Abstract
The nucleotide sequences of all three rRNA operons (rrnA, rrnB, and rrnC) of Sphingobium chungbukense DJ77 were determined. The three rrn operons have the same gene order (16S rRNA-tRNAIle-tRNAAla-23S rRNA-5S rRNA-tRNAfMet). The nucleotide sequences were identical over a 5,468 bp region spanning the 16S rRNA gene to the 5S rRNA gene. Variability was observed in the 5S rRNA-tRNAfMet spacer sequence of rrnB. The tRNAfMet gene sequences were identical except for two bases (T5794 and A5871 in rrnB, T5942 and A5956 in rrnA, but C5942 and G5956 in rrnC). Comparative sequence analyses of ribosomal RNA operons from DJ77 with those of the class Alphaproteobacteria, to which the genus Sphingobium belongs, reveal close evolutionary relationships with other members of the order Sphingomonadales.
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Arnvig, K.B., S. Pennell, B. Gopal, and M.J. Colston. 2004. A high-affinity interaction between NusA and the rrn nut site in Mycobacterium tuberculosis. Proc. Natl. Acad. Sci. USA 101, 8325–8330.
Burenjargal, M., Y.S. Lee, J.M. Yoo, Y.C. Kim, Y.M. Lee, S. Oh, Y.P. Yun, J.T. Hong, Y.B. Chung, D.C. Moon, and H.S. Yoo. 2007. Endogenous sphingolipid metabolites related to the growth in Sphingomonas chungbukensis. Arch. Pharm. Res. 30, 317–322.
Chenna, R., H. Sugawara, T. Koike, R. Lopez, T.J. Gibson, D.G. Higgins, and J.D. Thompson. 2003. Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res. 31, 3497–3500.
Goldberg, S.M., J. Johnson, D. Busam, T. Feldblyum, S. Ferriera, R. Friedman, A. Halpern, H. Khouri, S.A. Kravitz, F.M. Lauro, K. Li, Y.H. Rogers, R. Strausberg, G. Sutton, L. Tallon, T. Thomas, E. Venter, M. Frazier, and J.C. Venter. 2006. A Sanger/pyrosequencing hybrid approach for the generation of high-quality draft assemblies of marine microbial genomes. Proc. Natl. Acad. Sci. USA 103, 11240–11245.
Kim, S.J., J. Chun, K.S. Bae, and Y.C. Kim. 2000. Polyphasic assignments of an aromatic-degrading Pseudomonas sp., strain DJ77, in the genus Sphingomonas as Sphingomonas chungbukensis sp. nov. Int. J. Syst. Evol. Microbiol. 50, 1641–1647.
Koumi, P., H.E. Green, S. Hartley, D. Jordan, S. Lahec, R.J. Livett, K.W. Tsang, and D.M. Ward. 2004. Evaluation and validation of the ABI 3700, ABI 3100, and the MegaBACE 1000 capillary array electrophoresis instruments for use with short tandem repeat microsatellite typing in a forensic environment. Electrophoresis 25, 2227–2241.
Kwon, H.R. and Y.C. Kim. 2007. Nucleotide sequence and secondary structure of 5S rRNA from Sphingobium chungbukense DJ77. J. Microbiol. 45, 79–82.
Laslett, D. and B. Canback. 2004. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acid Res. 32, 11–16.
Lee, K.Y., H.R. Kown, W.H. Lee, and Y.C. Kim. 2005. Nucleotide sequence and secondary structure of 16S rRNA from Sphingomonas chungbukensis DJ77. Kor. J. Microbiol. 41, 125–129.
Morgan, E.A. 1986. Antitermination mechanisms in rRNA operons of Escherichia coil. J. Bacteriol. 168, 1–5.
Pal, R., S. Bala, M. Dadhwal, M. Kumar, G. Dhingra, O. Prakash, S.R. Prabagaran, S. Shivaji, J. Cullum, C. Holliger, and R. Lal. 2005. Hexachlorocyclohexane-degrading bacterial strains Sphingomonas paucimobilis B90A, UT26 and Sp+, having similar lin genes, represent three distinct species, Sphingobium indicum sp. nov., Sphingobium japonicum sp. nov. and Sphingobium francense sp. nov., and reclassification of [Sphingomonas] chungbukensis as Sphingobium chungbukense comb. nov. Int. J. Syst. Evol. Microbiol. 55, 1965–1972.
Sambrook, J., E.F. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual. 2nd ed. Cold Spring Harbor Laboratory, N.Y., USA.
Seo, J.S., H. Chong, H.S. Park, K.O. Yoon, C. Jung, J.J. Kim, J.H. Hong, H. Kim, J.H. Kim, J.I. Kil, C.J. Park, H.M. Oh, J.S. Lee, S.J. Jin, H.W. Um, H.J. Lee, S.J. Oh, J.Y. Kim, H.L. Kang, S.Y. Lee, K.J. Lee, and H.S. Kang. 2005. The genome sequence of the ethanologenic bacterium Zymomonas mobilis ZM4. Nat. Biotechnol. 23, 63–68.
Shin, H.J., S.J. Kim, and Y.C. Kim. 1997. Sequence analysis of the phnD gene encoding 2-hydroxymuconic semialdehyde hydrolase in Pseudomonas sp. strain DJ77. Biochem. Biophys. Res. Commun. 232, 288–291.
Silhavy, T.J., M.L. Berman, and L.W. Enquist. 1984. Drop dialysis of DNA preparations, p. 182. Experiments with Gene Fusions. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y., USA.
Song, J.Y., J.Y. Kwon, J.D. Choi, Y.C. Kim, and M.S. Shin. 2006. Pasting properties of non-waxy rice starch-hydrocolloid mixtures. Starch/Stärke 58, 223–230.
Zuker, M. 2003. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acid Res. 31, 3406–3415.
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Yeon, SM., Choi, BS. & Kim, YC. Organization of three rRNA (rrn) operons from Sphingobium chungbukense DJ77. J Microbiol. 46, 697–703 (2008). https://doi.org/10.1007/s12275-008-0193-0
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DOI: https://doi.org/10.1007/s12275-008-0193-0