1887

Abstract

The gene is universally present in bacterial species and encodes the RNA subunit of endoribonuclease P. In this study, was sequenced in 50 type strains and 29 additional strains of the genus . Putative secondary-structure models and possible interactions in RNase P RNA molecules are discussed. Phylogenetic relationships were studied and Bayesian, maximum-parsimony and minimum-evolution analyses supported six main clades that comprised 22 of the 50 species analysed. Phylogenetic inference was also studied for the 16S rRNA gene; it indicated a similar tree topology, but with weaker support values than for . Combined analysis of and 16S resulted in a phylogeny with significantly better support. Variability in the and 16S genes among all type strains, calculated as Shannon–Wiener information index values, was 0·45 for and 0·15 for 16S. Intraspecies proximity was assessed by principal coordinate analysis of for 32 strains of six closely related species (two clades) and showed species-specific clusters, but heterogeneity occurred in two species. It can be concluded that the gene is suitable for phylogenetic analysis of closely related taxa and has potential as a tool for species discrimination.

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2003-11-01
2024-03-29
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References

  1. Adnan S., Li N., Miura H., Hashimoto Y., Yamamoto H., Ezaki T. 1993; Covalently immobilized DNA plate for luminometric DNA-DNA hybridization to identify viridans streptococci in under 2 hours. FEMS Microbiol Lett 106:139–142 [CrossRef]
    [Google Scholar]
  2. Altman S., Kirsebom L. A. 1999; Ribonuclease P. In The RNA World pp 351–380Edited by Gesteland R. F., Cech T. R., Atkins J. F. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory;
    [Google Scholar]
  3. Baele M., Storms V., Haesebrouck F., Devriese L. A., Gillis M., Verschraegen G., de Baere T., Vaneechoutte M. 2001; Application and evaluation of the interlaboratory reproducibility of tRNA intergenic length polymorphism analysis (tDNA-PCR) for identification of Streptococcus species. J Clin Microbiol 39:1436–1442 [CrossRef]
    [Google Scholar]
  4. Bartie K. L., Wilson M. J., Williams D. W., Lewis M. A. O. 2000; Macrorestriction fingerprinting of “ Streptococcus milleri ” group bacteria by pulsed-field gel electrophoresis. J Clin Microbiol 38:2141–2149
    [Google Scholar]
  5. Beighton D., Hardie J. M., Whiley R. A. 1991; A scheme for the identification of viridans streptococci. J Med Microbiol 35:367–372 [CrossRef]
    [Google Scholar]
  6. Bentley R. W., Leigh J. A. 1995; Development of PCR-based hybridization protocol for identification of streptococcal species. J Clin Microbiol 33:1296–1301
    [Google Scholar]
  7. Bentley R. W., Leigh J. A., Collins M. D. 1991; Intrageneric structure of Streptococcus based on comparative analysis of small-subunit rRNA sequences. Int J Syst Bacteriol 41:487–494 [CrossRef]
    [Google Scholar]
  8. Brown J. W. 1999; The Ribonuclease P Database. Nucleic Acids Res 27:314 [CrossRef]
    [Google Scholar]
  9. De Gheldre Y., Vandamme P., Goossens H., Struelens M. J. 1999; Identification of clinically relevant viridans streptococci and analysis of transfer DNA intergenic spacer length polymorphism. Int J Syst Bacteriol 49:1591–1598 [CrossRef]
    [Google Scholar]
  10. Farrow J. A. E., Collins M. D. 1984; Taxonomic studies on streptococci of serological groups C, G and L and possibly related taxa. Syst Appl Microbiol 5:483–493 [CrossRef]
    [Google Scholar]
