메뉴 건너뛰기




Volumn 30, Issue 5, 2007, Pages 390-400

A prototype taxonomic microarray targeting the rpsA housekeeping gene permits species identification within the rhizobial genus Ensifer

Author keywords

Ensifer; Housekeeping gene; Oligonucleotide microarray; Species identification; Taxonomy

Indexed keywords

DNA; GENOMIC DNA; OLIGONUCLEOTIDE;

EID: 34250780068     PISSN: 07232020     EISSN: 16180984     Source Type: Journal    
DOI: 10.1016/j.syapm.2007.01.002     Document Type: Article
Times cited : (8)

References (51)
  • 1
    • 1942443733 scopus 로고    scopus 로고
    • Divergence and redundancy of 16S rRNA sequences in genomes with multiple rrn operons
    • Acinas S.G., Marcelino L.A., Klepac-Ceraj V., and Polz M.F. Divergence and redundancy of 16S rRNA sequences in genomes with multiple rrn operons. J. Bacteriol. 186 (2004) 2629-2635
    • (2004) J. Bacteriol. , vol.186 , pp. 2629-2635
    • Acinas, S.G.1    Marcelino, L.A.2    Klepac-Ceraj, V.3    Polz, M.F.4
  • 2
    • 0030875847 scopus 로고    scopus 로고
    • Thermodynamics and NMR of internal GT mismatches in DNA
    • Allawi H.T., and SantaLucia J. Thermodynamics and NMR of internal GT mismatches in DNA. Biochemistry 36 (1997) 10581-10594
    • (1997) Biochemistry , vol.36 , pp. 10581-10594
    • Allawi, H.T.1    SantaLucia, J.2
  • 5
    • 23044457732 scopus 로고    scopus 로고
    • Automatic selection of representative proteins for bacterial phylogeny
    • Bern M., and Goldberg D. Automatic selection of representative proteins for bacterial phylogeny. BMC Evol. Biol. 5 (2005) 34
    • (2005) BMC Evol. Biol. , vol.5 , pp. 34
    • Bern, M.1    Goldberg, D.2
  • 6
    • 22544432546 scopus 로고    scopus 로고
    • DNA chips for detection of bacterial pathogens
    • Blaskovic D., and Barak I. DNA chips for detection of bacterial pathogens. Biologia 60 (2005) 239-249
    • (2005) Biologia , vol.60 , pp. 239-249
    • Blaskovic, D.1    Barak, I.2
  • 8
    • 0034801924 scopus 로고    scopus 로고
    • Ralstonia taiwanensis sp. nov., isolated from root nodules of Mimosa species and sputum of a cystic fibrosis patient
    • Chen W.M., Laevens S., Lee T.M., Coenye T., De Vos P., Mergeay M., and Vandamme P. Ralstonia taiwanensis sp. nov., isolated from root nodules of Mimosa species and sputum of a cystic fibrosis patient. Int. J. Syst. Evol. Microbiol. 51 (2001) 1729-1735
    • (2001) Int. J. Syst. Evol. Microbiol. , vol.51 , pp. 1729-1735
    • Chen, W.M.1    Laevens, S.2    Lee, T.M.3    Coenye, T.4    De Vos, P.5    Mergeay, M.6    Vandamme, P.7
  • 9
    • 16844374904 scopus 로고    scopus 로고
    • Identification of clinically relevant viridans streptococci by an oligonucleotide array
    • Chen C.C., Teng L.J., Kaiung S., and Chang T.C. Identification of clinically relevant viridans streptococci by an oligonucleotide array. J. Clin. Microbiol. 43 (2005) 1515-1521
    • (2005) J. Clin. Microbiol. , vol.43 , pp. 1515-1521
    • Chen, C.C.1    Teng, L.J.2    Kaiung, S.3    Chang, T.C.4
  • 11
    • 15444377835 scopus 로고    scopus 로고
    • Rhizobial 16S rRNA and dnaK genes: mosaicism and the uncertain phylogenetic placement of Rhizobium galegae
    • Eardly B.D., Nour S.M., van Berkum P., and Selander R.K. Rhizobial 16S rRNA and dnaK genes: mosaicism and the uncertain phylogenetic placement of Rhizobium galegae. Appl. Environ. Microbiol. 71 (2005) 1328-1335
