Compilation of pseudomonad sequences present in a database on the structure of ribosomal RNA

Systematic and Applied Microbiology

Volumn 19, Issue 4, 1996, Pages 493-500

  Van De Peer, Yves ^a   Vancanneyt, Marc ^b   De Wachter, Rupert ^a  

^a UNIVERSITY OF ANTWERP   (Belgium)

^b GHENT UNIVERSITY   (Belgium)

Author keywords

Large ribosomal subunit RNA; Pseudomonads; Ribosomal RNA database; Secondary structure models; Small ribosomal subunit RNA

Indexed keywords

BACTERIAL RNA; RIBOSOME RNA;

ARTICLE; DATA BASE; NONHUMAN; PRIORITY JOURNAL; PSEUDOMONAS; RNA SEQUENCE; RNA STRUCTURE;

EID: 0030447540     PISSN: 07232020     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0723-2020(96)80022-1     Document Type: Article

References (31)

1. Anders, H. J., Kaetzke, A., Kampfer, P., Ludwig, W., Fuchs, G.: Taxonomic position of aromatic-degrading denitrifying pseudomonad strains K 172 and K 740 and their description as new members of the genera Thauera, as Thauera aromatica sp. nov., and Azoarcus, as Azoarcus evansii sp. nov., respectively, members of the beta subclass of the Proteobacteria. Int. J. Syst. Bacteriol. 45, 327-333 (1995)
2. Bennasar, A., Rossello-Mora, R., Lalucat, J., Moore, E. R.: 16S rRNA gene sequence analysis relative to genomovars of Pseudomonas stutzeri and proposal of Pseudomonas balearica sp. nov. Int. J. Syst. Bacteriol. 46, 200-205 (1996)
3. Benson, D. A., Boguski, M., Lipman, D. J., Ostell, J.: Genbank. Nucleic Acids Res. 24, 1-5 (1996)
4. Bowman, J., Sly, L., Hayward, A. C., Spiegel, Y., Stackebrandt, E.: Telluria mixta (Pseudomonas mixta, Bowman Sly, and Hayward 1988) gen. nov., comb. nov., and Telluria chitinolytica sp. nov.: soil-dwelling organisms which actively degrade polysaccharides. Int. J. Syst. Bacteriol. 43, 120-124 (1993)
5. De Rijk, P., De Wachter, R.: DCSE, an interactive tool for sequence alignment and secondary structure research. Comput. Applic. Biosci. 9, 735-740 (1993)
6. De Rijk, P., Van de Peer, Y., Chapelle, S., De Wachter, R.: Database on the structure of large ribosomal subunit RNA. Nucleic Acids Res. 22, 3495-3501 (1994)
7. De Rijk, P., Van de Peer, Y., De Wachter, R.: Database on the structure of large ribosomal subunit RNA. Nucleic Acids Res. 24, 92-97 (1996)
8. Dewhirst, F. E., Paster, B. J., Bright, P. L.: Chromobacterium, Eikenella, Kingella, Neisseria, Simonsiella and Vitreoscilla species comprise a major branch of the beta group Proteobacteria by 16S rRNA sequence comparison. Int. J. Syst. Bacteriol. 39, 258-266 (1989)
9. Dewhirst, F. E., Paster, B. C., la Fontaine, S., Rood, J. I.: Transfer of Kingella indologenes (Snell and Lapage 1976) to the genus Suttonella gen. nov. as Suttonella indologenes comb. nov.; transfer of Bacteroides nodosus (Beveridge 1941) to the genus Dichelobacter gen. nov. as Dichelobacter nodosus comb. nov.; and assignment of the genera Cardiobacterium, Dichelobacter, and Suttonella to Cardiobacteriaceae fam. nov. in the gamma division of Proteobacteria on the basis of 16S rRNA sequence comparison. Int. J. Syst. Bacteriol. 40, 426-433 (1990)
10. Dobron, S. J., McMeekin, T. A., Franzmann, P. D.: Phylogenetic relationships between some members of the genera Deleya, Halomonas, and Halovibrio. Int. J. Syst. Bacteriol. 43, 665-673 (1993)
11. Doolittle, W. F., Brown, J. R.: Tempo, mode, the progenote, and the universal root. Proc. Natl. Acad. Sci. USA 91, 6721-6728 (1994)
12. Felsenstein, J.: Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783-791 (1985)
13. Gutell, R. R., Larsen, N., Woese, C. R.: Lessons from an evolving rRNA: 16S and 23S rRNA structures from a comparative perspective. Microbiol. Rev. 58, 10-26 (1994)
