Predicting relatedness of bacterial genomes using the chaperonin-60 universal target (cpn60 UT): Application to Thermoanaerobacter species

Systematic and Applied Microbiology

Volumn 34, Issue 3, 2011, Pages 171-179

  Verbeke, Tobin J ^a   Sparling, Richard ^a   Hill, Janet E ^b   Links, Matthew G ^b,c   Levin, David ^a   Dumonceaux, Tim J ^c  

^a UNIVERSITY OF MANITOBA   (Canada)

^b UNIVERSITY OF SASKATCHEWAN   (Canada)

^c SASKATOON RESEARCH CENTRE   (Canada)

Author keywords

Chaperonin 60; Cpn60 universal target; Genome prediction; Heat shock protein; Taxonomic identification; Thermoanaerobacter

Indexed keywords

CHAPERONIN; OLIGONUCLEOTIDE; RECN PROTEIN;

ARTICLE; BACTERIAL GENE; BACTERIAL GENOME; BACTERIUM IDENTIFICATION; BACTERIUM ISOLATE; BASE PAIRING; DNA SEQUENCE; GENE AMPLIFICATION; MATHEMATICAL MODEL; NONHUMAN; PRIORITY JOURNAL; RPOA BACTERIAL GENE; SEQUENCE ALIGNMENT; THDF BACTERIAL GENE; THERMOANAEROBACTER; THERMOANAEROBACTER THERMOHYDROSULFURICUS;

BACTERIAL PROTEINS; CHAPERONIN 60; DNA PRIMERS; DNA, BACTERIAL; GENOME, BACTERIAL; LINEAR MODELS; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; PHYLOGENY; POLYMERASE CHAIN REACTION; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; THERMOANAEROBACTER;

BACTERIA (MICROORGANISMS); THERMOANAEROBACTER; THERMOANAEROBACTER THERMOHYDROSULFURICUS;

EID: 79954603471     PISSN: 07232020     EISSN: 16180984     Source Type: Journal    
DOI: 10.1016/j.syapm.2010.11.019     Document Type: Article

References (32)

