Application of the Ribonuclease P (RNase P) RNA Gene Sequence for Phylogenetic Analysis of the Genus Saccharomonospora

References

1. Brown J. W. 1997; The ribonuclease P database. Nucleic Acids Res 25:263–264
   [Google Scholar]
2. Brown J. W., Nolan J. M., Haas E. S., Rubio M. A. T., Major F., Pace N. R. 1996; Comparative analysis of ribonuclease P RNA using gene sequences from natural microbial populations reveals tertiary structural elements. Proc Natl AcadSci USA 93:3001–3006
   [Google Scholar]
3. Clayton R. A., Sutton G., Hinkle P. S., Bult C Jr, Fields C. 1995; Intraspecific variation in small-subunit rRNA sequences in Genbank : why single sequences may not adequately represent prokaryotic taxa. Int J Syst Bacteriol 45:595–599
   [Google Scholar]
4. Fox G. E., Wisotzkey J. D., Jurtshuk P. Jr 1992; How close is close: 16S rRNA sequence identity may not be sufficient to guarantee species identity. Int J Syst Bacteriol 42:166–170
   [Google Scholar]
5. Greene J. G., Treuhaft M. W., Arnsell R. M. 1981; Hyper-sensitivity pneumonitis due to Saccharomonospora viridis diagnosed by inhalation challenge. Ann Allergy 47:449–452
   [Google Scholar]
6. Greiner-Mai E., Kroppenstedt R. M., Korn-Wendisch F., Kutzner H. J. 1987; Morphological and biochemical characterization and emended descriptions of thermophilic actinomycetes species. Syst Appl Microbiol 9:97–109
   [Google Scholar]
7. Greiner-Mai E., Korn-Wendisch F., Kutzner H. J. 1988; Taxonomic revision of the genus Saccharomonospora and description of Saccharomonospora glauca sp. nov. Int J Syst Bacteriol 38:398–405
   [Google Scholar]
8. Gurtler V., Stanisich V. A. 1996; New approaches to typing and identification of bacteria using the 16S-23S rDNA spacer region. Microbiology 142:3–16
   [Google Scholar]
9. Gutell R. R., Larsen N., Woese C. R. 1994; Lessons from an evolving rRNA: 16S and 23S rRNA structures from a comparative perspective. Microbiol Rev 58:10–26
   [Google Scholar]
10. Haas E. S., Brown J. W., Pitulle C., Pace N. R. 1994; Further perspective on the catalytic core and secondary structure of ribonuclease P RNA. Proc Natl Acad Sci USA 91:2527–2531
    [Google Scholar]
11. Hain T., Ward-Rainey N., Kroppenstedt R. M., Stackebrandt E., Rainey F. A. 1997; Discrimination of Streptomyces albidoflavus strains based on the size and number of 16S-23S ribosomal DNA intergenic spacers. Int J Svst Bacteriol 47:202–206
    [Google Scholar]
12. Hofle M. 1990; Transfer RNAs as genotypic fingerprints of eubacteria. Arch Microbiol 153:299–304
    [Google Scholar]
13. Kamla V., Henrich B., Hadding U. 1996; Phylogeny based on elongation factor Tu reflects the phenotypic features of mycoplasma better than that based on 16S rRNA. Gene 171:83–87
    [Google Scholar]
14. Kim S.-B., Yoon J.-H., Kim H., Lee S. T., Park Y.-H., Goodfellow M. 1995; A phylogenetic analysis of the genus Saccharomonospora conducted with 16S rRNA gene sequences. Int J Syst Bacteriol 45:351–356
    [Google Scholar]
15. Lawrence N. P., Richman A., Amini R., Altman S. W. 1987; Heterologous enzyme function in Escherichia coli and the selection of genes encoding the catalytic RNA subunit of RNase P. Proc Natl Acad Sci USA 84:6825–6829
    [Google Scholar]
16. Leblond-Bourget N., Philippe H., Mangin I., Decaris B. 1996; 16S rRNA and 16S to 23S internal transcribed spacer sequence analyses reveal inter- and intraspecific Bifidobacterium phylogeny. Int J Syst Bacteriol 46:102–111
    [Google Scholar]
17. Maidak B. L., Olsen G. J., Larsen N., Overbeek R., McCaughey M. J., Woese C. R. 1997; The RDP (Ribosomal database project). Nucleic Acids Res 25:109–110
    [Google Scholar]
