Sequence heterogeneities of genes encoding 16S rRNAs in Paenibacillus polymyxa detected by temperature gradient gel electrophoresis

Journal of Bacteriology

Volumn 178, Issue 19, 1996, Pages 5636-5643

  Nübel, Ulrich ^a,c   Engelen, Bert ^a   Felsre, Andreas ^a,d   Snaidr, Jiri ^b   Wieshuber, Alois ^b   Amann, Rudolf I ^b   Ludwig, Wolfgang ^b   Backhaus, Horst ^a  

^a INSTITUTE FOR EPIDEMIOLOGY AND PATHOGEN DIAGNOSTICS   (Germany)

^b TECHNICAL UNIVERSITY OF MUNICH   (Germany)

^c MAX PLANCK INSTITUTE FOR MARINE MICROBIOLOGY   (Germany)

^d WAGENINGEN UNIVERSITY   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CELL CULTURE; CHROMOSOMAL LOCALIZATION; GEL ELECTROPHORESIS; GENE INSERTION; GENE SEQUENCE; GENE TARGETING; GENETIC HETEROGENEITY; OLIGONUCLEOTIDE PROBE; PAENIBACILLUS POLYMYXA; PLASMID; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROTEIN SECONDARY STRUCTURE; RNA GENE; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; SOUTHERN BLOTTING; STRUCTURE ACTIVITY RELATION;

EID: 0029796310     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/jb.178.19.5636-5643.1996     Document Type: Article

References (45)

