimilatory sulfate-reducing bacteria. FEMS Microbiol. Lett. 119, 303-308. 

Voltaire (1947) Candide or Optimism, translated by Butt J. Penguin, London von Dohlen CD, Kohler S, Alsop ST, McManus WR (2001) Mealybug P-proteobacterial ensymbionts contain y-proteobacterial symbionts. Nature 412 433-435 Vossbrinck CR, Maddox JV, Friedman S, Debrunner-Vossbrinck BA, Woese CR (1987) Ribosomal RNA sequence suggests microsporidia are extremely ancient eukaryotes. Nature 326 411-414... 

Vossbrinck CR, Maddox JV, Friedman S, Debrunner-Vossbrinck BA, Woese CR (1987) Ribosomal RNA sequence suggests microsporidia are extremely ancient eukaryotes. Nature 326 411-414... 

Wu, C. Shivakumar, S. (1994). Back-propagation and counter-propagation neural networks for phylogenetic classification of ribosomal RNA sequences. Nucleic Acids Res 22,4291-9. 

Although the primary domains—Bacteria, Archaea, and Eukarya—were originally classified on the basis of comparative ribosomal RNA sequencing, subsequent studies have shown that each kingdom can also be defined on the basis of other... 

Walker WF 5S ribosomal RNA sequences from Ascomycetes and evolutionary implications. Syst Appl Microbiol 1985 6 48-53. 

Hasegawa M, lida Y, Yano T, Takaiwa F, Miyata T Phylogenetic relationships among eukaryotic kingdoms inferred from ribosomal RNA sequences. J Mol Evol 1985 22 32-38. 

Klutzman CP Systematics of the ascomycetous yeasts assessed from ribosomal RNA sequence divergence. Antonie Van Leeuwenhoek 1993 63 165-174. 

Leclerc MC, Philippe H, Gueho E Phylogeny of dermatophytes and dimorphic fungi based on large subunit ribosomal RNA sequence comparisons. J Med Vet Mycol 1994 32 331-341. 

Discovering a new base pair. Examine the ribosomal RNA sequences in Figure 7.19. In sequences that do not contain Watson-Crick base pairs, what base tends to be paired with G Propose a structure for your new base pair. 

Molecular sequences reveal evolutionary relationships in ways and to an extent that classical phenotypic criteria, and even molecular functions, cannot. What can be seen only dimly, if at all, at higher levels of cellular organization becomes obvious in terms of molecular structures and sequences. This point is nowhere more dramatically illustrated than by the present situation, where at the level of the whole-cell phenotype the archaea and bacteria are, at best, difficult to distinguish, and the differences they do show are impossible to interpret unequivocally. However, the uniqueness of the two groups is blatant and readily interpretable on the molecular level. From the perspective of ribosomal RNA sequence and structure the living world divides into three distinct classes, corresponding to three very distinct rRNA types [48,49]. The same three classes... 

Figure 1 The distribution of autotrophic metabolic pathways among taxa within the three major domains of life (as inferred from ribosomal RNA sequences (Pace, 1997)). Specific metabolic pathways are indicated.

RNA. "Ribonucleic acid". The nucleic acid which carries the dna message into parts of the cell where it is interpreted and used. The 18s ribosomal rna sequence has been used in many groups of organisms to reconstruct phylogeny. 

A partial 16S ribosomal-RNA sequence of CPI 130 matched the genus Streptomyces, most closely the species verticillus. Therefore, this represents the first report of tartrolons from a Streptomyces species, since their only previously reported occurrence was in the myxobacterium Sorangium cellulosum [55, 57, 58]. 

B. Zingales, B. S. Stolf, R. P. Souto, O. Fernandes, and M. R. S. Briones, Epidemiology, biochemistry and evolution of Trypanosoma cruzi lineages based on ribosomal RNA sequences, Mem. Inst. Oswaldo Cruz., 94(Suppl. 1), (1999) 159-164. 

B3. Bottger, E. C., Rapid determination of bacterial ribosomal RNA sequences by direct sequencing of enzymically amplified DNA. FEMS Microbiol. Lett. 65, 171-176 (1989). 

---