Journal of Microbiology

NOTE] Complete Sequence and Organization of the Sphingobium chungbukense DJ77 pSY2 Plasmid: Sun-Mi Yeon , Young-Chang Kim; J. Microbiol. 2011;49(4):684-688. Published online September 2, 2011; DOI: https://doi.org/10.1007/s12275-011-1262-3

Abstract: Sphingobium chungbukense DJ77 is capable of metabolizing priority chemicals of human health concern such as polycyclic aromatic hydrocarbons (PAHs), extracellular polysaccharide (EPS), and antibiotics. Here, we report the complete DNA and genetic organization of the plasmid pSY2 from strain DJ77. A DNA sequence analysis revealed that pSY2 comprises 18,779 bp encoding 22 open reading frames (ORFs) with 59.5% G+C content. The ORFs on pSY2 were classified into DNA replication, conjugative function, transposition, plasmid stability/partition, and other functional groups (transport, fatty acid biosynthesis, stress, and growth rate regulation). Three ORFs on pSY2 were hypothetical proteins.

Characterization of Plasmid pSY3 in Sphingobium chungbukense DJ77: Sun-Mi Yeon , Young-Chang Kim; J. Microbiol. 2009;47(6):796-800. Published online February 4, 2010; DOI: https://doi.org/10.1007/s12275-009-0329-x

Abstract: This study determined the complete nucleotide sequence of the plasmid pSY3 from Sphingobium chungbukense DJ77. It was 35,735 bp long with a G+C content of 61.9%. Forty open reading frames (ORFs) were found. We predicted these ORFs would encode proteins associated with plasmid replication, conjugative transfer, transposition of genes, plasmid stability/partition, hypothetical protein, and some other functions. Genes for biodegradation were not found. No other plasmid homologous to pSY3 in the overall nucleotide sequence or gene organization could be found in the NCBI database.

Organization of Three rRNA (rrn) Operons from Sphingobium chungbukense DJ77: Sun-Mi Yeon , Beom-Soon Choi , Young-Chang Kim; J. Microbiol. 2008;46(6):697-703. Published online December 24, 2008; DOI: https://doi.org/10.1007/s12275-008-0193-0

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.

DNA Sequence of the phnN Gene for Benzaldehyde Dehydrogenase form Pseudomonas sp. DJ77 and Its Substrate Preference: Seong-Jae Kim , Soonyoung Hwang , Young-Chang Kim; J. Microbiol. 1999;37(4):224-228.

Abstract: Benzaldehyle dehydrogenase (BZDH), an enzyme involved in the degradation of toluene and xylenes, is encoded by the phnN gene of Pseudomonas sp. strain DJ77. We determined the nucleotide sequence of a DNA fragment of 1,803 base pairs which included the phnN gene. The fragment contained an open reading frame of 1,506 base pairs to accommodate th 55 kDa sized enzyme encoding BZDH. The enzyme efficiently oxidized benzaldehyde, salicylaldehyde, m-tolualdehyde and ps-tolualdehyde.

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