1887

Abstract

The 16S-23S and 23S-5S rRNA spacer DNA regions (spacer regions 1 and 2, respectively) from and were amplified by PCR. Their nucleotide sequences were established and a secondary structure model showing the interaction between the two spacer regions was built. Whereas lactococci and are characterized by a single type of spacer region 1, the enterococci show a high degree of variability in this region; thus the spacer regions 1 with and without tRNAwere characterized. However, as shown for lactococci and , the tRNAgene does not encode the 3'-terminal CCA trinucleotide. A putative antitermination signal is found downstream from the tRNAgene. Based on comparison with and , a double-stranded processing stem is proposed. In , one of the three different types of spacer region 1 contains no tRNA, but displays a 107 nt insertion that forms a long stem-loop structure. A similar insertion (115 nt in length) was found in and base compensatory mutations preserve the ability to form the long stem-loop structure. Such insertions may correspond to mobile intervening sequences, as found in the 23S rRNA coding sequences of some Gram-negative bacteria. The spacer regions 1 and 2 from the three subgroups of streptococci were compared, and except for the tRNAgene and the double-stranded processing sites, little similarity was found, which opens large possibilities for future development of DNA-based typing methods.

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1997-03-01
2021-08-05
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References

  1. Apirion D., Miczak A. 1993; RNA processing in prokaryotic cells. BioEssays 15:113–120
    [Google Scholar]
  2. Bacot C.M., Reeves R.H. 1991; Novel tRNA gene organization in the 16S-23S intergenic spacer of the Streptococcus pneumoniae rRNA gene cluster. J Bacteriol 173:4234–4236
    [Google Scholar]
  3. Barry T., Colleran G., Glennon M., Dunican L.K., Gannon F. 1991; . The 16s/23s ribosomal spacer region as a target for DNA probes to identify eubacteria. BCR Methods Appl 1:51–56
    [Google Scholar]
  4. Beimfohr C., Krause A., Amann R., Ludwig W., Schleifer K.H. 1993; In situ identification of lactococci, enterococci and streptococci. Syst Appl Microbiol 16:450–456
    [Google Scholar]
  5. Berg K.L., Squires C., Squires C.L. 1989; Ribosomal RNA operon anti-termination-function of leader and spacer region boxB-boxA sequences and their conservation in diverse microorganisms. . J Mol Biol 209:345–358
    [Google Scholar]
  6. Betzl D., Ludwig W., Schleifer K.H. 1990; Identification of lactococci and enterococci by colony hybridization with 23S rRNA-targeted oligonucleotide probes. Appl Environ Microbiol 56:2927–2929
    [Google Scholar]
  7. Borton G.J. 1993; Alscript: a tool to format multiple sequence alignments. Protein Eng 6:37–40
    [Google Scholar]
  8. Branlant C., Krol A., Machat M.A., Pouet J., Ebel J.P. 1981; Primary and secondary structures of Escherichia coli MRE 600 ribosomal RNA. Comparison with models of secondary structures for maize chloroplast 23S rRNA and for large portions of mouse and human 16S mitochondrial rRNAs. Nucleic Acids Res 9:4303–324
    [Google Scholar]
  9. Chiaruttini C., Milet M. 1993; Gene organization, primary structure and RNA processing analysis of a ribosomal RNA operon in Lactococcus lactis. . J Mol Biol 230:57–76
    [Google Scholar]
  10. De Man J.C, Rogosa M., Sharpe M. E. 1960; A medium for the cultivation of lactobacilli. J Appl Bacteriol 23:130–135
    [Google Scholar]
  11. Devriese L.A., Pot B., Collins M.D. 1993; Phenotypic identification of the genus Enterococcus and differentiation of phylogenetically distinct enterococcal species and species groups. J Appl Bacteriol 75:399–408
    [Google Scholar]
  12. van der Giessen J.W.B., Haring R.M., van der Zeijst B.A.M. 1994; Comparison of the 23S ribosomal RNA genes and the spacer region between the 16S and 23S rRNA genes of the closely related Mycobacterium avium and Mycobacterium para- tuberculosis and the fast-growing Mycobacterium phlei. . Microbiology 140:1103–1108
    [Google Scholar]
  13. Green C.J., Vold B.S. 1983; Sequence analysis of cluster of twenty-one tRNA genes in Bacillus subtilis. . Nucleic Acids Res 11:5763–5774
    [Google Scholar]
  14. Guédon G., Pébay M., Colmin C., Simonet J.M., Decaris B. 1992; . The 23S-5S spacer of two rRNA loci of Streptococcus salivarius subsp thermophilus include a promoter. Biochimie 74:585–588
    [Google Scholar]
  15. 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
    [Google Scholar]
  16. Hall L.M.C. 1994; Are point mutations or DNA rearrangements responsible for the restriction fragment length polymorphisms that are used to type bacteria ? . Microbiology 140:197–204
    [Google Scholar]
  17. Hall L.M.C., Duke B., Guiney M., Williams R. 1992; Typing of Enterococcus species by DNA restriction fragment analysis. J Clin Microbiol 30:915–919
    [Google Scholar]
  18. Harasawa R., Uemori T., Asada K., Kato I., Shiragami N. 1992; 〒boxA〓-like sequence between the 16S/23S spacer in rRNA operon of mycoplasmas. FEES Lett 297:209–211
