Application of the ribonuclease P (RNase P) RNA gene sequence for phylogenetic analysis of the genus Saccharomonospora

International Journal of Systematic Bacteriology

Volumn 48, Issue 4, 1998, Pages 1223-1230

  Cho, Myungsun ^a   Yoon, Jung Hoon ^a   Kim, Sam Bong ^a   Park, Yong Ha ^a  

^a Korea Research Institute of Bioscience and Biotechnology (KRIBB)   (South Korea)

Author keywords

Phylogeny; RNase P RNA gene sequence; Saccharomonospora

Indexed keywords

RIBONUCLEASE P; RIBOSOME DNA;

ACTINOBACTERIA; ARTICLE; BACTERIUM IDENTIFICATION; DNA DNA HYBRIDIZATION; GRAM POSITIVE BACTERIUM; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; SACCHAROMONOSPORA; SEQUENCE HOMOLOGY; TAXONOMY;

SACCHAROMONOSPORA AZUREA; SACCHAROMONOSPORA CAESIA;

EID: 0031784670     PISSN: 00207713     EISSN: None     Source Type: Journal    
DOI: 10.1099/00207713-48-4-1223     Document Type: Article

References (37)

1. Brown, J. W. (1997). The ribonuclease P database. Nucleic Acids Res 25, 263-264.
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 Acad Sci USA 93, 3001-3006.
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.
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.
5. Greene, J. G., Treuhaft, M. W. & Arnsell, R. M. (1981). Hypersensitivity pneumonitis due to Saccharomonospora viridis diagnosed by inhalation challenge. Ann Allergy 47, 449-452.
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.
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.
8. Gürtler, V. & Stanisich, V. A. (1996). New approaches to typing and identification of bacteria using the 16S-23S rDNA spacer region. Microbiology 142, 3-16.
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.
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.
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 Syst Bacteriol 47, 202-206.
12. Hofle, M. (1990). Transfer RNAs as genotypic fingerprints of eubacteria. Arch Microbiol 153, 299-304.
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.
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.
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.
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.
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.
18. Morse, D. P. & Schmidt, F. J. (1992). Sequences encoding the protein and RNA components of ribonuclease P from Streptomyces bikiniensis var. zorbonensis. Gene 117, 61-66.
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.
20. Pace, N. R. (1997). A molecular view of microbial diversity and the biosphere. Science 276, 734-740.
21. Pace, N. R. & Brown, J. W. (1995). Evolutionary perspective on the structure and function of ribonuclease P, a ribozyme. J Bacteriol 177, 1919-1928.
22. Runmao, H. (1987). Saccharomonospora azurea sp. nov., a new species from soil. Int J Syst Bacteriol 37, 60-61.
23. Runmao, H., Lin, C. & Guizhen, W. (1988). Saccharomonospora cyanea sp. nov. Int J Syst Bacteriol 38, 444-446.
24. Saitou, N. & Nei, M. (1987). The neighbor-joining method : a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406-425.
25. Sambrook, J., Fritsch, E. F. & Maniatis, T. (1989). Molecular Cloning: a Laboratory Manual, 2nd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory.
26. Shareck, F., Biely, P., Morosoli, R. & Kluepfel, D. (1995). Analysis of DNA flanking the xlnB locus of Streptomyces lividans reveals genes encoding acetyl xylan esterase and the RNA component of ribonuclease P. Gene 153, 105-109.
27. Skerman, V. B. D., McGowan, V. & Sneath, P. H. A. (editors) (1980). Approved lists of bacterial names. Int J Syst Bacteriol 30, 225-420.
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.
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.
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.
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.
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 16S rRNA sequences and a proposal to combine genera Amycolata and Pseudonocardia in an emended genus Pseudonocardia. Int J Syst Bacteriol 44, 292-299.
33. Woese, C. R. (1987). Bacterial evolution. Microbiol Rev 51, 221-271.
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.
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.
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 47, 661-669.
37. Yoon, J.-H., Lee, S. T., Kim, S.-B., Kim, W. Y., Goodfellow, M. & Park, Y.-H. (1997b). Restriction fragment length polymorphism analysis of PCR-amplified 16S ribosomal DNA for rapid identification of Saccharomonospora strains. Int J Syst Bacteriol 47, 111-114.