• Journal of Microbiology
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• v.45 no.6
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• pp.534-540
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• 2007

The Streptomyces coelicolor A3(2) genome contains six operons (rrnA to F) for ribosomal RNA synthesis. Transcription from rrnD occurs from four promoters (p1 to p4). We found that transcripts from the p1 and p3 promoters were most abundant in vivo in the early exponential phase. However, at later phases of exponential and stationary growth, transcripts from the p1 promoter decreased drastically, with the p3 and p4 transcripts constituting the major forms. Partially purified RNA polymerase supported transcription from the p3 and p4 promoters, whereas pure reconstituted RNA polymerase with core enzyme (E) and the major vegetative sigma factor ${\sigma}^{HrdB}$ ($E{\cdot}{\sigma}^{HrdB}$) did not. In order to assess any potential requirement for additional factor(s) that allow transcription from the p3 and p4 promoters, we fractionated a partially purified RNA polymerase preparation by denaturing gel filtration chromatography. We found that transcription from the p3 and p4 promoters required factor(s) of about 30-35 kDa in addition to RNAP holoenzyme ($E{\cdot}{\sigma}^{HrdB}$). Therefore, transcription from the p3 and p4 promoters, which contain a consensus -10 region but no -35 for ${\sigma}^{HrdB}$ recognition, are likely to be regulated by transcription factor(s) that modulate RNA polymerase holoenzyme activity in S. coelicolor.

• Korean Journal of Microbiology
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• v.30 no.6
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• pp.472-478
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• 1992

Synthesis of the pol gene products of HTLV-I requires rihosomes to shift frame twice in - I direction while translating genome-size mRNA. We havc made a lI1utagcni/cd RNA in which the gag and pro genes are aligned to allow synthe,.is of a largcr amount of the Gag-Pro-Pol polyproteins by a single frameshifting. Using this mutant, wc could examine the questions whether the predicted RNA secondary or tertiary structure downstream of the shift site is operative as a determinant for - I frameshifting. Deletion analysis showed that the stem-loop structure is essential for efficient frameshifting in the pro-pol overlap, but formation of a pseudoknot is less important.

• Animal cells and systems
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• v.12 no.3
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• pp.143-148
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• 2008

Heterogeneous nuclear ribonucleoprotein E1(hnRNP E1) is one of the primary pre-mRNA binding proteins in human cells. It consists of 356 amino acid residues and harbors three hnRNP K homology(KH) domains that mediate RNA-binding. The hnRNP E1 protein was shown to play important roles in mRNA stabilization and translational control. In order to enhance our understanding of the cellular functions of hnRNP E1, we searched for interacting proteins through a yeast two-hybrid screening while using HeLa cDNA library as target. One of the cDNA clones was found to be human ribosomal protein L18a cDNA(GenBank accession number BC071920). We demonstrated in this study that human ribosomal protein L18a, a constituent of ribosomal protein large subunit, interacts specifically with hnRNP E1 in the yeast two-hybrid system. Such an interaction was observed for the first time in this study, and was also verified by biochemical assay.

• Journal of Life Science
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• v.8 no.1
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• pp.32-39
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• 1998

The length and G/C concent of regions of an aphid rDNA unit that spans 13,061bo with 59% G/C content. flolowing belowing below are the those results, 5’ETS is 843bp in length with 69% G/C content, 18S is 2,469bp in length with 59% G/C content, ITS I is 229bp in length with 70% G/C content, 5.8S is 160bp in length with 63% G/C content, ITS II is 325bp in length with 70% G/C content, 28S is 4, 147bp in length with 60% G/C content, IGS is 4,888bp in length with 55% G/C content.

• Molecules and Cells
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• v.40 no.6
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• pp.410-417
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• 2017

Estimation of postmortem interval (PMI) is a key issue in the field of forensic pathology. With the availability of quantitative analysis of RNA levels in postmortem tissues, several studies have assessed the postmortem degradation of constitutively expressed RNA species to estimate PMI. However, conventional RNA quantification as well as biochemical and physiological changes employed thus far have limitations related to standardization or normalization. The present study focuses on an interesting feature of the subdomains of certain RNA species, in which they are site-specifically cleaved during apoptotic cell death. We found that the D8 divergent domain of ribosomal RNA (rRNA) bearing cell death-related cleavage sites was rapidly removed during postmortem RNA degradation. In contrast to the fragile domain, the 5' terminal region of 28S rRNA was remarkably stable during the postmortem period. Importantly, the differences in the degradation rates between the two domains in mammalian 28S rRNA were highly proportional to increasing PMI with a significant linear correlation observed in mice as well as human autopsy tissues. In conclusion, we demonstrate that comparison of the degradation rates between domains of a single RNA species provides quantitative information on postmortem degradation states, which can be applied for the estimation of PMI.