    • (2005) Appl. Environ. Microbiol. , vol.71 , pp. 1328-1335
    • Eardly, B.D.1    Nour, S.M.2    van Berkum, P.3    Selander, R.K.4
  • 12
    • 0030467103 scopus 로고    scopus 로고
    • Corresponding 16S rRNA gene segments in Rhizobiaceae and Aeromonas yield discordant phylogenies
    • Eardly B.D., Wang F.S., and van Berkum P. Corresponding 16S rRNA gene segments in Rhizobiaceae and Aeromonas yield discordant phylogenies. Plant and Soil 186 (1996) 69-74
    • (1996) Plant and Soil , vol.186 , pp. 69-74
    • Eardly, B.D.1    Wang, F.S.2    van Berkum, P.3
  • 13
    • 0029610851 scopus 로고
    • The RecA protein as a model molecule for molecular systematic studies of bacteria: comparison of trees of RecAs and 16S rRNAs from the same species
    • Eisen J.A. The RecA protein as a model molecule for molecular systematic studies of bacteria: comparison of trees of RecAs and 16S rRNAs from the same species. J. Mol. Evol. 41 (1995) 1105-1123
    • (1995) J. Mol. Evol. , vol.41 , pp. 1105-1123
    • Eisen, J.A.1
  • 15
    • 23744484693 scopus 로고    scopus 로고
    • Development of a new oligonucleotide array to identify staphylococcal strains at species level
    • Giammarinaro P., Leroy S., Chacornac J.P., Delmas J., and Talon R. Development of a new oligonucleotide array to identify staphylococcal strains at species level. J. Clin. Microbiol. 43 (2005) 3673-3680
    • (2005) J. Clin. Microbiol. , vol.43 , pp. 3673-3680
    • Giammarinaro, P.1    Leroy, S.2    Chacornac, J.P.3    Delmas, J.4    Talon, R.5
  • 16
    • 0034846156 scopus 로고    scopus 로고
    • Protein coding gene sequences: alternative phylogenetic markers or possible tools to compare ecological diversity in bacteria?
    • Giraffa G. Protein coding gene sequences: alternative phylogenetic markers or possible tools to compare ecological diversity in bacteria?. Current Genomics 2 (2001) 243-251
    • (2001) Current Genomics , vol.2 , pp. 243-251
    • Giraffa, G.1
  • 18
    • 7444221126 scopus 로고    scopus 로고
    • Potential of DNA microarrays for developing parallel detection tools (PDTs) for microorganisms relevant to biodefense and related research needs
    • Hashsham S.A., Wick L.M., Rouillard J.M., Gulari E., and Tiedje J.M. Potential of DNA microarrays for developing parallel detection tools (PDTs) for microorganisms relevant to biodefense and related research needs. Biosens. Bioelectron. 20 (2004) 668-683
    • (2004) Biosens. Bioelectron. , vol.20 , pp. 668-683
    • Hashsham, S.A.1    Wick, L.M.2    Rouillard, J.M.3    Gulari, E.4    Tiedje, J.M.5
  • 21
    • 33645754929 scopus 로고    scopus 로고
    • Application of DNA microarray technology for detection, identification, and characterization of food-borne pathogens
    • Kostrzynska M., and Bachand A. Application of DNA microarray technology for detection, identification, and characterization of food-borne pathogens. Can. J. Microbiol. 52 (2006) 1-8
    • (2006) Can. J. Microbiol. , vol.52 , pp. 1-8
    • Kostrzynska, M.1    Bachand, A.2
  • 24
    • 33947324049 scopus 로고    scopus 로고
    • M. Martens, M. Delaere, R. Coopman, P. De Vos, M. Gillis, A. Willems, Multilocus sequence analysis of Ensifer and related taxa, Int. J. Syst. Evol. Microbiol. 57 (2007), in press.