1. Amann, R. I., B. J. Binder, R. J. Olson, S. W. Chisholm, R. Devereux, and D. A. Stahl. 1990. Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl. Environ. Microbiol. 56:1919-1925.
2. Amann, R. I., L. Krumholz, and D. A. Stahl. 1990. Fluorescent-oligonucleotide probing of whole cells for determinative, phylogenetic, and environmental studies in microbiology. J. Bacteriol. 172:762-770.
3. Amann, R. I., W. Ludwig, and K. H. Schleifer. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59:143-169.
4. 3a.Anonymous. 1994. Validation of the publication of new names and new combinations previously effectively published outside the IJSB. List no. 51. Int. J. Syst. Bateriol. 44:852.
5. Ash, C., J. A. E. Farrow, S. Wallbanks, and M. D. Collins. 1991. Phylogenetic heterogeneity of the genus Bacillus revealed by comparative analysis of small-subunit-ribosomal RNA sequences. Lett. Appl. Microbiol. 13:202-206.
6. Ausubel, F. M., R. Brent, R. E. Kingston, D. D. Moore, J. A. Smith, J. G. Seidman, and K. Struhl. 1988. Preparation and analysis of DNA, p. 2.4.1.-2.4.5. In F. M. Ausubel (ed.), Current protocols in molecular biology. John Wiley & Sons, Inc., New York.
7. Belfort, M., M. E. Reaban, T. Coetzee, and J. Z. Dalgaard. 1995. Prokaryotic introns and inteins: a panoply of form and function. J. Bacteriol. 177:3897-3903.
8. Brosius, J., T. Dull, D. D. Sleeter, and H. F. Noller. 1981. Gene organization and primary structure of a ribosomal RNA operon from Escherichia coli. Proc. Natl. Acad. Sci. USA 75:4801-4805.
9. Carbon, P., C. Ehresmann, B. Ehresmann, and J.-P. Ebel. 1979. The complete nucleotide sequence of the ribosomal 16S rRNA from Escherichia coli. Eur. J. Biochem. 100:399-410.
10. Clayton, R. A., G. Sutton, P. S. Hinkle, Jr., C. Bult, and C. Fields. 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.
11. Cole, S. T., and I. Saint Girons. 1994. Bacterial genomics. FEMS Microbiol. Rev. 14:139-160.
12. Condon, C., D. Liveris, C. Squires, I. Schwartz, and C. L. Squires. 1995. rRNA operon multiplicity in Escherichia coli and the physiological implications of rrn inactivation. J. Bacteriol. 177:4152-4156.
13. Dryden, S., and S. Kaplan. 1990. Localization and structural analysis of the ribosomal RNA operons of Rhodobacter sphaeroides. Nucleic Acids Res. 18:7267-7277.
14. Fleischmann, R. D., M. D. Adams, O. While, R. A. Clayton, E. F. Krikness, A. R. Kerlavage, C. J. Bult, J.-F. Tomb, B. A. Dougherty, J. M. Merrick, K. McKenney, G. Sutton, W. FitzHugh, C. Fields, J. D. Gocayne, J. Scott, R. Shirley, L.-I. Liu, A. Glodek, J. M. Kelley, J. F. Weidman, C. A. Philips, T. Spreiggs, E. Hedblom, M. D. Cotton, T. R. Utterback, M. C. Hanna, D. T. Nguyen, D. M. Saudek, R. C. Brandon, L. D. Fine, J. L. Fritchman, J. L. Fuhrmann, N. S. M. Geoghagen, C. L. Gnehm, L. A. McDonald, K. V. Small, C. M. Fraser, H. O. Smith, and J. C. Venter. 1995. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269:496-512.
15. Fox, G. E., J. D. Wisotzkey, and P. Jurtshuk, 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.
16. Garnier, T., B. Canard, and S. T. Cole. 1991. Cloning, mapping, and molecular characterization of the rRNA operons of Clostridium perfringens. J. Bacteriol. 173:5431-5438.
17. Giovannoni, S. J. 1991. The polymerase chain reaction, p. 178-203. In E. Stackebrandl and M. Goodfellow (ed.), Nucleic acid techniques in bacterial systematics. John Wiley & Sons, Chichester, England.
18. Goovannoni, S. J., T. B. Britschgi, C. L. Moyer, and K. G. Field. 1990. Genetic diversity in Sargasso Sea bacterioplancton. Nature (London) 345:60-63.
19. Gunderson, J. H., M. L. Sogin, G. Wollett, M. Hollingdale, V. F. de la Cruz, A. P. Waters, and T. F. McCutchan. 1987. Structurally distinct, stage-specific ribosomes occur in Plasmodium. Science 238:933-937.
20. Gutell, R. R., N. Larsen, and C. R. Woese. 1994. Lessons from an evolving rRNA: 16S and 23S rRNA structures from a comparative perspective. Microbiol. Rev. 58:10-26.
21. Larsen, N., G. J. Olsen, B. L. Maidak, M. J. McCaughey, R. Overbeek, T. J. Macke, T. L. Marsh, and C. R. Woese. 1993. The ribosomal database project. Nucleic Acids Res. 21:3021-3023.
