• Korean Journal of Microbiology
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• v.44 no.2
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• pp.98-104
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• 2008

We constructed the null mutants of fission yeast Schizosaccharomyces pombe rsml gene that is thought to be involved in mRNA export. Though rsm1 gene is not essential for growth, the null mutant strain constructed by replacing the rsm1-coding region with an $kan^{r}$ gene showed growth retardation and mRNA export defects compared to wild type strain. We constructed double mutants which harbor rsm1 null allele and mutant allele of genes involved in mRNA export. The mex67 or npp106 null allele, when combined with rsm1 null allele, showed an additive effect on growth retardation and mRNA export defects. On the other hand, the thp1 null allele restored the defects of growth and mRNA export of rsm1 null mutant. These results suggest that rsm1 plays a role in mRNA export from the nucleus.

• Korean Journal of Microbiology
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• v.46 no.4
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• pp.401-404
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• 2010

Tho1 is a RNA-binding protein that assembles co-transcriptionally onto the nascent mRNA and is thought to be involved in mRNP biogenesis and mature mRNA export to cytoplasm in budding yeast. In fission yeast Schizosaccharomyces pombe, a homologue of THO1 (spTho1) was identified based on sequence alignment. A deletion mutant in a diploid strain was constructed by replacing one of spTho1-coding region with an ura4+ gene using one-step gene disruption method. Tetrad analysis showed that the spTho1 was not essential for growth. The spTho1 mutant did not show any defects of bulk mRNA export. However, over-expression of spTho1 from strong nmt1 promoter caused the growth defects and accumulation of poly(A)$^+$ RNA in the nucleus. These results suggest that spTho1 is involved in mRNA export from the nucleus to cytoplasm though it is not essential.

• Genomics & Informatics
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• v.12 no.2
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• pp.71-75
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• 2014

The tRNA structure contains conserved modifications that are responsible for its stability and are involved in the initiation and accuracy of the translation process. tRNA modification enzymes are prevalent in bacteria, archaea, and eukaryotes. tRNA Gm18 methyltransferase (TrmH) and tRNA $m^1G37$ methyltransferase (TrmD) are prevalent and essential enzymes in bacterial populations. TrmH involves itself in methylation process at the 2'-OH group of ribose at the 18th position of guanosine (G) in tRNAs. TrmD methylates the G residue next to the anticodon in selected tRNA subsets. Initially, $m^1G37$ modification was reported to take place on three conserved tRNA subsets ($tRNA^{Arg}$, $tRNA^{Leu}$, $tRNA^{Pro}$); later on, few archaea and eukaryotes organisms revealed that other tRNAs also have the $m^1G37$ modification. The present study reveals Gm18, $m^1G37$ modification, and positions of $m^1G$ that take place next to the anticodon in tRNA sequences. We selected extremophile organisms and attempted to retrieve the $m^1G$ and Gm18 modification bases in tRNA sequences. Results showed that the Gm18 modification G residue occurs in all tRNA subsets except three tRNAs ($tRNA^{Met}$, $tRNA^{Pro}$, $tRNA^{Val}$). Whereas the $m^1G37$ modification base G is formed only on $tRNA^{Arg}$, $tRNA^{Leu}$, $tRNA^{Pro}$, and $tRNA^{His}$, the rest of the tRNAs contain adenine (A) next to the anticodon. Thus, we hypothesize that Gm18 modification and $m^1G$ modification occur irrespective of a G residue in tRNAs.

