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Molecular characterization of the sequences of the 16S-23S rDNA internal spacer region (ISR) from isolates of Taylorella asinigenitalis.

Tazumi A, Ono S, Sekizuka T, Moore JE, Millar BC, Matsuda M - BMC Res Notes (2009)

Bottom Line: Thus, three ISRs were identified for each isolate, and therefore, at least three distinctly different ribosomal RNA operons were suggested to occur in the genome of T. asinigenitalis.This was also confirmed by Southern hybridization procedure.The present study represents a dendrogram constructed based on the nucleotide sequence data of 16S-23S rDNA ISR for T. asinigenitalis, which may aid in the phylogenetic positioning of T. asinigenitalis within the genus Taylorella, and in the molecular discrimination of T. asinigenitalis.

View Article: PubMed Central - HTML - PubMed

Affiliation: Laboratory of Molecular Biology, School of Environmental Health Sciences, Azabu University, Fuchinobe 1-17-71, Sagamihara 229-8501, Japan. de0702@azabu-u.ac.jp

ABSTRACT

Background: Sequence information on the 16S-23S rDNA internal spacer region (ISR) exhibits a large degree of sequence and length variation at both the genus and species levels. A primer pair for the amplification of 16S-23S rDNA ISR generated three amplicons for each of isolates of Taylorella asinigenitalis (UCD-1T, UK-1 and UK-2).

Findings: Following TA cloning and sequencing, the three isolates of T. asinigenitalis were demonstrated to possess three ISR units of different lengths. Although the three corresponding ISRs (A, B and C) were identified to be identical to each other (UK-1 and UK-2 isolates), the ISRs shared approximately 95.3-98.9% nucleotide sequence similarities between the UCD-1T and UK-1/-2 isolates. A typical order of two intercistronic tRNA genes (5'-tRNAIle-tRNAAla-3') with the different nucleotide spacers [44 through 51 base pairs (bp)] in length was identified among the isolates. The consensus sequences of the antiterminators of boxB and boxA were also identified in all ISRs. Thus, three ISRs were identified for each isolate, and therefore, at least three distinctly different ribosomal RNA operons were suggested to occur in the genome of T. asinigenitalis. This was also confirmed by Southern hybridization procedure.

Conclusion: The present study represents a dendrogram constructed based on the nucleotide sequence data of 16S-23S rDNA ISR for T. asinigenitalis, which may aid in the phylogenetic positioning of T. asinigenitalis within the genus Taylorella, and in the molecular discrimination of T. asinigenitalis.

No MeSH data available.


Nucleotide sequence alignments of the reagion including two intercistronic tRNA genes in the ISRs from the three isolates of T. asinigenitalis. Reference sequences of the ISR-A and -B from the NCTC11184T of T. equigenitalis are also shown for a comparison. Dots indicate identical bases; changes are explicitly indicated; positions identical in all isolates are marked by asterisks; two tRNA genes, for tRNAIle and tRNAAla, are underlined. Numbers at the left and right refer to nucleotide positions of the ISRs. Numbers in parentheses are the nucleotide positions accessible in the DDBJ/EMBL/GenBank (AB264283 – AB264291).
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Figure 2: Nucleotide sequence alignments of the reagion including two intercistronic tRNA genes in the ISRs from the three isolates of T. asinigenitalis. Reference sequences of the ISR-A and -B from the NCTC11184T of T. equigenitalis are also shown for a comparison. Dots indicate identical bases; changes are explicitly indicated; positions identical in all isolates are marked by asterisks; two tRNA genes, for tRNAIle and tRNAAla, are underlined. Numbers at the left and right refer to nucleotide positions of the ISRs. Numbers in parentheses are the nucleotide positions accessible in the DDBJ/EMBL/GenBank (AB264283 – AB264291).

Mentions: In relation to the 3' end of the ISR of T. asinigenitalis isolates, the probable 3' end of the ISR may represent the nucleotide position 989 of the NISR-A of T. equigenitalis NCTC11184T, since the nucleotide position 990 of the NISR-A of T. equigenitalis NCTC11184T [12] was previously deduced to be the possible 5' end of the 23S rDNA sequence of T. equigenitalis by the nucleotide sequence alignment and analysis of the ISR sequences, with the 5' end sequences of the 23S rDNA from several bacterial species (see Figure 2 in the paper described by Kagawa et al. (2006) [12].