14. Hildebrand, D. C., Palleroni, N. J., Henderson, M., Toth, J., Johnson, J. L.: Pseudomonas flavescens sp. nov., isolated from walnut blight cankers. Int. J. Syst. Bacteriol. 44, 410-415 (1994)
15. Hoepfl, P., Ludwig, W., Schleifer, K. H., Larsen, N.: The 23S ribosomal RNA higher-order structure of Pseudomonas cepacia and other prokaryotes. Eur. J. Biochem. 185, 355-364 (1989)
16. Kersters, K., Ludwig, W., Vancanneyt, M., De Vos, P., Gillis, M., Schleifer, K.-H.: Recent changes in the classification of the pseudomonads: an overview. Syst. Appl. Microbiol. (this issue)
17. Li, X., Del dot, T., Stackebrandt, E., Sly, L. I., Hayward, A. C.: Phylogenetic studies on rRNA group II Pseudomonas using 16S rRNA sequences. J. Appl. Microbiol. 74, 324-329 (1993)
18. Moore, E. R. B., Mau, M., Arnscheidt, A., Böttger, E. C., Hutson, R. A., Collins, M. D., Van de Peer, Y., De Wachter, R., Timmis, K. N.: The determination and comparison of the 16S rRNA gene sequences of the genus Pseudomonas (sensu stricto) and estimation of the natural intrageneric relationships. Syst. Appl. Microbiol. 196, 478-492 (1996)
19. Neefs, J.-M., Van de Peer, Y., De Rijk, f., Chapelle, S., De Wachter, R.: Compilation of small ribosomal subunit RNA structures. Nucleic Acids Res. 21, 3025-3049 (1993)
20. Nelles, L., Fang, B.-L., Volckaert, G., Vandenberghe, A., De Wachter, R.: Nucleotide sequence of a crustacean 18S ribosomal RNA gene and secondary structure of eukaryotic small subunit ribosomal RNAs. Nucleic Acids Res. 12, 8749-8768 (1984)
21. Rodriguez-Tomé, P., Stoehr, P., Cameron, G. N., Flores, T. P.: The European Bioinformatics Institute (EBI) databases. Nucleic Acids Res. 24, 6-13 (1996)
22. Takeuchi, M., Sawada, H., Oyaizu, H., Yakota, A.: Phylogenetic evidence for Sphingomonas and Rhizomonas as nonphotosynthetic members of the alpha-4 subclass of the proteobacteria. Int. J. Syst. Bacteriol. 44, 308-314 (1994)
23. Toschka, H. Y., Hoepfl, P., Ludwig, W., Schleifer, K. H., Ulbrich, N., Erdmann, V. A.: Complete Nucleotide Sequence of a 23S Ribosomal RNA gene from Pseudomonas aeruginosa. Nucleic Acids Res. 15, 7182 (1987)
24. Toschka, H. Y., Hoepfl, P., Ludwig, W., Schleifer, K. H., Ulbrich, N., Erdmann, V. A.: Complete nucleotide sequence of a 16S ribosomal RNA gene from Pseudomonas aeruginosa. Nucleic Acids Res. 16, 2348 (1988)
25. Van de Peer, Y., De Wachter, R.: TREECON: a software package for the construction and drawing of evolutionary trees. Comput. Applic. Biosci. 9, 177-182 (1993)
26. Van de Peer, Y., De Wachter, R.: TREECON for Windows: a software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment. Comput. Applic. Biosci. 10, 569-570 (1994)
27. Van de Peer, Y., Nicolaï, S., De Rijk, P., De Wachter, R.: Database on the structure of small ribosomal subunit RNA. Nucleic Acids Res. 24, 86-91 (1996)
28. Woese, C. R.: Bacterial evolution. Microbiol. Rev. 51, 221-271 (1987)
29. Yabuuchi, E., Kosako, Y., Oyaizu, H., Yano, I., Hotta, H., Hashimoto, Y., Ezaki, T., Arakawa, M.: Proposal of Burkholderia gen. nov. and transfer of seven species of the genus Pseudomonas homology group II to the new genus, with the type species Burkholderia cepacia (Palleroni and Holmes 1981) comb. nov. Microbiol. Immunol. 36, 1251-1275 (1992)
30. Yamamoto, S., Harayama, S.: PCR amplification and direct sequencing of gyrB genes with universal primers and their application to the detection and taxonomic analysis of Pseudomonas putida strains. Appl. Environ. Microbiol. 61, 1104-1109 (1995)
31. Yang, D., Oyaizu, Y., Oyaizu, H., Olsen, G. J., Woese, C. R.: Mitochondrial origins. Proc. Natl. Acad. Sci. USA 82, 4443-4447 (1985)