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Gene Review

16S  -  16S ribosomal RNA

Borrelia burgdorferi B31

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Disease relevance of 16S

  • To determine whether relapsing fever-like spirochetes associated with hard ticks may infect Ixodes ricinus ticks in central Europe, we screened questing ticks for 16S rDNA similar to that of Asian and American relapsing fever-like spirochetes [1].
  • Borrelia genus-specific oligonucleotides for the flagellin and 16S rRNA genes were used for amplification of DNA [2].
  • 16S rRNA mutations A1185G and C1186U, homologous to Escherichia coli nucleotides A1191 and C1192, conferred >2,200-fold and 1,300-fold resistance to spectinomycin, respectively [3].
  • We have determined and compared partial 16S rRNA sequences from 23 Lyme disease spirochete isolates and aligned these with 8 sequences previously presented [4].
  • In separate assays the 16S rRNA gene of Ehrlichia species and the 23S-5S rRNA spacer region of B. burgdorferi sensu lato were amplified and labeled by PCR [5].

High impact information on 16S

  • RESULTS: Two subjects were identified with nucleic acid for the 16S rRNA gene of C trachomatis [6].
  • These results have implications for the evolution of antibiotic resistance, because the 16S rRNA mutations conferring spectinomycin resistance have no significant fitness cost in vitro, and for the development of new selectable markers [3].
  • A 16S rRNA A1402G mutation, homologous to E. coli A1408, conferred >90-fold resistance to kanamycin and >240-fold resistance to gentamicin [3].
  • The methods used included: large restriction fragment pattern analysis of restriction enzyme MluI-digested genomic DNA, plasmid profiling, protein profiling, ribotyping using 5S, 16S, and 23S rDNA probes, and polymerase chain reaction amplification of the rrf (5S)-rrl (23S) intergenic spacer region [7].
  • Genetic fingerprints of bacterial populations were generated by temporal temperature gradient gel electrophoresis (TTGE) separation of individual polymerase chain reaction (PCR)-amplified 16S rRNA gene fragments, followed by DNA sequence analysis for bacterial identification [8].

Biological context of 16S


Anatomical context of 16S

  • We carried out a preliminary PCR survey of the blood of 15 dogs naturally exposed on ticks for the presence of the DNA of B. burgdorferi using primers complementary to the fragment of the gene encoding 16S rRNA of the small ribosome subunit [14].
  • Oligonucleotide primers used in the reaction flank a 244-base-pair representing part of the variable region V4 of the B. burgdorferi 16S rRNA from biopsies of patients with acrodermatitis, and in synovial fluid from a dog with arthritis [15].

Associations of 16S with chemical compounds

  • Here we report that (p)ppGpp levels in B. burgdorferi growing in BSK-II or BSK-H medium are not further increased by nutrient limitation or by serine hydroxamate-induced inhibition of protein synthesis and that the presence of (p)ppGpp during growth of N40 in BSK-H medium is not associated with decreased 16S rRNA synthesis [16].
  • The 16S rDNA sequencing resulted in a sequence identical to that described for Rickettsia helvetica, but the pattern obtained with RFLP of the citrate synthetase gene diverged from previously known patterns [9].
  • Microscopic examination of EDTA whole blood and nested PCR targeting A. phagocytophilum 16S rDNA gene fragment were carried out at enrolment [17].

Other interactions of 16S


Analytical, diagnostic and therapeutic context of 16S

  • All other PCR reactions were negative except for the pan bacterial 16S rRNA in the C trachomatis-positive subjects [6].
  • Strains were characterized and typed by 16S ribosomal RNA-specific polymerase chain reaction and determination of their large restriction fragment patterns using pulsed-field gel electrophoresis of MluI-digested genomic DNA [19].
  • Borrelia species were identified by 16S rRNA sequence analysis, which showed the presence of several species, some not yet defined, and a high prevalence of multiply infected ticks [20].
  • Decreased 16S rRNA synthesis was associated with the decreased growth rate of N40 seen during coculture with tick cells, which are growth conditions that were previously shown to decrease (p)ppGpp levels [16].
  • Comparative analysis of Borrelia isolates from southeastern USA based on randomly amplified polymorphic DNA fingerprint and 16S ribosomal gene sequence analyses [21].