• Korean Journal of Veterinary Research
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• v.38 no.4
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• pp.909-917
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• 1998

Six different sequences types(A through E and H) and a subtype(Bl) of the small subunit ribosomal RNA(SSUrRNA) gene were found in bovine Theileria isolates from different areas of Korea and Japan. The sequences were aligned and three hypervariable regions were observed in the nucleotide position ranges 212~231, 261~270 and 632~690. Five of the Theileria isolates yielded sequence type A; these were the field isolates KCB, KCN, and KCJ, and the laboratory stock KLS, all from Korea, and a single isolate from Japan (JHS). This sequence type is identical to the SSUrRNA gene sequence listed for Theileria buffeli (GenBank Accession No. Z15106) from Marula, Kenya. The Korean field isolate KKB yielded only a single sequence type (B), but multiple sequence types were found in some isolates. For example, KCB and JHS isolates yielded both types A and B ; isolate KKW showed types B and H; isolate KCN showed types A, C, and D ; and isolate KCJ showed types A, B, E, and a subtype B1. Finding of the multiple sequences SSUrRNA gene sequences suggests that bovine Theileria isolates from both Korea and Japan may consist of mixed populations.

• Environmental Engineering Research
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• v.14 no.1
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• pp.3-9
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• 2009

Microorganisms play an important role in the geochemical cycles, industry, environmental cleanup, and biotechnology among other fields. Given the high microbial diversity, identification of the microorganism is essential in understanding and managing the processes. One of the most popular and powerful method for microbial identification is comparative 16S rRNA gene analysis. Due to the highly conserved nature of this essential gene, sequencing and later comparison of it against known rRNA databases can provide assignment of the bacteria into the taxonomy, and the identity of its closest relatives. Isolation and sequencing of 16S rRNA genes directly from natural environments (either from DNA or RNA) can also be used to study the structure of the whole microbial community. Nowadays, novel sequencing technologies with massive outputs are giving researchers worldwide the chance to study the microbial world with a depth that was previously too expensive to achieve. In this article we describe commonly used research approaches for the study of individual microorganisms and microbial communities using the tools provided by Ribosomal Database Project website.

• The Korean Journal of Mycology
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• v.23 no.4 s.75
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• pp.318-324
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• 1995

The evolutionary relationships of the genus Trichoderma and related taxa were assessed using partial sequencing of 18S ribosomal RNA. Phylogenetic tree divided into three major groups; 1. Saccharomyces cerevisiae-Geotrichum klebahnii-Alternaria mali group; 2. Neurospora crassa-Aspergillus-Penicillium-Chrysosporium pannorum-Scopulariopsis sp. group; 3. Trichoderma group. The genus Trichoderma seemed to be phylogenetically separated from Saccharomyces cerevisiae, Aspergillus and Penicillium groups, and have passed through it's own evolutionary pathway.

• Journal of Life Science
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• v.25 no.9
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• pp.1007-1013
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• 2015

A COG (Cluster of Orthologous Groups of proteins) algorithm was applied to detect conserved genes in 711 prokaryotes. Only COG0080 (ribosomal protein L11) was common among all the 711 prokaryotes analyzed and 58 COGs were common in more than 700 prokaryotes. Nine COGs among 58, including COG0197 (endonuclease III) and COG0088 (ribosomal protein L4), were conserved in a form of one gene per one organism. COG0008 represented 1356 genes in 709 of the prokaryotes and this was the highest number of genes among 58 COGs. Twenty-two COGs were conserved in more than 708 prokaryotes. Of these, two were transcription related, four were tRNA synthetases, eight were large ribosomal subunits, seven were small ribosomal subunits, and one was translation elongation factor. Among 58 conserved COGs in more than 700 prokaryotes, 50 (86.2%) were translation related, and four (6.9%) were transcription related, pointing to the importance of protein-synthesis in prokaryotes. Among these 58 COGs, the most conserved COG was COG0060 (isoleucyl tRNA synthetase), and the least conserved was COG0143 (methionyl tRNA synthetase). Archaea and eubacteria were discriminated in the genomic analysis by the average distance and variation in distance of common COGs. The identification of these conserved genes could be useful in basic and applied research, such as antibiotic development and cancer therapeutics.

• Korean Journal of Environmental Biology
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• v.32 no.4
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• pp.382-388
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• 2014

Shortfin eel (Anguilla bicolor pacifica) is a species of commercial importance and its production is greatly affected due to the infection by Heterosporis anguillarum. In this study, we evaluated the effect of H. anguillarum infection on the growth of Shortfin eel. A disease that trunk muscle of cultured shortfin eel, Anguilla bicolor pacifica, were irregular and resulted in death, breakout of the commercial eel culture farm. We observed that the trunk muscle of infected eels were irregular and represented white or yellowish externally. Histopathologically, a great numbers of large or small spores and sporophorocysts were also observed in degenerated muscle layer. The cloning of specific gene of H. anguillarum, encoding small subunit ribosomal RNA (SSU-rRNA) was amplified by the polymerase chain reaction(PCR) from the muscle lesion of diseased eel. The size of clone gene is well matched with the size of small subunit ribosomal RNA of H. anguillarum and thus confirming the infection by H. anguillarum.