  11. 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 [CrossRef]
    [Google Scholar]
  12. Garnier F., Gerbaud G., Courvalin P., Galimand M. 1997; Identification of clinically relevant viridans group streptococci to the species level by PCR. J Clin Microbiol 35:2337–2341
    [Google Scholar]
  13. Gillespie B. E., Jayarao B. M., Oliver S. P. 1997; Identification of Streptococcus species by randomly amplified polymorphic deoxyribonucleic acid fingerprinting. J Dairy Sci 80:471–476 [CrossRef]
    [Google Scholar]
  14. Gower J. C. 1966; Some distance properties of latent root and vector methods used in multivariate analysis. Biometrika 53:325–338 [CrossRef]
    [Google Scholar]
  15. Gu X., Fu Y.-X., Li W.-H. 1995; Maximum likelihood estimation of the heterogeneity of substitution rate among nucleotide sites. Mol Biol Evol 12:546–557
    [Google Scholar]
  16. Haas E. S., Brown J. W. 1998; Evolutionary variation in bacterial RNase P RNAs. Nucleic Acids Res 26:4093–4099 [CrossRef]
    [Google Scholar]
  17. Haas E. S., Banta A. B., Harris J. K., Pace N. R., Brown J. W. 1996; Structure and evolution of ribonuclease P RNA in Gram-positive bacteria. Nucleic Acids Res 24:4775–4782 [CrossRef]
    [Google Scholar]
  18. Herrmann B., Winqvist O., Mattsson J. G., Kirsebom L. A. 1996; Differentiation of Chlamydia spp. by sequence determination and restriction endonuclease cleavage of RNase P RNA genes. J Clin Microbiol 34:1897–1902
    [Google Scholar]
  19. Herrmann B., Pettersson B., Everett K. D. E., Mikkelsen N. E., Kirsebom L. A. 2000; Characterization of the rnpB gene and RNase P RNA in the order Chlamydiales . Int J Syst Evol Microbiol 50:149–158 [CrossRef]
    [Google Scholar]
  20. Hillmann J. D., Andrews S. W., Painter S., Stashenko P. 1989; Adaptive changes in a strain of Streptococcus mutans during colonization of the human oral cavity. Microb Ecol Health Dis 2:231–239 [CrossRef]
    [Google Scholar]
  21. Huelsenbeck J. P., Crandall K. A. 1997; Phylogeny estimation and hypothesis testing using maximum likelihood. Annu Rev Ecol Syst 28:437–466 [CrossRef]
    [Google Scholar]
  22. Huelsenbeck J. P., Ronquist F. 2001; mrbayes: Bayesian inference of phylogenetic trees. Bioinformatics 17:754–755 [CrossRef]
    [Google Scholar]
  23. Jacobs J. A., Schot C. S., Bunschoten A. E., Schouls L. M. 1996; Rapid species identification of “ Streptococcus milleri ” strains by line blot hybridization: identification of a distinct 16S rRNA population closely related to Streptococcus constellatus . J Clin Microbiol 34:1717–1721
    [Google Scholar]
  24. Jacobs J. A., Schot C. S., Schouls L. M. 2000a; Haemolytic activity of the ‘ Streptococcus milleri group’ and relationship between haemolysis restricted to human red blood cells and pathogenicity in S. intermedius . J Med Microbiol 49:55–62
    [Google Scholar]
  25. Jacobs J. A., Schot C. S., Schouls L. M. 2000b; The Streptococcus anginosus species comprises five 16S rRNA ribogroups with different phenotypic characteristics and clinical relevance. Int J Syst Evol Microbiol 50:1073–1079 [CrossRef]
    [Google Scholar]
  26. Jayarao B. M., Dore J. J. Jr, Oliver S. P. 1992; Restriction fragment length polymorphism analysis of 16S ribosomal DNA of Streptococcus and Enterococcus species of bovine origin. J Clin Microbiol 30:2235–2240
    [Google Scholar]
  27. Kawamura Y., Hou X.-G., Sultana F., Miura H., Ezaki T. 1995; Determination of 16S rRNA sequences of Streptococcus mitis and Streptococcus gordonii and phylogenetic relationships among members of the genus Streptococcus . Int J Syst Bacteriol 45:406–408 [CrossRef]
