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Nucleotide Sequence and Secondary Structure of 16S rRNA from Sphingomonas chungbukensis DJ77  

Lee Kwan-Young (Life Sciences, Chungbuk National University)
Kwon Hae-Ryong (Life Sciences, Chungbuk National University)
Lee Won-Ho (Life Sciences, Chungbuk National University)
Kim Young-Chang (Biotechnology Research Institute, Chungbuk National University)
Publication Information
Korean Journal of Microbiology / v.41, no.2, 2005 , pp. 125-128 More about this Journal
Abstract
A 16S ribosomal RNA gene from S. chungbukensis DJ77 has been sequenced. This sequence had a length of 1,502 bp and was extended for 29 bp at 5' and for 37 bp at 3' from the partial sequence (1,435 bp) registered in 2000 year. Besides, 1 bp was newly added near to the 3' end. We made the secondary structure of the 16S rRNA based on E. coli model and found four specific regions. We found constant and variable regions in genus Sphingomonas as the result of multiple alignment of 16S rRNA gene sequences from Sphingomonas spp. and S. chungbukensis DJ77. We found a stem loop structure in S. chungbukensis DJ77, which was only discovered in C. jejuni to date. It showed the structural agreement despite the difference of the sequences from the both organisms. Finally, S. chungbukensis DJ77 belonged to cluster II (Sphingobium) group, after the classification using phylogenetic analysis and nucleotide signature analysis.
Keywords
16S rRNA; secondary structure; Sphingomonas chungbukensis;
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