  • 25
    • 3242891684 scopus 로고    scopus 로고
    • DIALIGN: multiple DNA and protein sequence alignment at BiBiServ
    • Morgenstern B. DIALIGN: multiple DNA and protein sequence alignment at BiBiServ. Nucleic Acids Res. 32 (2004) W33-W36
    • (2004) Nucleic Acids Res. , vol.32
    • Morgenstern, B.1
  • 26
    • 0030669211 scopus 로고    scopus 로고
    • rpoB sequence analysis as a novel basis for bacterial identification
    • Mollet C., Drancourt M., and Raoult D. rpoB sequence analysis as a novel basis for bacterial identification. Mol. Microbiol. 26 (1997) 1005-1011
    • (1997) Mol. Microbiol. , vol.26 , pp. 1005-1011
    • Mollet, C.1    Drancourt, M.2    Raoult, D.3
  • 27
    • 0035927646 scopus 로고    scopus 로고
    • Nodulation of legumes by members of the beta-subclass of Proteobacteria
    • Moulin L., Munive A., Dreyfus B., and Boivin-Masson C. Nodulation of legumes by members of the beta-subclass of Proteobacteria. Nature 411 (2001) 948-950
    • (2001) Nature , vol.411 , pp. 948-950
    • Moulin, L.1    Munive, A.2    Dreyfus, B.3    Boivin-Masson, C.4
  • 28
    • 0024553747 scopus 로고
    • Rapid extraction of bacterial genomic DNA with guanidium thiocyanate
    • Pitcher D.G., Saunders N.A., and Owen R.J. Rapid extraction of bacterial genomic DNA with guanidium thiocyanate. Lett. Appl. Microbiol. 8 (1989) 151-156
    • (1989) Lett. Appl. Microbiol. , vol.8 , pp. 151-156
    • Pitcher, D.G.1    Saunders, N.A.2    Owen, R.J.3
  • 29
    • 16344370555 scopus 로고    scopus 로고
    • GoArrays: highly dynamic and efficient microarray probe design
    • Rimour S., Hill D., Militon C., and Peyret P. GoArrays: highly dynamic and efficient microarray probe design. Bioinformatics 21 (2005) 1094-1103
    • (2005) Bioinformatics , vol.21 , pp. 1094-1103
    • Rimour, S.1    Hill, D.2    Militon, C.3    Peyret, P.4
  • 30
    • 10444271036 scopus 로고    scopus 로고
    • Allelic diversity and population structure in Oenococcus oeni as determined from sequence analysis of housekeeping genes
    • de las Rivas B., Marcobal A., and Munoz R. Allelic diversity and population structure in Oenococcus oeni as determined from sequence analysis of housekeeping genes. Appl. Environ. Microbiol. 70 (2004) 7210-7219
    • (2004) Appl. Environ. Microbiol. , vol.70 , pp. 7210-7219
    • de las Rivas, B.1    Marcobal, A.2    Munoz, R.3
  • 31
    • 0006793543 scopus 로고
    • Cloning and sequencing of a large fragment of the Atpd-Gene of Pirellula-marine - a contribution to the phylogeny of Planctomycetales
    • Ronner S., Liesack W., Wolters J., and Stackebrandt E. Cloning and sequencing of a large fragment of the Atpd-Gene of Pirellula-marine - a contribution to the phylogeny of Planctomycetales. Endocytobiosis Cell Res. 7 (1991) 219-229
    • (1991) Endocytobiosis Cell Res. , vol.7 , pp. 219-229
    • Ronner, S.1    Liesack, W.2    Wolters, J.3    Stackebrandt, E.4
  • 32
    • 11844271964 scopus 로고    scopus 로고
    • DNA microarray-based detection and identification of Chlamydia and Chlamydophila spp
    • Sachse K., Hotzel H., Slickers P., Ellinger T., and Ehricht R. DNA microarray-based detection and identification of Chlamydia and Chlamydophila spp. Mol. Cell. Probes 19 (2005) 41-50