    [Google Scholar]
  19. Hardie J.M. 1986; Genus Streptococcus Rosenbach 1884. . In Bergey〓s Manual of Systematic Bacteriology 2 pp. 1043–1047 Sneath P.H.A., Mair N.S., Sharpe M.E., Holt J.G. Edited by Baltimore: Williams & Wilkins;
    [Google Scholar]
  20. Hill C., Miller L.A., Klaenhamer T.R. 1990; Cloning, expression, and sequence determination of a bacteriophage fragment encoding bacteriophage resistance in Lactococcus lactis. . J Bacteriol 172:6419–426
    [Google Scholar]
  21. Jensen M.A., Webster J.A., Straus N. 1993; Rapid identification of bacteria on the basis of polymerase chain reaction- amplified ribosomal DNA spacer polymorphisms. Appl Environ Microbiol 59:945–952
    [Google Scholar]
  22. Ji Y., Kempsell K.E., Colston M.J., Cox R.A. 1994; Nucleotide sequences of the spacer-1, spacer-2 and trailer regions of the rrn operons and secondary structures of precursor 23S rRNAs and precursor 5S rRNAs of slow-growing mycobacteria. Microbiology 140:1763–1773
    [Google Scholar]
  23. Kilpper-Bälz R., Fischer G., Schleifer K.H. 1982; Nucleic acid hybridization of group N and group D streptococci. Curr Microbiol 7:245–250
    [Google Scholar]
  24. Konkel M.E., Marconi R.T., Head D.J., Cieplak W. 1994; Identification and characterization of an intervening sequence within the 23S ribosomal RNA genes of Campylobacter jejuni. . Mol Microbiol 14:235–241
    [Google Scholar]
  25. Le Bourgeois P., Lautier M., Van Den Berghe L, Gasson M.J. 1995; Physical and genetic map of the Lactococcus lactis subsp.cremoris MG1363 chromosome: comparison with that oi Lactococcus lactis subsp.lactis IL 1403 reveals a large genome inversion. J Bacteriol 177:2840–2850
    [Google Scholar]
  26. Loughney K., Lund E., Dahiberg J.E. 1982; tRNA genes are found between the 16S and the 23S rRNA genes in Bacillus subtilis. . Nucleic Acids Res 10:1607–1624
    [Google Scholar]
  27. Ludwig W., Seewaldt E., Kilpper-Bäz R., Schleifer K.H., Magrum L., Woese C.R., Fox G.E., Stackebrandt E. 1985; The phylogenetic position of Streptococcusand Enterococcus. . J Gen Microbiol 131:543–551
    [Google Scholar]
  28. Ludwig W., Kirchhof G., Klugbauer N. 13 other authors 1992; Complete 23S ribosomal RNA sequences of Gram-positive bacteria with a low DNA G -H C content. Syst Appl Microbiol 15:487–501
    [Google Scholar]
  29. Mundt J.O. 1986; Enterococci. . In Bergey’s Manual of Systematic Bacteriology, 2 pp. 1063–1065 Sneath P.H.A., Mair N.S., Sharpe M.E., Holt J.G. Edited By Baltimore: Williams & Wilkins;
    [Google Scholar]
  30. Nour M., Naïmi A., Beck G., Branlant C. 1995; 16S-23S and 23S-5S intergenic spacer regions of Streptococcus thermophilus and Streptococcus salivarius, primary and secondary structure. Curr Microbiol 31:270–278
    [Google Scholar]
  31. Ogasawara N., Moriya S., Yoshikawa H. 1983; Structure and organization of rRNA operons in the region of the replication origin of the Bacillus subtilis chromosome. Nucleic Acids Res 18:6301–6318
    [Google Scholar]
  32. Pébay M., Colmin C, Guédon G., De Gaspéri C., Decaris B., Simonet J.M. 1992; Detection of intraspecific DNA polymorphism in Streptococcus salivarius subspthermophilus by a homologous rDNA probe. Res Microbiol 143:37–46
    [Google Scholar]
  33. Pernodet J.L., Boccard F., Alegre M.T., Gagnat J., Guérineau M. 1989; Organization and nucleotide sequence of a ribosomal RNA gene cluster from Streptomyces ambofaciens. . Gene 79:33–6
    [Google Scholar]
  34. Pittet A.C., Hottinger H. 1989; Sequence of a hexameric tRNA gene cluster associated with rRNA genes in Lactobacillus bulgaricus. . Nucleic Acids Res 17:4873
    [Google Scholar]
  35. Potter S., Durovic P., Dennis P.P. 1995; Ribosomal RNA precursor processing by a eukaryotic U3 small nucleolar RNA- like molecule in an archaeon. Nature 268:1056–1060
    [Google Scholar]
  36. Sambrook J., Fritsch E.F., Maniatis T. 1989 Molecular Cloning: a Laboratory Manual, 2. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory;
    [Google Scholar]
  37. Schleifer K.H., Kilpper-Bälz R. 1987; Molecular and chemo- taxonomic approaches to the classification of streptococci, enterococci and lactococci: a review. Syst Appl Microbiol 10:1–19
    [Google Scholar]
  38. Sechi L.A., Daneo-Moore L. 1993; Characterization of intergenic spacers in two rrn operons of Enterococcus hirae ATCC 9790. J Bacteriol 175:3213–3219
    [Google Scholar]
  39. Tabor S., Richardson C.C. 1987; DNA sequence analysis with a modified bacteriophage T7 DNA polymerase. Proc Natl Acad Sci USA 844767–771
    [Google Scholar]
  40. 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]
  41. Whiley R.A., Duke B., Hardie J.M., Hall L.M.C. 1995; Heterogeneity among 16S-23S rRNA intergenic species within the 〒Streptococcus milleri group〓. Microbiology 141:1461–1467
    [Google Scholar]
  42. Williams A.M., Rodrigues U.M., Collins M.D. 1991; Intrageneric relationships of enterococci as determined by reverse transcriptase sequencing of small-subunit rRNA. Res Microbiol 142:67–74
    [Google Scholar]
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