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Paul Nardon - One of the best experts on this subject based on the ideXlab platform.

  • moleCular CharaCterization of the prinCipal symbiotiC baCteria of the weevil sitophilus oryzae a peCuliar g C Content of an endoCytobiotiC dna
    Journal of Molecular Evolution, 1998
    Co-Authors: Abdelaziz Heddi, Hubert Charles, Chaque Khatchadourian, Guy Bonnot, Paul Nardon
    Abstract:

    The prinCipal intraCellular symbiotiC baCteria of the Cereal weevil Sitophilus oryzae were CharaCterized using the sequenCe of the 16S rDNA gene (rrs gene) and G + C Content analysis. Polymerase Chain reaCtion amplifiCation with universal eubaCterial primers of the rrs gene showed a single expeCted sequenCe of 1,501 bp. Comparison of this sequenCe with the available database sequenCes plaCed the intraCellular baCteria of S. oryzae as members of the EnterobaCteriaCeae family, Closely related to the free-living baCteria, Erwinia herbiCola and EsCheriChia Coli, and the endoCytobiotiC baCteria of the tsetse fly and aphids. Moreover, by high-performanCe liquid Chromatography, we measured the genomiC G + C Content of the S. oryzae prinCipal endoCytobiotes (SOPE) as 54%, while the known genomiC G + C Content of most intraCellular baCteria is about 39.5%. Furthermore, based on the third Codon position G + C Content and the rrs gene G + C Content, we demonstrated that most intraCellular baCteria exCept SOPE are A + T biased irrespeCtive of their phylogenetiC position. Finally, using the hsp60 gene sequenCe, the Codon usage of SOPE was Compared with that of two phylogenetiCally Closely related baCteria: E. Coli, a free-living baCterium, and BuChnera aphidiCola, the intraCellular symbiotiC baCteria of aphids. Taken together, these results show a peCuliar and distinCtly different DNA Composition of SOPE with respeCt to the other obligate intraCellular baCteria, and, Combined with biologiCal and bioChemiCal data, they eluCidate the evolution of symbiosis in S. oryzae.

  • moleCular CharaCterization of the prinCipal symbiotiC baCteria of the weevil sitophilus oryzae a peCuliar g C Content of an endoCytobiotiC dna
    Journal of Molecular Evolution, 1998
    Co-Authors: Abdelaziz Heddi, Hubert Charles, Chaque Khatchadourian, Guy Bonnot, Paul Nardon
    Abstract:

    The prinCipal intraCellular symbiotiC baCteria of the Cereal weevil Sitophilus oryzae were CharaCterized using the sequenCe of the 16S rDNA gene (rrs gene) and G + C Content analysis. Polymerase Chain reaCtion amplifiCation with universal eubaCterial primers of the rrs gene showed a single expeCted sequenCe of 1,501 bp. Comparison of this sequenCe with the available database sequenCes plaCed the intraCellular baCteria of S. oryzae as members of the EnterobaCteriaCeae family, Closely related to the free-living baCteria, Erwinia herbiCola and EsCheriChia Coli, and the endoCytobiotiC baCteria of the tsetse fly and aphids. Moreover, by high-performanCe liquid Chromatography, we measured the genomiC G + C Content of the S. oryzae prinCipal endoCytobiotes (SOPE) as 54%, while the known genomiC G + C Content of most intraCellular baCteria is about 39.5%. Furthermore, based on the third Codon position G + C Content and the rrs gene G + C Content, we demonstrated that most intraCellular baCteria exCept SOPE are A + T biased irrespeCtive of their phylogenetiC position. Finally, using the hsp60 gene sequenCe, the Codon usage of SOPE was Compared with that of two phylogenetiCally Closely related baCteria: E. Coli, a free-living baCterium, and BuChnera aphidiCola, the intraCellular symbiotiC baCteria of aphids. Taken together, these results show a peCuliar and distinCtly different DNA Composition of SOPE with respeCt to the other obligate intraCellular baCteria, and, Combined with biologiCal and bioChemiCal data, they eluCidate the evolution of symbiosis in S. oryzae.

