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. 1996 Aug;34(8):1897–1902. doi: 10.1128/jcm.34.8.1897-1902.1996

Differentiation of Chlamydia spp. by sequence determination and restriction endonuclease cleavage of RNase P RNA genes.

B Herrmann 1, O Winqvist 1, J G Mattsson 1, L A Kirsebom 1
PMCID: PMC229149  PMID: 8818877

Abstract

The amplification of DNA from Chlamydia trachomatis by PCR with degenerated primers yielded a 345-bp fragment of the putative RNase P RNA gene. From the deduced DNA sequence of this gene in C. trachomatis, a modified primer pair was designed. The primer pair was subsequently used to obtain the corresponding gene products from Chlamydia pneumoniae and Chlamydia psittaci. Sequence comparisons revealed similarities of 76.6% between C. trachomatis and C. pneumoniae, 79.5% between C. trachomatis and C. psittaci, and 84.7% between C. pneumoniae and C. psittaci. Furthermore, the three species were differentiated by fragment length polymorphism analysis after restriction enzyme cleavage of the PCR products. Sequence variations among 14 serotypes of C. trachomatis were confined to one purine base substitution in the putative RNase P RNA gene of lymphogranuloma venereum strains L1 to L3. Complete sequence similarity was found for nine strains of C. pneumoniae of different geographic origins. Taken together, our results indicate a possibility of the general application of this method in clinical bacteriology. Analysis of the secondary structures of the putative RNase P RNA genes from the different Chlamydia species suggested that a novel structural element in the domain of RNase P RNA is involved in base pairing with the 3'-terminal CCA motif of a tRNA precursor. This structure has not previously been found among RNase P RNAs of members of the division Bacteria.