1. Acinas S.G., Marcelino L.A., Klepac-Ceraj V., Polz M.F. Divergence and redundancy of 16S rRNA sequences in genomes with multiple rrn operons. J. Bacteriol. 2004, 186:2629-2635.
2. Adékambi T., Drancourt M., Raoult D. The rpoB gene as a tool for clinical microbiologists. Trends Microbiol. 2009, 17:37-45.
3. Arahal D.R., Sanchez E., Macian M.C., Garay E. Value of recN sequences for species identification and as a phylogenetic marker within the family " Leuconostocaceae" Int. Microbiol. 2008, 11:33-39.
4. Clavel T., Lippman R., Gavini F., Dore J., Blaut M. Clostridium saccharogumia sp. nov. and Lactonifactor longoviformis gen. nov., sp. nov., two novel human faecal bacteria involved in the conversion of the dietary phytoestrogen secoisolariciresinol diglucoside. Syst. Appl. Microbiol. 2007, 30:16-26.
5. Cooper J.E., Feil E.J. Multilocus sequence typing - what is resolved?. Trends Microbiol. 2004, 12:373-377.
6. Crocetti G.R., Hugenholtz P., Bond P.L., Schuler A., Keller J., Jenkins D., Blackall L.L. Identification of polyphosphate-accumulating organisms and design of 16S rRNA-directed probes for their detection and quantitation. Appl. Environ. Microbiol. 2000, 66:1175-1182.
7. Fardeau M.L., Bonilla Salinas M., L'Haridon S., Jeanthon C., Verhe F., Cayol J.L., Patel B.K., Garcia J.L., Ollivier B. Isolation from oil reservoirs of novel thermophilic anaerobes phylogenetically related to Thermoanaerobacter subterraneus: reassignment of T. subterraneus, Thermoanaerobacter yonseiensis, Thermoanaerobacter tengcongensis and Carboxydibrachium pacificum to Caldanaerobacter subterraneus gen. nov., sp. nov., comb. nov. as four novel subspecies. Int. J. Syst. Evol. Microbiol. 2004, 54:467-474.
8. Gevers D., Cohan F.M., Lawrence J.G., Spratt B.G., Coenye T., Feil E.J., Stackebrandt E., Van de Peer Y., Vandamme P., Thompson F.L., Swings J. Re-evaluating prokaryotic species. Nat. Rev. Microbiol. 2005, 3:733-739.
9. Glazunova O.O., Raoult D., Roux V. Partial sequence comparison of the rpoB, sodA, groEL and gyrB genes within the genus Streptococcus. Int. J. Syst. Evol. Microbiol. 2009, 59:2317-2322.
10. Harvey S.H., Krien M.J., O'Connell M.J. Structural maintenance of chromosomes (SMC) proteins, a family of conserved ATPases. Genome Biol. 2002, 3. REVIEWS3003.
11. Hemmingsen S.M., Woolford C., van der Vies S.M., Tilly K., Dennis D.T., Georgopoulos C.P., Hendrix R.W., Ellis R.J. Homologous plant and bacterial proteins chaperone oligomeric protein assembly. Nature 1988, 333:330-334.
12. Hill J.E., Penny S.L., Crowell K.G., Goh S.H., Hemmingsen S.M. cpnDB: a chaperonin sequence database. Genome Res. 2004, 14:1669-1675.
13. Hill J.E., Town J.R., Hemmingsen S.M. Improved template representation in cpn60 polymerase chain reaction (PCR) product libraries generated from complex templates by application of a specific mixture of PCR primers. Environ. Microbiol. 2005, 8:741-746.
14. Kuhnert P., Korczak B.M., Stephan R., Joosten H., Iversen C. Phylogeny and prediction of genetic similarity of Cronobacter and related taxa by multilocus sequence analysis (MLSA). Int. J. Food Microbiol. 2009, 136:152-158.
15. Loren J.G., Farfan M., Minana-Galbis D., Fuste M.C. Prediction of whole-genome DNA G+C content within the genus Aeromonas based on housekeeping gene sequences. Syst. Appl. Microbiol. 2010, 33:237-242.
16. Ludwig W. Nucleic acid techniques in bacterial systematics and identification. Int. J. Food Microbiol. 2007, 120:225-236.
17. Lund P.A. Multiple chaperonins in bacteria - why so many?. FEMS Microbiol. Rev. 2009, 33:785-800.
18. Meintanis C., Chalkou K.I., Kormas K.A., Lymperopoulou D.S., Katsifas E.A., Hatzinikolaou D.G., Karagouni A.D. Application of rpoB sequence similarity analysis, REP-PCR and BOX-PCR for the differentiation of species within the genus Geobacillus. Lett. Appl. Microbiol. 2008, 46:395-401.
19. Pei A.Y., Oberdorf W.E., Nossa C.W., Agarwal A., Chokshi P., Gerz E.A., Jin Z., Lee P., Yang L., Poles M., Brown S.M., Sotero S., Desantis T., Brodie E., Nelson K., Pei Z. Diversity of 16S rRNA genes within individual prokaryotic genomes. Appl. Environ. Microbiol. 2010, 76:3886-3897.
20. Pontes D.S., Lima-Bittencourt C.I., Chartone-Souza E., Amaral Nascimento A.M. Molecular approaches: advantages and artifacts in assessing bacterial diversity. J. Ind. Microbiol. Biotechnol. 2007, 34:463-473.
21. Rasko D.A., Ravel J., Økstad O.A., Helgason E., Cer R.Z., Jiang L., Shores K.A., Fouts D.E., Tourasse N.J., Angiuoli S.V., Kolonay J., Nelson W.C., Kolstø A.B., Fraser C.M., Read T.D. The genome sequence of Bacillus cereus ATCC 10987 reveals metabolic adaptations and a large plasmid related to Bacillus anthracis pXO1. Nucleic Acids Res. 2004, 32:977-988.
22. Richter M., Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc. Natl. Acad. Sci. U.S.A. 2009, 106:19126-19131.
23. Saitou N., Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 1987, 4:406-425.
24. Schloss P.D., Handelsman J. Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl. Environ. Microbiol. 2005, 71:1501-1506.
25. Sparling R., Islam R., Cicek N., Carere C., Chow H., Levin D.B. Formate synthesis by Clostridium thermocellum during anaerobic fermentation. Can. J. Microbiol. 2006, 52:681-688.
26. Stackebrandt E., Frederiksen W., Garrity G.M., Grimont P.A., Kampfer P., Maiden M.C., Nesme X., Rossello-Mora R., Swings J., Truper H.G., Vauterin L., Ward A.C., Whitman W.B. Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int. J. Syst. Evol. Microbiol. 2002, 52:1043-1047.
27. Tamura K., Dudley J., Nei M., Kumar S. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol. Biol. Evol. 2007, 24:1596-1599.
28. Thompson J.D., Higgins D.G., Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994, 22:4673-4680.
29. Wang L.T., Lee F.L., Tai C.J., Kasai H. Comparison of gyrB gene sequences, 16S rRNA gene sequences and DNA-DNA hybridization in the Bacillus subtilis group. Int. J. Syst. Evol. Microbiol. 2007, 57:1846-1850.
30. Weng F.Y., Chiou C.S., Lin P.H.P., Yang S.S. Application of recA and rpoB sequence analysis on phylogeny and molecular identification of Geobacillus species. J. Appl. Microbiol. 2009, 107:452-464.
31. Zeigler D.R. Application of a recN sequence similarity analysis to the identification of species within the bacterial genus Geobacillus. Int. J. Syst. Evol. Microbiol. 2005, 55:1171-1179.
32. Zeigler D.R. Gene sequences useful for predicting relatedness of whole genomes in bacteria. Int. J. Syst. Evol. Microbiol. 2003, 53:1893-1900.