• Bulletin of the Korean Chemical Society
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• v.20 no.11
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• pp.1335-1339
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• 1999

The function of 5S rRNA, a constituent of a large subunit of ribosome, is not clearly known yet. To identify RNA motifs interacting with 5S rRNA, and thereby to get an insight into the function of 5S rRNA in the ribosome, a SELEX (Systematic Evolution of Ligands by Exponential Enrichment) experiment was performed. RNA molecules binding to Escherichia coli 5S rRNA were selected from a 48-mer random sequence library through 12 rounds of selection, cloned, and sequenced. Two groups of the selected RNA molecules had the consensus sequences GCGG and GUGAAA, respectively, which are present in the segment, G688 through A696, of E. coli 16S rRNA. The gel mobility shift assay showed that 5S rRNA interacted with the 16S rRNA fragment containing the GCGG and GUGAAA sequences. The enzymatic protection experiment shows that the A29CCUGA34 and G51AAGUG56 sequences of 5S rRNA and the C680AGG683 and G688CGG691 sequences of the 16S rRNA fragment are involved in the interaction between the two RNA molecules. On the basis of this observation, we suggest that 5S rRNA and 16S rRNA play a role for the association of two ribosomal subunits.

• Korean Journal of Microbiology
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• v.45 no.4
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• pp.430-434
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• 2009

Bacterial 16S rRNA gene sequences have been widely used for the studies on molecular phylogeny, evolutional history, and molecular detections. Bacterial genomes have multiple rRNA operons, of which gene sequences sometimes are variable. In the present study, heterogeneity of the Vibrio 16S rRNA gene sequences were investigated. Vibrio 16S rRNA sequences were obtained from GenBank databases, considering the completion of gene annotation of Vibrio genome sequences. These included V. cholerae, V. harveyi, V. parahaemolyticus, V. splendidus, and V. vulnificus. Chromosome 1 of the studied Vibrio had 7~10 copies of the 16S rRNA gene, and their intragenomic variations were less than 0.9% dissimilarity (more than 99.1% DNA similarity). Chromosome 2 had none or single 16S rRNA gene. Intragenomic 16S rRNA genotypes were detected at least 5 types (V. vulnificus #CMCP6) to 8 types (V. parahaemolyticus #RIMD 2210633, V. harveyi #ATCC BAA-1116). These suggest that Vibrio has high heterogeneity of the 16S rRNA gene sequences.

• Journal of Microbiology
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• v.33 no.2
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• pp.136-141
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• 1995

From a cluster of structural rRNA genes which has previsouly been cloned (Hwang and Kim, in submission; J. Microbiol. Biotechnol.), a 1.0-kb Eco RI fragment of DNA which shows significant homology to the 25S and rRNA s of Tricholoma matsutake was used for sequence analysis. Nucleotide sequence was bidirectionally determined using delection series of the DNA fragment. Comparing the resultant 1016-base sequence with sequences in the database, both the 3'end of 25S-rRNA gene and 5S rRNA gene were searched. The 5S rRNA gene is 118-bp in length and is located 158-bp downstream of 3'end of the 25S rRNA gene. IGSI and IGS2 (partial) sequences are also contained in the fragment. Multiple alignment of the 5S rRNA sequences was carried out with 5S rRNA sequences from some members of the subdivision Basidiomycotina obtained from the database. Polygenetic analysis with distance matrix established by Kimura's 2-parameter method and phylogenetic tree by UPGMA method proposed that T. matsutake is closely related to efibulobasidium allbescens. Secondary structure of 5S rRNA was also hypothesized to show similar topology with its generally accepted eukaryotic counterpart.

• Animal cells and systems
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• v.4 no.1
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• pp.77-85
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• 2000

This study has demonstrated the molecular variation of 5S rRNA genes in 15 Allium subgenus Rhizirideum and 1 Allium subg. Allium. For cloning of the 5S rRNA genes, PCR products were obtained from amplification with oligonucleotide primers which were derived from the conserved coding region of 5S rRNA genes. These amplified PCR products were cloned and identified by FISH and sequence analysis. The 5S rRNA loci were primarily located on chromosomes 5 and/or 7 in diploid species and various chromosomes in alloploid species. The size of the coding region of 5S rRNA genes was 120 bp in all the species and the sequences were highly conserved within Allium species. The sizes of nontranscribed spacer (NTS) region were varied from 194 bp (A. dektiude-fustykisum, 2n=16) to 483 bp (A. sativum). Two kinds of NTS regions were observed in A. victorialis var. platyphyllum a diploid, A. wakegi an amphihaploid, A. sacculiferum, A. grayi, A. deltoide-fistulosum and A. wenescens all allotetraploids, while most diploid species showed only one NTS region. The species containing two components of NTS region were grouped with different diploid species in a phylogenetic tree analysis using the sequences of 5S rRNA genes and adjacent non-coding regions.

