Use of rpoB sequences for phylogenetic study of Mycoplasma species

FEMS Microbiology Letters

Volumn 226, Issue 2, 2003, Pages 299-305

  Kim, Kil Soo ^a,e   Ko, Kwan Soo ^b,f   Chang, Myoung Woong ^c   Hahn, Tae Wook ^d   Hong, Seong Karp ^b   Kook, Yoon Hoh ^b  

^a Seoul National University   (South Korea)

^b Seoul National University Hospital   (South Korea)

^c Kosin University College of Medicine   (South Korea)

^d Kangwon National University   (South Korea)

^e Hanyang University   (South Korea)

^f INFECTIOUS DISEASE RESEARCH INSTITUTE   (United States)

Author keywords

Mycoplasma; Phylogeny; rpoB; Ureaplasma

Indexed keywords

DNA; RIBOSOME DNA; RNA POLYMERASE BETA SUBUNIT; DNA DIRECTED RNA POLYMERASE; RNA 16S;

ACHOLEPLASMA LAIDLAWII; AMINO ACID SEQUENCE; ARTICLE; DNA SEQUENCE; ENZYME ASSAY; MYCOPLASMA; MYCOPLASMA ANATIS; MYCOPLASMA ARTHRITIDIS; MYCOPLASMA BUCCULE; MYCOPLASMA GALLISEPTICUM; MYCOPLASMA GENITALIUM; MYCOPLASMA HOMINIS; MYCOPLASMA HYOPNEUMONIAE; MYCOPLASMA HYORHINIS; MYCOPLASMA IOWAE; MYCOPLASMA LIPOPHILUM; MYCOPLASMA ORALE; MYCOPLASMA PENETRANS; MYCOPLASMA PIRUM; MYCOPLASMA PNEUMONIAE; MYCOPLASMA PRIMATUM; MYCOPLASMA PULLORUM; MYCOPLASMA PULMONIS; MYCOPLASMA SALIVARIUM; MYCOPLASMA SPERMATOPHILUM; MYCOPLASMA SYNOVIAE; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; PHYLOGENY; PRIORITY JOURNAL; SEQUENCE ANALYSIS; SPECIES; UREAPLASMA; UREAPLASMA PARVUM; UREAPLASMA UREALYTICUM; BACTERIAL GENE; CHEMISTRY; CLASSIFICATION; COMPARATIVE STUDY; GENETICS; MOLECULAR GENETICS; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY;

MYCOPLASMA; MYCOPLASMATALES; UREAPLASMA;

AMINO ACID SEQUENCE; DNA, RIBOSOMAL; DNA-DIRECTED RNA POLYMERASES; GENES, BACTERIAL; MOLECULAR SEQUENCE DATA; MYCOPLASMA; PHYLOGENY; RNA, RIBOSOMAL, 16S; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID; SEQUENCE HOMOLOGY, NUCLEIC ACID; UREAPLASMA;

EID: 0642285654     PISSN: 03781097     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0378-1097(03)00618-9     Document Type: Article

References (25)

