• 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.

• Korean Journal of Microbiology
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• v.48 no.4
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• pp.319-324
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• 2012

In this study, we investigated molecular divergences and phylogenetic characteristics of the 16S ribosomal RNA (rRNA) and RNA polymerase beta subunit (rpoB) gene sequences from the order Oscillatoriales (Cyanobacteria). The rpoB of Oscillatoriales showed higher genetic divergence when compared with those of 16S rRNA (p-distance: rpoB=0.270, 16S=0.109), and these differences were statistically significant (Student t-test, p<0.001). Phylogenetic trees of 16S rRNA and rpoB were generally compatible; however, rpoB tree clearly separated the compared Oscillatoriales taxa, with higher phylogenetic resolution. In addition, parsimony analyses showed that rpoB gene evolved 2.40-fold faster than 16S rRNA. These results suggest that the rpoB is a useful gene for the molecular phylogenetics and species discrimination in the order Oscillatoriales.

• 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.26 no.2
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• pp.106-112
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• 1988

We have examined the structures and cellular distributions of the SV40 late RNAs present in monkey cells at late times after infection. One particular RNA species, spliced at residue 373(373-RNA), was found to be as abundant as the major late 16S RNAs. This result was unexpected since previous reports showed that the molecular ratio of the 373-spliced 19S RNA to 16S RNA is approximately 0.1 among either cytoplasmic polyadenylated or polysomal viral RNAs. Both sedimentation and electrophoretic analysis indicated that the 373-RNA was approximately 16S to 19S in size. Therefore, it was not a splicing intermediate or the product of premature termination of transcription within the late leader region. Whereas most SV40 late 16S RNA is polyadenylated and located in the cytoplasm, the majority of 373-RNA was found to lack poly A, and be located in the nucleus.

• Journal of the Korean Chemical Society
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• v.46 no.2
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• pp.157-163
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• 2002

To identify RNA motifs interacting with $tRNA^{Val}$, a SELEX(Systematic Evolution of Ligands by Exponential Enrichment) was applied. Random DNA library which contains a region of ran-domized 48-mer oligonucleotide flanked by conserved sequ ence primers was transcribed into RNA pool using T7 RNA polymerase and RNA aptamers were selected with $tRNA^{Val}$ -immobilized affinity column through 14 rounds of SELEX. Some of the resulting aptamers contained a consensus sequence similar to the sequence in the loop regions of three rRNAs; C43GAAC47 sequence of 5S rRNA, G1491AAGU1495, G1379UUCC1383 sequence of 16S rRNA and C1064UUAG1068, G2110UGUA2114, C2480GACGG2485, A2600CAGU2604 sequence of 23S rRNA. These results suggest that $tRNA^{Val}$ can interact with 5S rRNA, 16S rRNA and 23S rRNA with variety in ribosome.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.36 no.3
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• pp.239-246
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• 2003

We have examined the 16S-23S rRNA intergenic spacer region (ISR) of Vibrio vulnificus KCTC 2959. ISRs were amplified by primers complementary to conserved regions of 16S and 23S rRNA genes. ISR amplicons were cloned and sequenced. Analysis of the ISR sequences showed that V. vulnificus KCTC 2959 contains five types of polymorphic ISRs. Size of ISRs ranged from 424 to 741 bp in length and the number of tRNA genes ranged from one to four. The ISRs were designated as ISR-E $(tRNA^{Glu}),\;ISR-IA\;(tRNA^{Ile}-tRNA^{Ala})$, ISR-EKV $(tRNA^{Glu}-tRNA^{Lys}-tRNA^{Val})$, ISR-IAV $(tRNA^{Ile}-tRNA^{Ala}-tRNA^{val})$ and ISR-EKAV $(tRNA^{Glu}-tRNA^{Lys}-tRNA^{Ala}-tRNA^{Val})$ based on their tRNA genes. Multiple alignment of representative sequences from different Vibrio species revealed several domains of high sequence variability. We used the sequences of variable domains to design species-specific primer for detection PCR. Specificity of the primers was examined using genomic DNA prepared from 18 different Vibrio species. The results showed that the PCR using primers designed in this study can be used to detect V. vulnificus from other Vibrio species.

• Korean Journal of Microbiology
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• v.46 no.3
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• pp.296-302
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• 2010

Microcystis (Cyanobacteria, Chroococcales) is one of the green tide-causing organisms in freshwaters, and some species produce microcystin that is hepatotoxin. In the aspects of freshwater quality controls and health concerns, therefore it is necessary to manage the harmful organisms. In the present study, RNA polymerase beta subunit (rpoB) gene sequences of Microcystis were determined and characterized in order to use a potential marker for the molecular detections of the species. Microcystis rpoB showed high divergences of DNA similarity and genetic distances when compared with those of 16S rRNA, and the molecular differences were statistically significant (Student t-test, p<0.05). Parsimony analyses showed the rpoB gene evolves more than 2-fold faster than 16S rRNA. In addition, phylogeny of the rpoB gene separated each M. aeruginosa strain more clearly compared with a 16S rRNA tree. This study found that the order Chroococcales, including Microcystis, has approximately two rRNA operons and single copy of the rpoB gene in their chromosomes. These results suggest that the rpoB gene is a useful marker for the molecular phylogenetics and the detection of Microcystis.

• Journal of Life Science
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• v.13 no.6
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• pp.856-864
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• 2003

The 16S rRNA gene is the most common gene in the phylogenetic analysis of procaryotes. However very high conservative of 16S rRNA has limitation in the discrimination of highly related organisms, hence other molecule was applied in this study and the result was compared with that of 16S rRNA. Three COGs (Clusters of Orthologous of protein) were only detected in 42 procaryotes ; transcription elongation facto. (COG0195), bacterial DNA primase (COG0358) and uridylate kinase (COG0528). Uridylate kinase gene was selected because of the similarity and one single copy number in each genome. Bacteria, belong to same genus, and Archaebacteria were same position with high bootstrap value in phylogenetic tree like the tree of 16S rRNA. However, alpha and epsilon Proteobcteria showed different position and Spirochaetales of Eubarteria was grouped together with Archaebacteria unlike the result of 16S rRNA. Uridylate kinase may compensate the problem of very high conservative of 16S rRNA gene and it would help to access more accurate discrimination and phylogenetic analysis of bacteria.

• 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.

• Environmental Engineering Research
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• v.19 no.4
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• pp.317-329
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• 2014

The diversity of cyanobacteria in Sri Lanka was studied in different water reservoirs, paddy fields, brackish water and tsunami affected areas using light microcopy, 16S rRNA sequences, followed by phylogenetic analysis. Based on light microscopy, 24 genera were identified from environmental samples belonging to the orders Chroococcales, Oscillatoriales, Pleurocapsales and Nostocales. In cultures, 33 genera were identified from all five cyanobacterial orders, including Stigonematales. Based on 16S rRNA gene sequences and their morphology, two isolates were identified up to species level, 72 to genus level, one isolate up to family and 11 up to order level. Twelve isolates couldn't be assigned to any taxonomic level. The results of 16S rRNA gene sequences along with the phylogenetic analysis indicated that some cyanobacterial isolates could be accommodated to genus or order level. The 16S rRNA sequence analysis data in this study confirmed that order Nostocales and order Pleurocapsales cyanobacteria are monophyletic while orders Chroococcales, Oscillatoriales and Stigonematales cyanobacteria are polyphyletic. Polyphasic approach including the combination of light microscopy, cultures and the analysis of 16S rRNA gene sequences provide a promising approach to ascertain the diversity of cyanobacteria in different habitats.