  1. Relapsing fever-like spirochetes infecting European vector tick of Lyme disease agent. Richter, D., Schlee, D.B., Matuschka, F.R. Emerging Infect. Dis. (2003) [Pubmed]
  2. Identification of an uncultivable Borrelia species in the hard tick Amblyomma americanum: possible agent of a Lyme disease-like illness. Barbour, A.G., Maupin, G.O., Teltow, G.J., Carter, C.J., Piesman, J. J. Infect. Dis. (1996) [Pubmed]
  3. Mutations conferring aminoglycoside and spectinomycin resistance in Borrelia burgdorferi. Criswell, D., Tobiason, V.L., Lodmell, J.S., Samuels, D.S. Antimicrob. Agents Chemother. (2006) [Pubmed]
  4. Development of polymerase chain reaction primer sets for diagnosis of Lyme disease and for species-specific identification of Lyme disease isolates by 16S rRNA signature nucleotide analysis. Marconi, R.T., Garon, C.F. J. Clin. Microbiol. (1992) [Pubmed]
  5. Detection and identification of Ehrlichia, Borrelia burgdorferi sensu lato, and Bartonella species in Dutch Ixodes ricinus ticks. Schouls, L.M., Van De Pol, I., Rijpkema, S.G., Schot, C.S. J. Clin. Microbiol. (1999) [Pubmed]
  6. Chlamydia trachomatis nucleic acids can be found in the synovium of some asymptomatic subjects. Schumacher, H.R., Arayssi, T., Crane, M., Lee, J., Gerard, H., Hudson, A.P., Klippel, J. Arthritis Rheum. (1999) [Pubmed]
  7. Molecular subtyping of Borrelia burgdorferi sensu lato isolates from five patients with solitary lymphocytoma. Picken, R.N., Strle, F., Ruzic-Sabljic, E., Maraspin, V., Lotric-Furlan, S., Cimperman, J., Cheng, Y., Picken, M.M. J. Invest. Dermatol. (1997) [Pubmed]
  8. Molecular analysis of microbial communities identified in different developmental stages of Ixodes scapularis ticks from Westchester and Dutchess Counties, New York. Moreno, C.X., Moy, F., Daniels, T.J., Godfrey, H.P., Cabello, F.C. Environ. Microbiol. (2006) [Pubmed]
  9. Characterization of a spotted fever group Rickettsia from Ixodes ricinus ticks in Sweden. Nilsson, K., Jaenson, T.G., Uhnoo, I., Lindquist, O., Pettersson, B., Uhlén, M., Friman, G., Påhlson, C. J. Clin. Microbiol. (1997) [Pubmed]
  10. Characterization of Borrelia lusitaniae sp. nov. by 16S ribosomal DNA sequence analysis. Le Fleche, A., Postic, D., Girardet, K., Peter, O., Baranton, G. Int. J. Syst. Bacteriol. (1997) [Pubmed]
  11. Analysis of base-pairing potentials between 16S rRNA and 5' UTR for translation initiation in various prokaryotes. Osada, Y., Saito, R., Tomita, M. Bioinformatics (1999) [Pubmed]
  12. Physical map of the linear chromosome of the bacterium Borrelia burgdorferi 212, a causative agent of Lyme disease, and localization of rRNA genes. Davidson, B.E., MacDougall, J., Saint Girons, I. J. Bacteriol. (1992) [Pubmed]
  13. Strain typing of Borrelia burgdorferi, Borrelia afzelii, and Borrelia garinii by using multiple-locus variable-number tandem repeat analysis. Farlow, J., Postic, D., Smith, K.L., Jay, Z., Baranton, G., Keim, P. J. Clin. Microbiol. (2002) [Pubmed]
  14. Molecular evidence of the presence of Borrelia burgdorferi sensu lato in blood samples taken from dogs in Poland. Skotarczak, B., Wodecka, B. Annals of agricultural and environmental medicine : AAEM. (2003) [Pubmed]
  15. Detection of Borrelia burgdorferi DNA in human skin biopsies and dog synovial fluid by the polymerase chain reaction. Salinas-Meléndez, J.A., Tamez-González, R., Welsh-Lozano, O., Barrera-Saldaãna, H.A. Rev. Latinoam. Microbiol. (1995) [Pubmed]
  16. Characterization of the stringent response and rel(Bbu) expression in Borrelia burgdorferi. Bugrysheva, J., Dobrikova, E.Y., Sartakova, M.L., Caimano, M.J., Daniels, T.J., Radolf, J.D., Godfrey, H.P., Cabello, F.C. J. Bacteriol. (2003) [Pubmed]
  17. Etiology of tick-borne febrile illnesses in adult residents of North-Eastern Poland: report from a prospective clinical study. Grzeszczuk, A., Ziarko, S., Kovalchuk, O., Stańczak, J. Int. J. Med. Microbiol. (2006) [Pubmed]
  18. Prevalence of granulocytic Ehrlichia and Borrelia burgdorferi sensu lato in Ixodes ricinus ticks collected from Southwestern Finland and from Vormsi Island in Estonia. Mäkinen, J., Vuorinen, I., Oksi, J., Peltomaa, M., He, Q., Marjamäki, M., Viljanen, M.K. APMIS (2003) [Pubmed]
  19. Identification of three species of Borrelia burgdorferi sensu lato (B. burgdorferi sensu stricto, B. garinii, and B. afzelii) among isolates from acrodermatitis chronica atrophicans lesions. Picken, R.N., Strle, F., Picken, M.M., Ruzic-Sabljic, E., Maraspin, V., Lotric-Furlan, S., Cimperman, J. J. Invest. Dermatol. (1998) [Pubmed]
  20. Detection and typing of Borrelia burgdorferi sensu lato in Ixodes ricinus ticks attached to human skin by PCR. Liebisch, G., Sohns, B., Bautsch, W. J. Clin. Microbiol. (1998) [Pubmed]
  21. Comparative analysis of Borrelia isolates from southeastern USA based on randomly amplified polymorphic DNA fingerprint and 16S ribosomal gene sequence analyses. Lin, T., Oliver, J.H., Gao, L. FEMS Microbiol. Lett. (2003) [Pubmed]
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