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Selected References

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  1. Brown J. W., Haas E. S., Gilbert D. G., Pace N. R. The Ribonuclease P database. Nucleic Acids Res. 1994 Sep;22(17):3660–3662. doi: 10.1093/nar/22.17.3660. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Brown J. W., Pace N. R. Ribonuclease P RNA and protein subunits from bacteria. Nucleic Acids Res. 1992 Apr 11;20(7):1451–1456. doi: 10.1093/nar/20.7.1451. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Cates W., Jr, Wasserheit J. N. Genital chlamydial infections: epidemiology and reproductive sequelae. Am J Obstet Gynecol. 1991 Jun;164(6 Pt 2):1771–1781. doi: 10.1016/0002-9378(91)90559-a. [DOI] [PubMed] [Google Scholar]
  4. Cousineau B., Cerpa C., Lefebvre J., Cedergren R. The sequence of the gene encoding elongation factor Tu from Chlamydia trachomatis compared with those of other organisms. Gene. 1992 Oct 12;120(1):33–41. doi: 10.1016/0378-1119(92)90006-b. [DOI] [PubMed] [Google Scholar]
  5. Darr S. C., Brown J. W., Pace N. R. The varieties of ribonuclease P. Trends Biochem Sci. 1992 May;17(5):178–182. doi: 10.1016/0968-0004(92)90262-8. [DOI] [PubMed] [Google Scholar]
  6. Fox G. E., Wisotzkey J. D., Jurtshuk P., Jr How close is close: 16S rRNA sequence identity may not be sufficient to guarantee species identity. Int J Syst Bacteriol. 1992 Jan;42(1):166–170. doi: 10.1099/00207713-42-1-166. [DOI] [PubMed] [Google Scholar]
  7. Fukushi H., Hirai K. Proposal of Chlamydia pecorum sp. nov. for Chlamydia strains derived from ruminants. Int J Syst Bacteriol. 1992 Apr;42(2):306–308. doi: 10.1099/00207713-42-2-306. [DOI] [PubMed] [Google Scholar]
  8. Gardiner K., Pace N. R. RNase P of Bacillus subtilis has a RNA component. J Biol Chem. 1980 Aug 25;255(16):7507–7509. [PubMed] [Google Scholar]
  9. Gaydos C. A., Palmer L., Quinn T. C., Falkow S., Eiden J. J. Phylogenetic relationship of Chlamydia pneumoniae to Chlamydia psittaci and Chlamydia trachomatis as determined by analysis of 16S ribosomal DNA sequences. Int J Syst Bacteriol. 1993 Jul;43(3):610–612. doi: 10.1099/00207713-43-3-610. [DOI] [PubMed] [Google Scholar]
  10. Gaydos C. A., Quinn T. C., Bobo L. D., Eiden J. J. Similarity of Chlamydia pneumoniae strains in the variable domain IV region of the major outer membrane protein gene. Infect Immun. 1992 Dec;60(12):5319–5323. doi: 10.1128/iai.60.12.5319-5323.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Grayston J. T., Campbell L. A., Kuo C. C., Mordhorst C. H., Saikku P., Thom D. H., Wang S. P. A new respiratory tract pathogen: Chlamydia pneumoniae strain TWAR. J Infect Dis. 1990 Apr;161(4):618–625. doi: 10.1093/infdis/161.4.618. [DOI] [PubMed] [Google Scholar]
  12. Green C. J., Vold B. S. A cluster of nine tRNA genes between ribosomal gene operons in Bacillus subtilis. J Bacteriol. 1992 May;174(10):3147–3151. doi: 10.1128/jb.174.10.3147-3151.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Green C. J., Vold B. S. Staphylococcus aureus has clustered tRNA genes. J Bacteriol. 1993 Aug;175(16):5091–5096. doi: 10.1128/jb.175.16.5091-5096.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Guerrier-Takada C., Gardiner K., Marsh T., Pace N., Altman S. The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme. Cell. 1983 Dec;35(3 Pt 2):849–857. doi: 10.1016/0092-8674(83)90117-4. [DOI] [PubMed] [Google Scholar]
  15. Hansen F. G., Hansen E. B., Atlung T. Physical mapping and nucleotide sequence of the rnpA gene that encodes the protein component of ribonuclease P in Escherichia coli. Gene. 1985;38(1-3):85–93. doi: 10.1016/0378-1119(85)90206-9. [DOI] [PubMed] [Google Scholar]
  16. Hultman T., Ståhl S., Hornes E., Uhlén M. Direct solid phase sequencing of genomic and plasmid DNA using magnetic beads as solid support. Nucleic Acids Res. 1989 Jul 11;17(13):4937–4946. doi: 10.1093/nar/17.13.4937. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Kirsebom L. A., Svärd S. G. Base pairing between Escherichia coli RNase P RNA and its substrate. EMBO J. 1994 Oct 17;13(20):4870–4876. doi: 10.1002/j.1460-2075.1994.tb06814.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. LaGrandeur T. E., Darr S. C., Haas E. S., Pace N. R. Characterization of the RNase P RNA of Sulfolobus acidocaldarius. J Bacteriol. 1993 Aug;175(16):5043–5048. doi: 10.1128/jb.175.16.5043-5048.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Macfarlane J. T., Macrae A. D. Psittacosis. Br Med Bull. 1983 Apr;39(2):163–167. doi: 10.1093/oxfordjournals.bmb.a071810. [DOI] [PubMed] [Google Scholar]
  20. Odeh M., Oliven A. Chlamydial infections of the heart. Eur J Clin Microbiol Infect Dis. 1992 Oct;11(10):885–893. doi: 10.1007/BF01962368. [DOI] [PubMed] [Google Scholar]
  21. Saikku P., Leinonen M., Mattila K., Ekman M. R., Nieminen M. S., Mäkelä P. H., Huttunen J. K., Valtonen V. Serological evidence of an association of a novel Chlamydia, TWAR, with chronic coronary heart disease and acute myocardial infarction. Lancet. 1988 Oct 29;2(8618):983–986. doi: 10.1016/s0140-6736(88)90741-6. [DOI] [PubMed] [Google Scholar]
  22. Stark B. C., Kole R., Bowman E. J., Altman S. Ribonuclease P: an enzyme with an essential RNA component. Proc Natl Acad Sci U S A. 1978 Aug;75(8):3717–3721. doi: 10.1073/pnas.75.8.3717. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Wagels G., Rasmussen S., Timms P. Comparison of Chlamydia pneumoniae isolates by western blot (immunoblot) analysis and DNA sequencing of the omp 2 gene. J Clin Microbiol. 1994 Nov;32(11):2820–2823. doi: 10.1128/jcm.32.11.2820-2823.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Weisburg W. G., Hatch T. P., Woese C. R. Eubacterial origin of chlamydiae. J Bacteriol. 1986 Aug;167(2):570–574. doi: 10.1128/jb.167.2.570-574.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Weiss S. G., Newcomb R. W., Beem M. O. Pulmonary assessment of children after chlamydial pneumonia of infancy. J Pediatr. 1986 May;108(5 Pt 1):659–664. doi: 10.1016/s0022-3476(86)81037-x. [DOI] [PubMed] [Google Scholar]
  26. Yuan Y., Zhang Y. X., Watkins N. G., Caldwell H. D. Nucleotide and deduced amino acid sequences for the four variable domains of the major outer membrane proteins of the 15 Chlamydia trachomatis serovars. Infect Immun. 1989 Apr;57(4):1040–1049. doi: 10.1128/iai.57.4.1040-1049.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]

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