• Microbiology and Biotechnology Letters
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• v.32 no.3
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• pp.218-223
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• 2004

Myxobacteria are Gram-negative soil bacteria known to be a rich source of potentially useful secondary metabolites. We have isolated 204 strains of bacteriolytic myxobacteria from soil samples collected in Korea and determined their 16S rRNA sequences. Sequence analysis of the partially determined 16S rRNA sequences has suggested that 132 isolates (65% of total isolates) belong to the genus Myxococcus and 59 isolates (29% of total isolates) belong to the genus Corallococcus. Meanwhile, 4 isolates appear to be Archangium spp. and the other 4 isolates appear to be Stigmatella spp. Genera of the remained 5 isolates have not been identified because their 16S rRNA sequences are distantly related to those of known myxobacteria.

• Korean Journal of Microbiology
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• v.32 no.3
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• pp.177-181
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• 1994

The sequences of the cytoplasmic 5S rRNAs(EMBL accession number X73589 and X73890) from two polupores, Ganoderma applanatum and Schizopora paradoxa, were determined by the direct chemical method for sequencing RNA and compared to the sequences of 9 reported mushrooms. 5S rRNAs of Ganoderma applanatum and Schizopora paradoxa consisted of 118 bases and fit the secondary structure model of the 5S rRNAs of basidiomycetes proposed by Huysmans et al. Based on Kimura’s K_nuc values, the closest fungus to Ganoderma applanatum was Ceratobasidium cornigerum and the one to Schizopora paradoxa was Bjerkandera adusta. When the secondary structures of 5S rRNAs of 11 mushrooms were compared the base substitution occurred at helix regions more than at loop regions. When a phylogenetic tree was constructed using the Neighbor program of the PHYLIP package, it partially discriminated and separated the mushrooms of the Hymenomycetes by the order.

• Journal of the Korean Chemical Society
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• v.42 no.2
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• pp.209-213
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• 1998

The higher order structure of Pseudomonas alcaligenes 5S rRNA has been investigated by using ($\eta^{6}$-mesitylene) manganese (Ⅰ) tricarbonyl hexafluorophosphate[MTH-Mn (Ⅰ)], dimethylpyrocarbonate, potassium permanganate as chemical probes. The sequences cleaved strongly by MTH-Mn (Ⅰ) on the tertiary structure of the 5S rRNA are $G_{12}AUGG_{16}$ of loop a, $G_{51}AAGUGAAGC_{60}$ of the region b-C, $U_{65}-AGCG_{69}$. of the region B-a, and $G_{72}AUGG_{76}$ of loop d. Based on such cleavage patterns of 5S rRNA by MTH-Mn(Ⅰ) and other chemical probes, we presume that the sequences strongly cleaved form pocket-like structure as in the the corner of L structure of $tRNA^{Phe}$. We also presume that the region b-C and loop d together play a role of hinge in forming the pocket-like structure in the 5S rRNA.

• BMB Reports
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• v.29 no.2
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• pp.133-136
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• 1996

The affinity cleavage reagent Methidiumpropyl-EDTA-Iron(II) is applied to the structural analysis of 5S rRNA. Analysis of cleavage sites induced by MPE-Fe(II) on 5S rRNA shows that MPE intercalates easily between the unstable base pairs or into the bulges, thereby it strongly cuts the nucleosides nearby. The stable helical stems A, B, D and E as well as loop d are weakly cut. Most of the single-stranded loops are not cleaved. Based on the cleavage pattern of the 5S rRNA by MPE-Fe(II) and RNase V1, we suggest that MPE-Fe(II) may be used as a potential chemical probe in searching for the unstable helical regions of RNA, and for the sequences that appear to be involved in folding and distorting 5S rRNA.

• Journal of the Korea Academia-Industrial cooperation Society
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• v.18 no.1
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• pp.141-147
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• 2017

In this study, a meta-analysis of fecal bacteria in dogs was conducted using 16S rRNA gene sequences that have been recovered from cloning and Sanger sequencing. For this meta-analysis, we retrieved all 16S rRNA gene sequences recovered from fecal bacteria in dogs in the RDP database (Release 11, Update 3). A total of 420 sequences were identified from the RDP database, 42 of which were also recovered from cultured isolates. The 420 sequences were assigned to five phyla, of which Firmicutes was the most predominant phylum, accounting for 55.2% of all 420 sequences. Bacteroidetes was the second most predominant phylum, accounting for 32.1% of the 420 sequences, followed by Actinobacteria (6.4%), Fusobacteria (3.8%), and Proteobacteria (2.4%). The genus Bacteroides within Bacteroidetes was the largest, representing 30.0% of all 420 sequences, while the putative genus Clostridium XI within Firmicutes was the second largest, representing 27.4% of all 420 sequences. A total of 82 operational taxonomic units (OTUs) that are putative species were identified from the retrieved sequences. The results of this study will improve understanding of the diversity of fecal bacteria in dogs and guide future studies on the health and well-being of dogs.

• Korean Journal of Microbiology
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• v.41 no.2
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• pp.125-128
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• 2005

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.