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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.


A phylogenetic tree constructed based on the nucleotide sequence information of the ISRs, by using the UPGMA method. Values, 0.1, in the figure represent evolutionary distances.
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Figure 1: A phylogenetic tree constructed based on the nucleotide sequence information of the ISRs, by using the UPGMA method. Values, 0.1, in the figure represent evolutionary distances.

Mentions: The PCR primer pair (ISR-Tef and ISR-5r) used for the amplification of the segments containing the 16S-23S rDNA ISRs of the three T. asinigenitalis isolates produced three amplicons of approximately 930 to 1,050 bp in length for the three isolates, respectively (data not shown). This may imply that T. asinigenitalis possesses at least three ISR units of different lengths. Subsequently, nine purified and cloned fragments, containing the ISRs, were subjected to TA cloning and sequencing. The sequences corresponding to the PCR primers (ISR-Tef/-5r) were excluded from the sequence data and further analysis in the present study. The sequences containing the two 16S-23S rDNA ISRs from T. equigenitalis NCTC11184T (AB113653 and AB113656) were also compared. The genetic relatedness of the ISRs is shown in Figure 1.


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)

A phylogenetic tree constructed based on the nucleotide sequence information of the ISRs, by using the UPGMA method. Values, 0.1, in the figure represent evolutionary distances.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 1: A phylogenetic tree constructed based on the nucleotide sequence information of the ISRs, by using the UPGMA method. Values, 0.1, in the figure represent evolutionary distances.
Mentions: The PCR primer pair (ISR-Tef and ISR-5r) used for the amplification of the segments containing the 16S-23S rDNA ISRs of the three T. asinigenitalis isolates produced three amplicons of approximately 930 to 1,050 bp in length for the three isolates, respectively (data not shown). This may imply that T. asinigenitalis possesses at least three ISR units of different lengths. Subsequently, nine purified and cloned fragments, containing the ISRs, were subjected to TA cloning and sequencing. The sequences corresponding to the PCR primers (ISR-Tef/-5r) were excluded from the sequence data and further analysis in the present study. The sequences containing the two 16S-23S rDNA ISRs from T. equigenitalis NCTC11184T (AB113653 and AB113656) were also compared. The genetic relatedness of the ISRs is shown in Figure 1.

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.