    [Google Scholar]
  28. Kawamura Y., Whiley R. A., Shu S.-E., Ezaki T., Hardie J. M. 1999; Genetic approaches to the identification of the mitis group within the genus Streptococcus . Microbiology 145:2605–2613
    [Google Scholar]
  29. Kikuchi K., Enari T., Totsuka K., Shimizu K. 1995; Comparison of phenotypic characteristics, DNA-DNA hybridization results, and results with a commercial rapid biochemical and enzymatic reaction system for identification of viridans group streptococci. J Clin Microbiol 33:1215–1222
    [Google Scholar]
  30. Kilian M., Mikkelsen L., Henrichsen J. 1989; Taxonomic studies of viridans streptococci: description of Streptococcus gordonii sp. nov. and emended descriptions of Streptococcus sanguis (White and Niven 1946), Streptococcus oralis (Bridge and Sneath 1982), and Streptococcus mitis (Andrewes and Horder 1906). Int J Syst Bacteriol 39:471–484 [CrossRef]
    [Google Scholar]
  31. Lawrence J., Yajko D. M., Hadley W. K. 1985; Incidence and characterization of beta-hemolytic Streptococcus milleri and differentiation from S. pyogenes (group A), S. equisimilis (group C), and large-colony group G streptococci. J Clin Microbiol 22772–777
    [Google Scholar]
  32. Legendre P., Anderson M. J. 1998 distpcoa program Département de Sciences Biologiques, Université de Montréal;
    [Google Scholar]
  33. Legendre P., Anderson M. J. 1999; Distance-based redundancy analysis: testing multi-species responses in multi-factorial ecological experiments. Ecol Monogr 69:1–24 [CrossRef]
    [Google Scholar]
  34. Ludwig W., Weizenegger M., Kilpper-Bälz R., Schleifer K. H. 1988; Phylogenetic relationships of anaerobic streptococci. Int J Syst Bacteriol 38:15–18 [CrossRef]
    [Google Scholar]
  35. Maidak B. L., Cole J. R., Lilburn T. G. 7 other authors 2001; The RDP-II (Ribosomal Database Project. Nucleic Acids Res 29:173–174 [CrossRef]
    [Google Scholar]
  36. Manachini P. L., Flint S. H., Ward L. J. H., Kelly W., Fortina M. G., Parini C., Mora D. 2002; Comparison between Streptococcus macedonicus and Streptococcus waius strains and reclassification of Streptococcus waius (Flint et al . 1999) as Streptococcus macedonicus (Tsakalidou et al . 1998). Int J Syst Evol Microbiol 52:945–951 [CrossRef]
    [Google Scholar]
  37. Massire C., Jaeger L., Westhof E. 1998; Derivation of the three-dimensional architecture of bacterial ribonuclease P RNAs from comparative sequence analysis. J Mol Biol 279:773–793 [CrossRef]
    [Google Scholar]
  38. Nubel U., Engelen B., Felske A., Snaidr J., Wieshuber A., Amann R. I., Ludwig W., Backhaus H. 1996; Sequence heterogeneities of genes encoding 16S rRNAs in Paenibacillus polymyxa detected by temperature gradient gel electrophoresis. J Bacteriol 178:5636–5643
    [Google Scholar]
  39. Pannucci J. A., Haas E. S., Hall T. A., Harris J. K., Brown J. W. 1999; RNase P RNAs from some Archaea are catalytically active. Proc Natl Acad Sci U S A 96:7803–7808 [CrossRef]
    [Google Scholar]
  40. Posada D., Crandall K. A. 1998; modeltest: testing the model of DNA substitution. Bioinformatics 14:817–818 [CrossRef]
    [Google Scholar]
  41. Poyart C., Quesne G., Coulon S., Berche P., Trieu-Cuot P. 1998; Identification of streptococci to species level by sequencing the gene encoding the manganese-dependent superoxide dismutase. J Clin Microbiol 36:41–47
    [Google Scholar]