    • (2005) Mol. Cell. Probes , vol.19 , pp. 41-50
    • Sachse, K.1    Hotzel, H.2    Slickers, P.3    Ellinger, T.4    Ehricht, R.5
  • 34
    • 84984934354 scopus 로고    scopus 로고
    • Molecular interactions on microarrays
    • Southern E., Mir K., and Shchepinov M. Molecular interactions on microarrays. Nat. Genet. 21 (1999) 5-9
    • (1999) Nat. Genet. , vol.21 , pp. 5-9
    • Southern, E.1    Mir, K.2    Shchepinov, M.3
  • 35
    • 0029742228 scopus 로고    scopus 로고
    • Four unnamed species of nonsymbiotic rhizobia isolated from the rhizosphere of Lotus corniculatus
    • Sullivan J.T., Eardly B.D., van Berkum P., and Ronson C.W. Four unnamed species of nonsymbiotic rhizobia isolated from the rhizosphere of Lotus corniculatus. Appl. Environ. Microbiol. 62 (1996) 2818-2825
    • (1996) Appl. Environ. Microbiol. , vol.62 , pp. 2818-2825
    • Sullivan, J.T.1    Eardly, B.D.2    van Berkum, P.3    Ronson, C.W.4
  • 36
    • 84939594966 scopus 로고    scopus 로고
    • D.L. Swofford, PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods), Version 4, 2002.
  • 37
    • 0031574072 scopus 로고    scopus 로고
    • The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools
    • Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., and Higgins D.G. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25 (1997) 4876-4882
    • (1997) Nucleic Acids Res. , vol.25 , pp. 4876-4882
    • Thompson, J.D.1    Gibson, T.J.2    Plewniak, F.3    Jeanmougin, F.4    Higgins, D.G.5
  • 39
    • 0036959851 scopus 로고    scopus 로고
    • Burkholderia tuberum sp. nov. and Burkholderia phymatum sp. nov., nodulate the roots of tropical legumes
    • Vandamme P., Goris J., Chen W.M., de Vos P., and Willems A. Burkholderia tuberum sp. nov. and Burkholderia phymatum sp. nov., nodulate the roots of tropical legumes. Syst. Appl. Microbiol. 25 (2002) 507-512
    • (2002) Syst. Appl. Microbiol. , vol.25 , pp. 507-512
    • Vandamme, P.1    Goris, J.2    Chen, W.M.3    de Vos, P.4    Willems, A.5
  • 41
    • 0028343191 scopus 로고
    • Evolutionary relationships among eubacterial groups as inferred from GroEL (chaperonin) sequence comparisons
    • Viale A.M., Arakaki A.K., Soncini F.C., and Ferreyra R.G. Evolutionary relationships among eubacterial groups as inferred from GroEL (chaperonin) sequence comparisons. Int. J. Syst. Bacteriol. 44 (1994) 527-533
    • (1994) Int. J. Syst. Bacteriol. , vol.44 , pp. 527-533
    • Viale, A.M.1    Arakaki, A.K.2    Soncini, F.C.3    Ferreyra, R.G.4
  • 42
    • 25144442706 scopus 로고    scopus 로고
    • Molecular systematics of rhizobia based on maximum likelihood and Bayesian phylogenies inferred from rrs, atpD, recA and nifH sequences, and their use in the classification of Sesbania microsymbionts from Venezuelan wetlands
    • Vinuesa P., Silva C., Lorite M.J., Izaguirre-Mayoral M.L., Bedmar E.J., and Martinez-Romero E. Molecular systematics of rhizobia based on maximum likelihood and Bayesian phylogenies inferred from rrs, atpD, recA and nifH sequences, and their use in the classification of Sesbania microsymbionts from Venezuelan wetlands. Syst. Appl. Microbiol. 28 (2005) 702-716
    • (2005) Syst. Appl. Microbiol. , vol.28 , pp. 702-716