Wolfgang Ludwig - One of the best experts on this subject based on the ideXlab platform.

  • speCifiC oligonuCleotide probes for in situ deteCtion of a major group of gram positive baCteria with low dna g C Content
    Systematic and Applied Microbiology, 1999
    Co-Authors: Harald Meier, Wolfgang Ludwig, Rudolf Amann, Karlheinz Schleifer
    Abstract:

    Summary Almost one thousand 16S rRNA sequenCes of Gram-positive baCteria with a low DNA G+C Content from publiC databases were analyzed using the ARB software paCkage. A signature region was identified between positions 354 and 371 ( E. Coli numbering) for the BaCillus sub-branCh of the Gram-positive baCteria with a low DNA G+C Content, the former orders BaCillales and LaCtobaCillales . Three oligonuCleotide probes, namely LGC354A, LGC354B, and LGC354C, were designed to target this diagnostiC site. Their fluoresCent derivatives were suitable for whole Cell deteCtion by fluoresCenCe in situ hybridization (FISH). Hybridization Conditions were adjusted for differentiation of target and related non-target referenCe speCies. When applying FISH to whole baCterial Cells in a sample of aCtivated sludge from a Communal wastewater treatment plant, members of the BaCillus sub-branCh were deteCted at levels from 0.01% of Cells in samples fixed with paraformaldehyde to over 8 perCent in the same samples fixed with ethanol and treated with lysozyme. The problems of quantitative in situ analysis of Gram-positive baCteria with a low DNA G+C Content in biofilm floCs are disCussed and reCommendations made. Members of the BaCillus sub-branCh were deteCted in different abundanCes in aCtivated sludge samples from different wastewater plants.

  • in situ probing of gram positive baCteria with high dna g C Content using 23s rrna targeted oligonuCleotides
    Microbiology, 1994
    Co-Authors: Carsten Roller, Wolfgang Ludwig, Rudolf Amann, Michael Wagner, Karlheinz Schleifer
    Abstract:

    23S-rRNA-targeted oligonuCleotide probes were designed for the phylogenetiC group ‘Gram-positive baCteria with high G + C Content of DNA’ (GPBHGC). A sequenCe idiosynCrasy in two adjaCent base pairs in the stem of helix 69 in domain IV of the 23S rRNA is present in all hitherto analysed strains of GPBHGC. An oligonuCleotide probe targeted to this region hybridized only with strains of GPBHGC and was suCCessfully used for in situ monitoring of these Cells in aCtivated sludge. Another unique feature of the 23S rRNA moleCules of GPBHGC is a large insertion in domain III. FluoresCent oligonuCleotides targeted to the highly variable regions of the rRNA within the insertions of CorynebaCterium glutamiCum DSM 20300T, AureobaCterium testaCeum DSM 20166 and BrevibaCterium sp. DSM 20165 hybridized speCifiCally to their target strains, whereas probing with oligonuCleotides Complementary to the rRNA-Coding strand of the 23S rDNA and to the spaCer between 16S and 23S rRNA of C. glutamiCum did not result in deteCtable fluoresCenCe. This Confirmed that the large 23S insertions are indeed present in 23S rRNAs of GPBHGC and provide potential target sites for highly speCifiC nuCleiC aCid probes.

  • Complete 23s ribosomal rna sequenCes of gram positive baCteria with a low dna g C Content
    Systematic and Applied Microbiology, 1992
    Co-Authors: Wolfgang Ludwig, Gudrun Kirchhof, Norbert Klugbauer, Michael Weizenegger, Doris Betzl, Mathias Ehrmann, Christian Hertel, Sabine Jilg, Ralf Tatzel, Horst Zitzelsberger
    Abstract:

    Summary The Complete 23S rRNA primary struCtures of 14 gram-positive baCteria with a low DNA G+C Content were determined. The sequenCes were Compared with 50 published as well as unpublished Complete 23S rRNA sequenCes from baCteria. Based on previously published models, higher order struCture analyses were performed and a Consensus higher order struCture model of the 23S rRNA from gram-positive baCteria with a low DNA G+C Content was established. A tree refleCting the phylogenetiC relationships among gram-positive baCteria with a low DNA G+C Content was reConstruCted and Compared with a phylogenetiC tree based on a Comparable data set of 16S rRNA sequenCes. The topologies of the trees are in good agreement.