  42. Poyart C., Quesne G., Trieu-Cuot P. 2002; Taxonomic dissection of the Streptococcus bovis group by analysis of manganese-dependent superoxide dismutase gene ( sodA ) sequences: reclassification of ‘ Streptococcus infantarius subsp. coli ’ as Streptococcus lutetiensis sp. nov. and of Streptococcus bovis biotype II.2 as Streptococcus pasteurianus sp. nov. Int J Syst Evol Microbiol 52:1247–1255 [CrossRef]
    [Google Scholar]
  43. Rodriguez F., Oliver J. L., Marin A., Medina J. R. 1990; The general stochastic model of nucleotide substitution. J Theor Biol 142:485–501 [CrossRef]
    [Google Scholar]
  44. Rudney J. D., Larson C. J. 1994; Use of restriction fragment polymorphism analysis of rRNA genes to assign species to unknown clinical isolates of oral viridans streptococci. J Clin Microbiol 32:437–443
    [Google Scholar]
  45. Saruta K., Matsunaga T., Hoshina S., Kono M., Kitahara S., Kanemoto S., Sakai O., Machida K. 1995; Rapid identification of Streptococcus pneumoniae by PCR amplification of ribosomal DNA spacer region. FEMS Microbiol Lett 132:165–170 [CrossRef]
    [Google Scholar]
  46. Schmidhuber S., Ludwig W., Schleifer K. H. 1988; Construction of a DNA probe for the specific identification of Streptococcus oralis . J Clin Microbiol 26:1042–1044
    [Google Scholar]
  47. Shannon C. E., Weaver W. 1949 The Mathematical Theory of Communication Urbana, IL: University of Illinois Press;
    [Google Scholar]
  48. Skaar I., Gaustad P., Tønjum T., Holm B., Stenwig H. 1994; Streptococcus phocae sp. nov., a new species isolated from clinical specimens from seals. Int J Syst Bacteriol 44:646–650 [CrossRef]
    [Google Scholar]
  49. 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 [CrossRef]
    [Google Scholar]
  50. Swofford D. L. 2000 paup*. Phylogenetic Analysis Using Parsimony (*and other methods), release 4 for Apple Macintosh, Intel, Linux and SGI/Irix Sunderland, MA: Sinauer Associates;
    [Google Scholar]
  51. Tamura K., Nei M. 1993; Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 10:512–526
    [Google Scholar]
  52. Tanner M. A., Cech T. R. 1995; An important RNA tertiary interaction of group I and group II introns is implicated in gram-positive RNase P RNAs. RNA 1:349–350
    [Google Scholar]
  53. Tardif G., Sulavik M. C., Jones G. W., Clewell D. B. 1989; Spontaneous switching of the sucrose-promoted colony phenotype in Streptococcus sanguis . Infect Immun 57:3945–3948
    [Google Scholar]
  54. Waddell P. J., Penny D. 1996; Evolutionary trees of apes and humans from DNA sequences. In Handbook of Human Symbolic Evolution pp 53–73Edited by Lock A., Peters C. R. Oxford: Oxford University Press;
    [Google Scholar]
  55. Whatmore A. M., Whiley R. A. 2002; Re-evaluation of the taxonomic position of Streptococcus ferus . Int J Syst Evol Microbiol 52:1783–1787 [CrossRef]
    [Google Scholar]
  56. Whiley R. A., Duke B., Hardie J. M., Hall L. M. C. 1995; Heterogeneity among 16S–23S rRNA intergenic spacers of species within the ‘ Streptococcus milleri group’. Microbiology 141:1461–1467 [CrossRef]
    [Google Scholar]
  57. Whiley R. A., Hall L. M. C., Hardie J. M., Beighton D. 1997; Genotypic and phenotypic diversity within Streptococcus anginosus . Int J Syst Bacteriol 47:645–650 [CrossRef]
    [Google Scholar]
  58. Wiener N. 1949 Extrapolation, Interpolation, and Smoothing of Stationary Time Series: with Engineering Applications New York: Wiley;
    [Google Scholar]
  59. Yang Z. 1993; Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites. Mol Biol Evol 10:1396–1401
    [Google Scholar]
  60. Yang Z. 1994; Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J Mol Evol 39:306–314 [CrossRef]
    [Google Scholar]
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