• Bulletin of the Korean Chemical Society
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• v.29 no.6
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• pp.1137-1140
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• 2008

M1 RNA, the catalytic subunit of Escherichia coli RNase P, is an essential ribozyme that processes the 5' leader sequence of tRNA precursors (ptRNAs). Using KS2003, an E. coli strain generating only low levels of M1 RNA, which showed growth defects, we examined whether M1 RNA is involved in polycistronic mRNA processing or degradation. Microarray analysis of total RNA from KS2003 revealed six polycistronic operon mRNAs (acpP-fabF, cysDNC, flgAMN, lepAB, phoPQ, and puuCBE) showing large differences in expression between the adjacent genes in the same mRNA transcript compared with the KS2001 wild type strain. Model substrates spanning an adjacent pair of genes for each polycistronic mRNA were tested for RNase P cleavage in vitro. Five model RNAs (cysNC, flgMN, lepAB, phoPQ, and puuBE) were cleaved by RNase P holoenzyme but not by M1 RNA alone. However, the cleavages occurred at non-ptRNA-like cleavage sites, with much less efficiency than the cleavage of ptRNA. Since cleavage products generated by RNase P from a polycistronic mRNA can have different in vivo stabilities, our results suggest that RNase P cleavage may lead to differential expression of each cistron.

• Microbiology and Biotechnology Letters
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• v.30 no.1
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• pp.68-72
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• 2002

To obtain a yeast mutant with high RNA content and high growth rate, Saccharomyces cerevisiae MTY62 was mutated with ethylmethane sulfonate. Among the selected mutants that were sensitive to the high concentration of KCl, M40-10 strain was finally selected due to its rapid cell growth and high RNA content in the tube and baffled-flask cultures. In the batch culture of M40-10 mutant, the maximum specific growth rate ($\mu_{max}$) of $0.38 h^{-1}$ , RNA concentration of 3210 mg-RNA/1, and RNA content of 183 mg-RNA/g-DCW were obtained, which were 23%, 15%, and 12% increased levels, respectively, compared to those of MTY62 parent strain. The intermittent fed-batch culture of M40-10 strain resulted in the maximum cell concentration of 35.6 g-DCW/1, RNA concentration of 5677 mg/1, and RNA content of 160 mg-RNA/g-DCW. Through the constant fed-batch culture, the maximum cell concentration of 46.4 g-DCW/1, RNA concentration of 6270 mg-RNA/1, and RNA content of 135 mg-RNA/g-DCW were obtained. At the 20 h culture time in the fed-batch cultures of M40-10 strain, the cell and RNA concentrations were increased by 30% and 10%, respectively, over the parent strain MTY62. In addition, it was also found that the accumulated RNA within the mutant cell was not degraded until the end of fed-batch cultivation, indicating that the M40-10 cell is a mutant with weak acidic RNase activity.y.

• Genomics & Informatics
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• v.17 no.1
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• pp.10.1-10.3
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• 2019

To identify miRNA-mRNA interaction pairs associated with binary phenotypes, we propose a hierarchical structural component model for miRNA-mRNA integration (HisCoM-mimi). Information on known mRNA targets provided by TargetScan is used to perform HisCoM-mimi. However, multiple databases can be used to find miRNA-mRNA signatures with known biological information through different algorithms. To take these additional databases into account, we present our advanced application software for HisCoM-mimi for binary phenotypes. The proposed HisCoM-mimi supports both TargetScan and miRTarBase, which provides manually-verified information initially gathered by text-mining the literature. By integrating information from miRTarBase into HisCoM-mimi, a broad range of target information derived from the research literature can be analyzed. Another improvement of the new HisCoM-mimi approach is the inclusion of updated algorithms to provide the lasso and elastic-net penalties for users who want to fit a model with a smaller number of selected miRNAs and mRNAs. We expect that our HisCoM-mimi software will make advanced methods accessible to researchers who want to identify miRNA-mRNA interaction pairs related with binary phenotypes.