22. Liesack, W., and E. Stackebrandt. 1989. Evidence for unlinked rrm operons in the planctomycete Pirellula marina, J. Bacteriol. 171:5025-5030.
23. Meyer, C. G., E. Tannich, J. Harders, K. Henco, and R. D. Horstmann. 1991. Direct sequencing of variable HLA gene segments after in vitro amplification and allele separation by temperature-gradient gel electrophoresis. J. Immunol. Methods 142:251-256.
24. Muyzer, G., E. C. de Waal, and A. G. Uitterlinden. 1993. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl. Environ. Microbiol. 59:695-700.
25. Mylvaganam, S., and P. P. Dennis. 1992. Sequence heterogeneity between the two genes encoding 16S rRNA from the halophilic archaebacterium Haloarcula marismortui. Genetics 130:399-410.
26. Neefs, J. M., Y. V. de Peer, L. Hendriks, and R. de Wachter. 1990. Compilation of small ribosomal subunit RNA sequences, Nucleic Acids Res. 18: 2237-2242.
27. Ogasawara, N., S. Nakai, and H. Joshikawa. 1994. Systematic sequencing of the 180 kilobase region of the Bacillus subtilis chromosome containing the replication origin. DNA Res. 1:1-14.
28. Peterson, R. C., J. L. Doering, and D. D. Brown. 1980. Characterization of two Xenopus somatic 5S DNAs and one minor oocyte-specific 5S DNA. Cell 20:131-141.
29. Rosenbaum, V., and D. Riesner. 1987. Temperature-gradient gel electrophoresis; thermodynamic analysis of nucleic acids and proteins in purified form and in cellular extruds. Biophys. Chem. 26:235-246.
30. Rössler, D., W. Ludwig, K. H. Schleifer, C. Lin, T. J. McGill, J. D. Wisotzkey, P. Jurtshuk, Jr., and G. E. Fox. 1991. Phylogenetic diversity in the genus Bacillus as seen by 16S rRNA sequencing studies. Syst. Appl. Microbiol. 14:266-269.
31. Rudner, R., A.-M. White, B. Studamire, D. Liu, W. Lam, W. Samarrai, and C. J. Barangan. 1993. Heterogeneity in expression of ribosormal RNA operons in Bacillus subtilis, abstr. H-257, p. 23d. In Abstracts of the 93rd General Meeting of the American Society for Microbiology 1993. American Society for Microbiology, Washington, D.C.
32. Saiki, R. K., D. H. Gelfand, S. Stoffel, S. J. Scharf, R. Higuchi, G. T. Horn, K. B. Mullis, and H. A. Erlich. 1488. Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239:487-491.
33. Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
34. Sheffield, V. C., D. R. Cox, L. S. Lerman, and R. M. Myers. 1989. Attachment of a 40-base-pair G+C-rich sequence (GC-clamp) to genomic DNA fragments by the polymerase chain reaction results in improved detection of single-base changes. Proc. Natl. Acad. Sci. USA 86:232-236.
35. Sogin, M. L. 1990. Amplification of ribosomal RNA genes for molecular evolution studies, p. 307-314. In M. A. Innis, D. H. Gelfand, J. J. Sninsky, and T. J. White (ed.), PCR protocols, a guide to methods and applications. Academic Press, San Diego, Calif.
36. 34a.Söller, R., E. Stackebrandt, and G. Krupp. Personal communication.
37. Stackebrandt, E., and B. M. Goebel. 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.
38. Steger, G. 1994. Thermal denaturation of double-stranded nucleic acids: prediction of temperatures critical for gradient gel electrophoresis and polymerase chain reaction. Nucleic Acids Res. 22:2760-2768.
39. Suzuki, T., and K. Yamasato. 1994. Phylogeny of spore-forming lactic acid bacteria based on 16S rRNA gene sequences. FEMS Microbiol. Lett. 115: 13-17.
40. van Wezel, G. P., E. Vijgenboom, and L. Bosch. 1991. A comparative study of the ribosomal RNA operons of Streptomyces coelicolor A3(2) and sequence analysis of rRNA. Nucleic Acids Res. 19:4399-4403.
41. Wagner, R. 1994. The regulation of ribosomal RNA synthesis and bacterial cell growth. Arch. Microbiol. 161:100-109.
42. Wich, G., L. Siebold, and A. Böck. 1987. Divergent evolution of 5S rRNA genes in Methanococcus, Z. Naturforsch. 42c:373-380.
43. Widom, R. L., E. D. Jarvis, G. LaFauci, and R. Rudner. 1988. Instability of rRNA operons in Bacillus subtilis. J. Bacteriol. 170:605-610.
44. Woese, C. R. 1987. Bacterial evolution. Microbiol. Rev. 51:221-271.
45. Zarda, B., R. Amann, G. Wallner, and K.-H. Schleifer. 1991. Identification of single bacterial cells using digoxigenin-labeled, rRNA-targeted oligonucleotides. J. Gen. Microbiol. 137:2823-2830.