18. Morse D. P., 8i Schmidt F. J. 1992; Sequences encoding the protein and RNA components of ribonuclease P from Streptomyces bikiniensis var. zorbonensis. Gene 117:61–66
    [Google Scholar]
19. Nonomura H., Ohara Y. 1971; Distribution of actinomycetes in soil. X. New genus and species of monosporic actinomycetes. J Ferment Technol 49:895–903
    [Google Scholar]
20. Pace N. R. 1997; A molecular view of microbial diversity and the biosphere. Science 276:734–740
    [Google Scholar]
21. Pace N. R., Brown J. W. 1995; Evolutionary perspective on the structure and function of ribonuclease P, a ribozyme. J Bacteriol 111:1919–1928
    [Google Scholar]
22. Runmao H. 1987; Saccharomonospora azurea sp. nov., a new species from soil. Int J Syst Bacteriol 37:60–61
    [Google Scholar]
23. Runmao H., Lin C., Guizhen W. 1988; Saccharomonospora cyanea sp. nov. Int J Syst Bacteriol 38:444–446
    [Google Scholar]
24. Saitou N., Nei M. 1987; The neighbor-joining method : a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425
    [Google Scholar]
25. Sambrook J., Fritsch E. F., Maniatis T. 1989; Molecular Cloning: a Laboratory Manual. , 2. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory;
    [Google Scholar]
26. Shareck F., Biely P., Morosoli R., Kluepfel D. 1995; Analysis of DNA flanking the xlnB locus ofStreptomyces lividans reveals genes encoding acetyl xylan esterase and the RNA component of ribonuclease P. Gene 153:105–109
    [Google Scholar]
27. Skerman V. B. D., McGowan V., Sneath P. H. A. 1980; Approved lists of bacterial names. Int J Syst Bacteriol 30:225–420
    [Google Scholar]
28. Stackebrandt E., Goebel B. M. 1994; Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44:846–849
    [Google Scholar]
29. Thompson J. D., Higgins D. G., Gibson T. J. 1994; clustal w : improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680
    [Google Scholar]
30. Valsangiacomo C., Balmelli T., Piffaretti J.-C. 1997; A phylogenetic analysis of Borrelia burgdorferi sensu lato based on sequence information from the hbb gene, coding for a histone-like protein. Int J Syst Bacteriol 47:1–10
    [Google Scholar]
31. Vandamme P., Pot B., Gillis M., De Vos P., Kersters K., Swings J. 1996; Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol Rev 60:407–438
    [Google Scholar]
32. Warwick S., Bowen T., McVeigh H., Embley T. M. 1994; A phylogenetic analysis of the family Pseudonocardiacea and the genera Actinokineospora and Saccharothrix with 16Ss rRNA sequences and a proposal to combine genera Amycolata and Pseudonocardia in an emended genus Pseudonocardia . Int J Svst Bacteriol 44:292–299
    [Google Scholar]
33. Woese C. R. 1987; Bacterial evolution. Microbiol Rev 51:221–271
    [Google Scholar]
34. Yoon J.-H., Kim H., Kim S.-B., Kim H.-J., Kim W. Y., Lee S. T., Goodfellow M., Park Y.-H. 1996a; Identification of Saccharomonospora strains with genomic DNA fragments and rRNA gene probes. Int J Syst Bacteriol 46:502–505
    [Google Scholar]
35. Yoon J.-H., Lee S. T., Shin Y. K., Kim S.-B., Kim H.-J., Goodfellow M., Park Y.-H. 1996b; Rapid identification of Saccharomonospora strains by multiplex PCR using species-specific primers within the 16S rRNA gene. J Microbiol Methods 27:89–95
    [Google Scholar]
36. Yoon J.-H., Lee S.T., Kim S.-B., Goodfellow M., Park Y.-H. 1997a; Inter- and intraspecific genetic analysis of the genus Saccharomonospora with 16S to 23S ribosomal DNA (rDNA) and 23S to 5S rDNA internally transcribed spacer sequences. Int J Syst Bacteriol 41:661–669
    [Google Scholar]
37. Yoon J.-H., Lee S.T., Kim S.-B., Kim W. Y., Goodfellow M., Park Y.-H. 1997b; estriction fragment length polymorphism analysis of PCR-amplified 16S ribosomal DNA for rapid identification of Saccharomonospora strains. Int J Syst Bacteriol 47:111–114
    [Google Scholar]