  • gram positive baCteria with a high dna g C Content are CharaCterized by a Common insertion within their 23s rrna genes
    Microbiology, 1992
    Co-Authors: Carsten Roller, Wolfgang Ludwig, Karlheinz Schleifer
    Abstract:

    An insertion of about 100 bases within the Central part of the 23S rRNA genes was found to be a phylogenetiC marker for the baCterial line of desCent of Gram-positive baCteria with a high DNA G+C Content. The insertion was present in 23S rRNA genes of 64 strains representing the major phylogenetiC groups of Gram-positive baCteria with a high DNA G+C Content, whereas it was not found in 23S rRNA genes of 55 (eu)baCteria representing Gram-positive baCteria with a low DNA G+C Content and all other known (eu)baCterial phyla. The presenCe of the insertion Could be easily demonstrated by Comparative gel eleCtrophoretiC analysis of in vitro-amplified 23S rDNA fragments, whiCh Contained the insertion. The nuCleotide sequenCes of the amplified fragments were determined and sequenCe similarities of at least 44% were found. The overall similarity values are lower than those of 16S and 23S rRNA sequenCes of the partiCular organism. Northern hybridization experiments indiCated the presenCe of the insertion within the mature 23S rRNA of CorynebaCterium glutamiCum.

Karlheinz Schleifer - One of the best experts on this subject based on the ideXlab platform.

  • speCifiC oligonuCleotide probes for in situ deteCtion of a major group of gram positive baCteria with low dna g C Content
    Systematic and Applied Microbiology, 1999
    Co-Authors: Harald Meier, Wolfgang Ludwig, Rudolf Amann, Karlheinz Schleifer
    Abstract:

    Summary Almost one thousand 16S rRNA sequenCes of Gram-positive baCteria with a low DNA G+C Content from publiC databases were analyzed using the ARB software paCkage. A signature region was identified between positions 354 and 371 ( E. Coli numbering) for the BaCillus sub-branCh of the Gram-positive baCteria with a low DNA G+C Content, the former orders BaCillales and LaCtobaCillales . Three oligonuCleotide probes, namely LGC354A, LGC354B, and LGC354C, were designed to target this diagnostiC site. Their fluoresCent derivatives were suitable for whole Cell deteCtion by fluoresCenCe in situ hybridization (FISH). Hybridization Conditions were adjusted for differentiation of target and related non-target referenCe speCies. When applying FISH to whole baCterial Cells in a sample of aCtivated sludge from a Communal wastewater treatment plant, members of the BaCillus sub-branCh were deteCted at levels from 0.01% of Cells in samples fixed with paraformaldehyde to over 8 perCent in the same samples fixed with ethanol and treated with lysozyme. The problems of quantitative in situ analysis of Gram-positive baCteria with a low DNA G+C Content in biofilm floCs are disCussed and reCommendations made. Members of the BaCillus sub-branCh were deteCted in different abundanCes in aCtivated sludge samples from different wastewater plants.

  • in situ probing of gram positive baCteria with high dna g C Content using 23s rrna targeted oligonuCleotides
    Microbiology, 1994
    Co-Authors: Carsten Roller, Wolfgang Ludwig, Rudolf Amann, Michael Wagner, Karlheinz Schleifer
    Abstract:

    23S-rRNA-targeted oligonuCleotide probes were designed for the phylogenetiC group ‘Gram-positive baCteria with high G + C Content of DNA’ (GPBHGC). A sequenCe idiosynCrasy in two adjaCent base pairs in the stem of helix 69 in domain IV of the 23S rRNA is present in all hitherto analysed strains of GPBHGC. An oligonuCleotide probe targeted to this region hybridized only with strains of GPBHGC and was suCCessfully used for in situ monitoring of these Cells in aCtivated sludge. Another unique feature of the 23S rRNA moleCules of GPBHGC is a large insertion in domain III. FluoresCent oligonuCleotides targeted to the highly variable regions of the rRNA within the insertions of CorynebaCterium glutamiCum DSM 20300T, AureobaCterium testaCeum DSM 20166 and BrevibaCterium sp. DSM 20165 hybridized speCifiCally to their target strains, whereas probing with oligonuCleotides Complementary to the rRNA-Coding strand of the 23S rDNA and to the spaCer between 16S and 23S rRNA of C. glutamiCum did not result in deteCtable fluoresCenCe. This Confirmed that the large 23S insertions are indeed present in 23S rRNAs of GPBHGC and provide potential target sites for highly speCifiC nuCleiC aCid probes.

  • gram positive baCteria with a high dna g C Content are CharaCterized by a Common insertion within their 23s rrna genes
    Microbiology, 1992
    Co-Authors: Carsten Roller, Wolfgang Ludwig, Karlheinz Schleifer
    Abstract:

    An insertion of about 100 bases within the Central part of the 23S rRNA genes was found to be a phylogenetiC marker for the baCterial line of desCent of Gram-positive baCteria with a high DNA G+C Content. The insertion was present in 23S rRNA genes of 64 strains representing the major phylogenetiC groups of Gram-positive baCteria with a high DNA G+C Content, whereas it was not found in 23S rRNA genes of 55 (eu)baCteria representing Gram-positive baCteria with a low DNA G+C Content and all other known (eu)baCterial phyla. The presenCe of the insertion Could be easily demonstrated by Comparative gel eleCtrophoretiC analysis of in vitro-amplified 23S rDNA fragments, whiCh Contained the insertion. The nuCleotide sequenCes of the amplified fragments were determined and sequenCe similarities of at least 44% were found. The overall similarity values are lower than those of 16S and 23S rRNA sequenCes of the partiCular organism. Northern hybridization experiments indiCated the presenCe of the insertion within the mature 23S rRNA of CorynebaCterium glutamiCum.

Markus Goker - One of the best experts on this subject based on the ideXlab platform.

  • taxonomiC use of dna g C Content and dna dna hybridization in the genomiC age
    International Journal of Systematic and Evolutionary Microbiology, 2014
    Co-Authors: Jan P Meierkolthoff, Hanspeter Klenk, Markus Goker
    Abstract:

    The G+C Content of a genome is frequently used in taxonomiC desCriptions of speCies and genera. In the past it has been determined using Conventional, indireCt methods, but it is nowadays reasonable to CalCulate the DNA G+C Content direCtly from the inCreasingly available and affordable genome sequenCes. The expeCted inCrease in aCCuraCy, however, might alter the way in whiCh the G+C Content is used for drawing taxonomiC ConClusions. We here re-estimate the literature assumption that the G+C Content Can vary up to 3–5 % within speCies using genomiC datasets. The resulting G+C Content differenCes are Compared with DNA–DNA hybridization (DDH) similarities CalCulated in siliCo using the GGDC web server, with 70 % similarity as the gold standard threshold for speCies boundaries. The results indiCate that the G+C Content, if Computed from genome sequenCes, varies no more than 1 % within speCies. StatistiCal models based on larger differenCes alone Can rejeCt the hypothesis that two strains belong to the same speCies. BeCause DDH similarities between two non-type strains oCCur in the genomiC datasets, we also examine to what extent and under whiCh Conditions suCh a similarity Could be <70 % even though the similarity of either strain to a type strain was ≥70 %. In theory, their similarity Could be as low as 50 %, whereas empiriCal data suggest a boundary Closer (but not identiCal) to 70 %. However, it is shown that using a 50 % boundary would not affeCt the ConClusions regarding the DNA G+C Content. HenCe, we suggest that disCrepanCies between G+C Content data provided in speCies desCriptions on the one hand and those reCalCulated after genome sequenCing on the other hand ≥1 % are due to signifiCant inaCCuraCies of the applied Conventional methods and aCCordingly Call for emendations of speCies desCriptions.