    • Vinuesa, P.1    Silva, C.2    Lorite, M.J.3    Izaguirre-Mayoral, M.L.4    Bedmar, E.J.5    Martinez-Romero, E.6
  • 43
    • 0042922317 scopus 로고    scopus 로고
    • Microarray-based identification of thermophilic Campylobacter jejuni, C. coli, C. lari, and C. upsaliensis
    • Volokhov D., Chizhikov V., Chumakov K., and Rasooly A. Microarray-based identification of thermophilic Campylobacter jejuni, C. coli, C. lari, and C. upsaliensis. J. Clin. Microbiol. 41 (2003) 4071-4080
    • (2003) J. Clin. Microbiol. , vol.41 , pp. 4071-4080
    • Volokhov, D.1    Chizhikov, V.2    Chumakov, K.3    Rasooly, A.4
  • 45
    • 2442673171 scopus 로고    scopus 로고
    • Nucleic acid amplification strategies for DNA microarray-based pathogen detection
    • Vora G.J., Meador C.E., Stenger D.A., and Andreadis J.D. Nucleic acid amplification strategies for DNA microarray-based pathogen detection. Appl. Environ. Microbiol. 70 (2004) 3047-3054
    • (2004) Appl. Environ. Microbiol. , vol.70 , pp. 3047-3054
    • Vora, G.J.1    Meador, C.E.2    Stenger, D.A.3    Andreadis, J.D.4
  • 46
    • 0023184331 scopus 로고
    • Bacterial evolution
    • Woese C.R. Bacterial evolution. Microbiol. Rev. 51 (1987) 221-271
    • (1987) Microbiol. Rev. , vol.51 , pp. 221-271
    • Woese, C.R.1
  • 48
    • 0028948030 scopus 로고
    • PCR amplification and direct sequencing of gyrB genes with universal primers and their application to the detection and taxonomic analysis of Pseudomonas putida strains
    • Yamamoto S., and Harayama S. PCR amplification and direct sequencing of gyrB genes with universal primers and their application to the detection and taxonomic analysis of Pseudomonas putida strains. Appl. Environ. Microbiol. 61 (1995) 1104-1109
    • (1995) Appl. Environ. Microbiol. , vol.61 , pp. 1104-1109
    • Yamamoto, S.1    Harayama, S.2
  • 49
    • 0033764790 scopus 로고    scopus 로고
    • Phylogeny of the genus Pseudomonas: intrageneric structure reconstructed from the nucleotide sequences of gyrB and rpoD genes
    • Yamamoto S., Kasai H., Arnold D.L., Jackson R.W., Vivian A., and Harayama S. Phylogeny of the genus Pseudomonas: intrageneric structure reconstructed from the nucleotide sequences of gyrB and rpoD genes. Microbiology 146 (2000) 2385-2394
    • (2000) Microbiology , vol.146 , pp. 2385-2394
    • Yamamoto, S.1    Kasai, H.2    Arnold, D.L.3    Jackson, R.W.4    Vivian, A.5    Harayama, S.6
  • 51
    • 0141698715 scopus 로고    scopus 로고
    • The genus name Ensifer Casida 1982 takes priority over Sinorhizobium Chen et al. 1988, and Sinorhizobium morelense Wang et al. 2002 is a later synonym of Ensifer adhaerens Casida 1982. Is the combination "Sinorhizobium adhaerens" (Casida 1982) Willems et al. 2003 legitimate? Request for an Opinion
    • Young J.M. The genus name Ensifer Casida 1982 takes priority over Sinorhizobium Chen et al. 1988, and Sinorhizobium morelense Wang et al. 2002 is a later synonym of Ensifer adhaerens Casida 1982. Is the combination "Sinorhizobium adhaerens" (Casida 1982) Willems et al. 2003 legitimate? Request for an Opinion. Int. J. Syst. Evol. Microbiol. 53 (2003) 2107-2110
    • (2003) Int. J. Syst. Evol. Microbiol. , vol.53 , pp. 2107-2110
    • Young, J.M.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.