1. Waites, K.B. and Taylor-Robinson, D. (1999) Mycoplasma and Ureaplasma. In: Manual of Clinical Microbiology, 7th Edn. (Murray, P.R., Ed.), pp. 582-794. American Society for Microbiology, Washington, DC.
2. Razin S., Yogev D., Naot Y. Molecular biology and pathogenicity of Mycoplasmas. Microbiol. Mol. Biol. Rev. 62:1998;1094-1156.
3. Yoshida T., Maeda S.-I., Deguchi T., Ishiko H. Phylogeny-based rapid identification of mycoplasmas and ureaplasmas from urethritis patients. J. Clin. Microbiol. 40:2002;105-110.
4. Pettersson B., Uhlén M., Johansson K.-E. Phylogeny of some mycoplasmas from ruminants based on 16S rRNA sequences and definition of a new cluster within the hominis group. Int. J. Syst. Bacteriol. 46:1996;1093-1098.
5. Weisburg W.G., Tully J.G., Rose D.L., Petzel J.P., Oyaizu H., Yang D., Mandelco L., Sechrest J., Lawrence T.G., Van Etten J., Maniloff J., Woese C.R. A phylogenetic analysis of the mycoplasmas: basis for their classification. J. Bacteriol. 171:1989;6455-6467.
6. Pettersson B., Tully J.G., Bölske G., Johansson K.-E. Updated phylogenetic description of the Mycoplasma hominis cluster (Weisburg et al., 1989) based on 16S rDNA sequences. Int. J. Syst. Evol. Microbiol. 50:2000;290-301.
7. Woese C.R., Kandler O., Wheelis M.L. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eukarya. Proc. Natl. Acad. Sci. USA. 87:1990;4576-4579.
8. Pettersson B., Bölske G., Thiaucourt F., Uhlén M., Johansson K.-E. Molecular evolution of Mycoplasma capricolum subsp. capripneumoniae strains, based on polymorphisms in the 16S rRNA genes. J. Bacteriol. 180:1998;2350-2358.
9. Königsson M.H., Bölske G., Johansson K.-E. Intraspecific variation in the 16S rRNA gene sequences of Mycoplasma agalactiae and Mycoplasma bovis strains. Vet. Microbiol. 85:2002;209-220.
10. Palys T., Nakamura K., Cohan F.M. Discovery and classification of ecological diversity in the bacterial world: the role of DNA sequence data. Int. J. Syst. Bacteriol. 47:1997;1145-1156.
11. Mollet C., Drancourt M., Raoult D. rpoB sequence analysis as a novel basis for bacterial identification. Mol. Microbiol. 26:1997;1005-1011.
12. Kim B.-J., Lee S.-H., Lyu M.-A., Kim S.-J., Bai G.-H., Kim S.-S., Chae G.-T., Kim E.-C., Cha C.-Y., Kook Y.-H. Identification of mycobacterial species by comparative sequence analysis of the RNA polymerase gene (rpoB). J. Clin. Microbiol. 37:1999;1714-1720.
13. Lee S.-H., Kim B.-J., Kim J.-H., Park K.-H., Kim S.-J., Kook Y.-H. Differentiation of Borrelia burgdorferi sensu lato on the basis of RNA polymerase gene (rpoB) sequences. J. Clin. Microbiol. 38:2000;2557-2562.
14. Ko K.S., Lee H.K., Park M.-Y., Lee K.-H., Yun Y.-J., Woo S.-Y., Miyamoto H., Kook Y.-H. Application of RNA polymerase β-subunit gene (rpoB) sequences for the molecular differentiation of Legionella species. J. Clin. Microbiol. 40:2002;2653-2658.
15. Swofford, D.L. (1999) PAUP*: Phylogenetic Analysis Using Parsimony (* and Other Methods), version 4. Sinauer Associates, Sunderland, MA.
16. Farris J.S., Källersjö M., Kluge A.G., Bult C. Testing significance of incongruence. Cladistics. 10:1995;315-319.
17. Cunningham C.W. Can three incongruence tests predict when data should be combined? Mol. Biol. Evol. 14:1997;733-740.
18. Ovchinnikov Y.A., Monastyrskaya G.S., Gubanov V.V., Guryev S.O., Chertov O.U., Modyanov N.N., Grinkevich V.A., Makarova I.A., Marchenko T.V., Polovikova I.N., Lipkin V.M., Sverdlov E.D. The primary structure of Escherichia coli RNA polymerase: nucleotide sequence of the rpoB gene and amino acid sequence of the beta-subunit. Eur. J. Biochem. 116:1981;621-629.
19. Gaurivaud P., Laigret F., Bove J.-M. Insusceptibility of members of the class Mollucutes to rifampin: studies of the Spiroplasma citri RNA polymerase β-subunit gene. Antimicrob. Agents Chemother. 40:1996;858-862.
20. Denamur E., Lecointre G., Darlu P., Tenaillon O., Acquaviva C., Sayada C., Sunjevaric I., Rothstein R., Elion J., Taddei F., Radman M., Matic I. Evolutionary implications of the frequent horizontal transfer of mismatch repair genes. Cell. 103:2000;711-721.
21. Rawadi G., Dujeancourt-Henry A., Lemercier B., Roulland-Dussoix D. Phylogenetic position of rare human mycoplasmas, Mycoplasma faucium, M. buccale, M. primatum and M. spermatophilum, based on 16S rRNA gene sequences. Int. J. Syst. Bacteriol. 48:1998;305-309.
22. Roux V., Rydkina E., Eremeeva M., Raoult D. Citrate synthase gene comparison, a new tool for phylogenetic analysis, and its application for the richettsiae. Int. J. Syst. Bacteriol. 47:1997;252-261.
23. Renesto P., Gouvernet J., Drancourt M., Roux V., Raoult D. Use of rpoB gene analysis for detection and identification of Bartonella species. J. Clin. Microbiol. 39:2001;430-437.
24. Drancourt M., Raoult D. rpoB gene sequence-based identification of Staphylococcus species. J. Clin. Microbiol. 40:2002;1333-1338.
25. Taddei F., Matic I., Godelle B., Radman M. To be a mutator, or how pathogenic and commensal bacteria can evolve rapidly. Trends Microbiol. 5:1997;427-429.