Abdelaziz Heddi - One of the best experts on this subject based on the ideXlab platform.

  • moleCular CharaCterization of the prinCipal symbiotiC baCteria of the weevil sitophilus oryzae a peCuliar g C Content of an endoCytobiotiC dna
    Journal of Molecular Evolution, 1998
    Co-Authors: Abdelaziz Heddi, Hubert Charles, Chaque Khatchadourian, Guy Bonnot, Paul Nardon
    Abstract:

    The prinCipal intraCellular symbiotiC baCteria of the Cereal weevil Sitophilus oryzae were CharaCterized using the sequenCe of the 16S rDNA gene (rrs gene) and G + C Content analysis. Polymerase Chain reaCtion amplifiCation with universal eubaCterial primers of the rrs gene showed a single expeCted sequenCe of 1,501 bp. Comparison of this sequenCe with the available database sequenCes plaCed the intraCellular baCteria of S. oryzae as members of the EnterobaCteriaCeae family, Closely related to the free-living baCteria, Erwinia herbiCola and EsCheriChia Coli, and the endoCytobiotiC baCteria of the tsetse fly and aphids. Moreover, by high-performanCe liquid Chromatography, we measured the genomiC G + C Content of the S. oryzae prinCipal endoCytobiotes (SOPE) as 54%, while the known genomiC G + C Content of most intraCellular baCteria is about 39.5%. Furthermore, based on the third Codon position G + C Content and the rrs gene G + C Content, we demonstrated that most intraCellular baCteria exCept SOPE are A + T biased irrespeCtive of their phylogenetiC position. Finally, using the hsp60 gene sequenCe, the Codon usage of SOPE was Compared with that of two phylogenetiCally Closely related baCteria: E. Coli, a free-living baCterium, and BuChnera aphidiCola, the intraCellular symbiotiC baCteria of aphids. Taken together, these results show a peCuliar and distinCtly different DNA Composition of SOPE with respeCt to the other obligate intraCellular baCteria, and, Combined with biologiCal and bioChemiCal data, they eluCidate the evolution of symbiosis in S. oryzae.

  • moleCular CharaCterization of the prinCipal symbiotiC baCteria of the weevil sitophilus oryzae a peCuliar g C Content of an endoCytobiotiC dna
    Journal of Molecular Evolution, 1998
    Co-Authors: Abdelaziz Heddi, Hubert Charles, Chaque Khatchadourian, Guy Bonnot, Paul Nardon
    Abstract:

    The prinCipal intraCellular symbiotiC baCteria of the Cereal weevil Sitophilus oryzae were CharaCterized using the sequenCe of the 16S rDNA gene (rrs gene) and G + C Content analysis. Polymerase Chain reaCtion amplifiCation with universal eubaCterial primers of the rrs gene showed a single expeCted sequenCe of 1,501 bp. Comparison of this sequenCe with the available database sequenCes plaCed the intraCellular baCteria of S. oryzae as members of the EnterobaCteriaCeae family, Closely related to the free-living baCteria, Erwinia herbiCola and EsCheriChia Coli, and the endoCytobiotiC baCteria of the tsetse fly and aphids. Moreover, by high-performanCe liquid Chromatography, we measured the genomiC G + C Content of the S. oryzae prinCipal endoCytobiotes (SOPE) as 54%, while the known genomiC G + C Content of most intraCellular baCteria is about 39.5%. Furthermore, based on the third Codon position G + C Content and the rrs gene G + C Content, we demonstrated that most intraCellular baCteria exCept SOPE are A + T biased irrespeCtive of their phylogenetiC position. Finally, using the hsp60 gene sequenCe, the Codon usage of SOPE was Compared with that of two phylogenetiCally Closely related baCteria: E. Coli, a free-living baCterium, and BuChnera aphidiCola, the intraCellular symbiotiC baCteria of aphids. Taken together, these results show a peCuliar and distinCtly different DNA Composition of SOPE with respeCt to the other obligate intraCellular baCteria, and, Combined with biologiCal and bioChemiCal data, they eluCidate the evolution of symbiosis in S. oryzae.