• The korean journal of orthodontics
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• v.39 no.4
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• pp.248-256
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• 2009

Objective: The aim of this study was to determine if human PDL cells can produce osteoclastogenic mRNA and examine how compressive stress affects the expression of osteoclastogenic mRNA in human PDL cells. Methods: Human PDL cells were obtained from biscupids extracted for orthodontic treatment. The compressive force was adjusted by increasing the number of cover glasses. PDL cells were subjected to a compressive force of 0.5, 1.0, 2.0, 3.0 or $4.0\;g/cm^2$ for 0.5, 1.5, 6, 24 or 48 hours. Reverse transcription polymerase chain reaction (RT-PCR) analysis was performed to examine levels of M-CSF, IL-$1{\beta}$, RANKL, OPG mRNA expression. Results: Human PDL cells could produce M-CSF mRNA. Human PDL cells under compressive stress showed increased M-CSF, IL-$1{\beta}$ and RANKL mRNAs expression in a force (up to $2\;g/cm^2$) and time-dependent manner. However, OPG mRNA expression was constant regardless of the level and duration of stress. Conclusions: Continuous compressive stress induced the mRNA expression of osteoclastogenic cytokines including M-CSF, RANKL, IL-$1{\beta}$ in PDL cells. Together with an unchanged OPG mRNA level, these results suggest that compressive stress-induced osteoclastogenesis in vivo is partly controlled by M-CSF, RANKL and IL-$1{\beta}$ expression in PDL cells.

• Korean Journal of Microbiology
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• v.48 no.2
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• pp.171-174
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• 2012

THOC1/Hpr1 is one subunit of THO complex that is an evolutionally conserved assembly involved in the mRNP packaging and mRNA export during transcription elongation. In fission yeast Schizosaccharomyces pombe, an ortholog (spHpr1) of THOC1/Hpr1 was identified based on sequence alignment. A deletion mutant in a diploid strain was constructed by replacing one of spHpr1-coding region with a $kan^r$ gene using one-step gene disruption method. Tetrad analysis showed that the sphpr1 is essential for growth. Over-expression of sphpr1 from strong nmt1 promoter caused no defects of growth and mRNA export. However, repression of the sphpr1 expression resulted in growth inhibition accompanied by accumulation of poly$(A)^+$ RNA in the nucleus. These results suggest that spHpr1 is involved in mRNA export from the nucleus to cytoplasm.

• The Korean Journal of Zoology
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• v.39 no.1
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• pp.115-121
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• 1996

To investigate gestational profiles in gene expression of placental lactogen I fpL4), PL-lI and Pit-1, RNA samples were extracted from the placentas of pregnant day 12 to 20 at 2 day intervals. Northern blots showed changes in gene expression of PL4, - 11 and Pit-i. Sizes of PL-l and -II mRNA were changed and amounts of PL-I, -H and Pit-1 mRNA increased during progress of gestation. To examine the effect of estrogen on the gene expression of PL-I, -Il and Pit-1, pregnant female rats were ovariectomized (OVX) and daily injected with estradiol (OVX + E). OVX markedly lowered the amount of PL4 and 41 mRNA, and shifted niRNA size from 1 kb to i 3 kb in PL-l mRNA and 0.6 kb to i kb in PL-ll mRNA, respectively. OVX had no effect on the mRNA size of Pit-1, but markedly attenuated Pit-1 mRNA level. Estrogen injection reversed the effect of OVX on the size-shift but not on the amount of PL4 and -Il mRNA. Replacement of E partially recovered OVX-induced inhibition of Pit-i mRNA level. Present results suggest that estrogen may play a pivotal role on the gene expression of PL-l and -Il such as alternative RNA splicing and/or polyadenylation, and Pit-1 may be involved in the gene expression of PL-l and 41 by estrogen.

• Korean Journal of Microbiology
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• v.26 no.1
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• pp.27-31
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• 1988

Biosynthesis and processing of cytoplasmic mRNA from heterogenous nuclear RNA (hn-RNA) in Aspergillus phoenicis were studied by $^{3}H$-uridine labeling and synchronous culture techniques during their life cycle. Incorporations of $^{3}H$-uridine into hn-RNA and mRNA were most rapid in vesicle-phialide fromation stage and diminished in hyphal growth stage. The processing of cytoplasmic mRNA from hn-RNA was proceeded more rapidly in hyphal growth and conidiophore formation stages than in conidia and vesicle-phialide formation stages. The specific radioactivities of hn-RNA and mRNA were very high in vesicle-phialide formation stage.