Molecular characterization of the sequences of the 16S-23S rDNA internal spacer region (ISR) from isolates of Taylorella asinigenitalis.

Tazumi A, Ono S, Sekizuka T, Moore JE, Millar BC, Matsuda M - BMC Res Notes (2009)

Nucleotide sequence alignments of the reagion including two intercistronic tRNA genes in the ISRs from the three isolates of T. asinigenitalis. Reference sequences of the ISR-A and -B from the NCTC11184T of T. equigenitalis are also shown for a comparison. Dots indicate identical bases; changes are explicitly indicated; positions identical in all isolates are marked by asterisks; two tRNA genes, for tRNAIle and tRNAAla, are underlined. Numbers at the left and right refer to nucleotide positions of the ISRs. Numbers in parentheses are the nucleotide positions accessible in the DDBJ/EMBL/GenBank (AB264283 – AB264291).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2666751&req=5

Figure 2: Nucleotide sequence alignments of the reagion including two intercistronic tRNA genes in the ISRs from the three isolates of T. asinigenitalis. Reference sequences of the ISR-A and -B from the NCTC11184T of T. equigenitalis are also shown for a comparison. Dots indicate identical bases; changes are explicitly indicated; positions identical in all isolates are marked by asterisks; two tRNA genes, for tRNAIle and tRNAAla, are underlined. Numbers at the left and right refer to nucleotide positions of the ISRs. Numbers in parentheses are the nucleotide positions accessible in the DDBJ/EMBL/GenBank (AB264283 – AB264291).
Mentions: In relation to the 3' end of the ISR of T. asinigenitalis isolates, the probable 3' end of the ISR may represent the nucleotide position 989 of the NISR-A of T. equigenitalis NCTC11184T, since the nucleotide position 990 of the NISR-A of T. equigenitalis NCTC11184T [12] was previously deduced to be the possible 5' end of the 23S rDNA sequence of T. equigenitalis by the nucleotide sequence alignment and analysis of the ISR sequences, with the 5' end sequences of the 23S rDNA from several bacterial species (see Figure 2 in the paper described by Kagawa et al. (2006) [12].

Bottom Line: Thus, three ISRs were identified for each isolate, and therefore, at least three distinctly different ribosomal RNA operons were suggested to occur in the genome of T. asinigenitalis.This was also confirmed by Southern hybridization procedure.The present study represents a dendrogram constructed based on the nucleotide sequence data of 16S-23S rDNA ISR for T. asinigenitalis, which may aid in the phylogenetic positioning of T. asinigenitalis within the genus Taylorella, and in the molecular discrimination of T. asinigenitalis.

View Article: PubMed Central - HTML - PubMed

Affiliation: Laboratory of Molecular Biology, School of Environmental Health Sciences, Azabu University, Fuchinobe 1-17-71, Sagamihara 229-8501, Japan. de0702@azabu-u.ac.jp

ABSTRACT

Background: Sequence information on the 16S-23S rDNA internal spacer region (ISR) exhibits a large degree of sequence and length variation at both the genus and species levels. A primer pair for the amplification of 16S-23S rDNA ISR generated three amplicons for each of isolates of Taylorella asinigenitalis (UCD-1T, UK-1 and UK-2).

Findings: Following TA cloning and sequencing, the three isolates of T. asinigenitalis were demonstrated to possess three ISR units of different lengths. Although the three corresponding ISRs (A, B and C) were identified to be identical to each other (UK-1 and UK-2 isolates), the ISRs shared approximately 95.3-98.9% nucleotide sequence similarities between the UCD-1T and UK-1/-2 isolates. A typical order of two intercistronic tRNA genes (5'-tRNAIle-tRNAAla-3') with the different nucleotide spacers [44 through 51 base pairs (bp)] in length was identified among the isolates. The consensus sequences of the antiterminators of boxB and boxA were also identified in all ISRs. Thus, three ISRs were identified for each isolate, and therefore, at least three distinctly different ribosomal RNA operons were suggested to occur in the genome of T. asinigenitalis. This was also confirmed by Southern hybridization procedure.

Conclusion: The present study represents a dendrogram constructed based on the nucleotide sequence data of 16S-23S rDNA ISR for T. asinigenitalis, which may aid in the phylogenetic positioning of T. asinigenitalis within the genus Taylorella, and in the molecular discrimination of T. asinigenitalis.

No MeSH data available.