• Molecules and Cells
• /
• v.39 no.5
• /
• pp.367-374
• /
• 2016

Since the RNA world hypothesis was proposed, a large number of regulatory noncoding RNAs (ncRNAs) have been identified in many species, ranging from microorganisms to mammals. During the characterization of these newly discovered RNAs, RNAs having both coding and noncoding functions were discovered, and these were considered bifunctional RNAs. The recent use of computational and high-throughput experimental approaches has revealed increasing evidence of various sources of bifunctional RNAs, such as protein-coding mRNAs with a noncoding isoform and long ncRNAs bearing a small open reading frame. Therefore, the genomic diversity of Janusfaced RNA molecules that have dual characteristics of coding and noncoding indicates that the functional roles of RNAs have to be revisited in cells on a genome-wide scale. Such studies would allow us to further understand the complex gene-regulatory network in cells. In this review, we discuss three major genomic sources of bifunctional RNAs and present a handful of examples of bifunctional RNA along with their functional roles.

• International Journal of Industrial Entomology and Biomaterials
• /
• v.18 no.1
• /
• pp.33-40
• /
• 2009

A vitellogenin cDNA was cloned from the bumblebee Bombus ignitus. The cDNA encoding B. ignitus vitellogenin (BiVg) is 5473 bases long with an open reading frame of 1773 amino acid residues. BiVg possesses two consensus (RXXR/S) cleavage sites and has the conserved DGXR and GL/ICG motif near its C-terminus. The deduced amino acid sequence of BiVg cDNA showed significant similarity with hymenopteran Vgs (51% identity to Apis mellifera Vg, and $33{\sim}36%$ to other insect Vgs). The BiVg cDNA was expressed as a 200-kDa polypeptide in baculovirus-infected insect Sf9 cells. Northern and Western blot analyses showed the expression of BiVg in fat bodies of pupae and adults. In queens, the expression of BiVg was first detected in late pupal stage fat bodies, and secreted BiVg was also observed in late pupal stage hemolymph.

• BMB Reports
• /
• v.32 no.4
• /
• pp.409-413
• /
• 1999

The cDNA encoding CMP-NeuAc:lactosylceramide ${\alpha}2$,3-sialyltransferase (GM3 synthase) was isolated from a human fetal brain cDNA library using sequence information obtained from amino acid sequences found in the conserved regions of the previously-cloned mouse GM3 synthase (mST3Gal V) and human sialyltransferases. The cDNA sequence included an open reading frame coding for 362 amino acids, and the primary structure of this enzyme predicted all the structural features characteristic of other sialyltransferases, including a type II membrane protein topology and both sialylmotifs. Comparative analysis of this cDNA with mST3Gal V showed 85% and 86% identity of the nucleotide and amino acid residues, respectively. The expression of this gene is highly restricted in both human fetal and adult tissues.

• Journal of Korean Society of Steel Construction
• /
• v.9 no.2 s.31
• /
• pp.221-228
• /
• 1997

The main purpose of this paper is to determine the dynamic optimal shapes of simple beam-columns with the constant volume. The parabolic function is chosen as the variable equation for the depth of regular polygon cross-section. The ordinary differential equation including the effect of axial load is applied to calculate the natural frequencies. The Runge-Kutta and Regula-Falsi methods are used to integrate the differential equation and compute the frequencies, respectively. Then the dynamic optimal shape whose lowest natural frequency is highest is determined by reading the critical value of the frequency versus section ratio curve plotted by the frequency data. In the numerical examples, the simple beam-columns are analysed and the numerical results of this study are shown in tables and figures.

• Journal of Microbiology and Biotechnology
• /
• v.17 no.1
• /
• pp.74-80
• /
• 2007

An enantioselective lipase gene (esf) for the kinetic resolution of optically active (S)-flurbiprofen was cloned from the new strain Serratia marcescens ES-2. The esf gene was composed of a 1,845-bp open reading frame encoding 614 amino acid residues with a calculated molecular mass of 64,978 Da. The lipase expressed in E. coli was purified by a three-step procedure, and it showed preferential substrate specificity toward the medium-chain-length fatty acids. The esf gene encoding the enantioselective lipase was reintroduced into the parent strain S. marcescens ES-2 for secretory overexpression. The transformant S. marcescens BESF secreted up to 217kU/ml of the enantioselective lipase, about 54-fold more than the parent strain, after supplementing 3.0% Triton X-207. The kinetic resolution of (S)-flurbiprofen was carried out even at an extremely high (R,S)-flurbiprofen ethyl ester [(R,S)-FEE] concentration of 500 mM, 130 kU of the S. marcescens ES-2 lipase per mmol of (R,S)-FEE, and 1,000 mM of succinyl ${\beta}-cyclodextrin$ as the dispenser at $37^{\circ}C$ for 12h, achieving the high enantiomeric excess and conversion yield of 98% and 48%, respectively.

• International Journal of Industrial Entomology and Biomaterials
• /
• v.5 no.1
• /
• pp.93-102
• /
• 2002

We have cloned and characterized the complete fibroin light chain gene from the silkworm Baekok-Jam, Bombyx mori, a recommended variety in Korea. It consists of seven exons and six introns. It consists of 14,663 nucleotides long with an open reading frame of 786 nucleotides that encodes a protein of 262 amino acid residues with a molecular mass of approximately 26,000 dalton. The amino acid alignment revealed that the Baekok-Jam fibroin light chain had 98.5 % protein sequence identity to J139 strain: differed at four amino acid positions (11, 46, 80 and 123). The Northern hybridization analysis showed that the Baekok-Jam fibroin light chain gene was specifically expressed in the posterior silk gland.

• Journal of Microbiology and Biotechnology
• /
• v.10 no.5
• /
• pp.670-676
• /
• 2000

Several clones obtained from Serratia marcescens stimulated E. coli TP2139 (${\Delta}lac, \;{\Delta} crp$) cells to use maltose as a carbon source. The crp gene clone, pCKB12, was confirmed to stimulate the $\beta$-galactosidase activity, by Southern hybridization [31]. The nucleotide sequence of the crp region consisting of 1,979 bp was determined. The sequencing of the fragment led to the identification of two open reading frames: One of these, the crp gene, encoded 210 amino acid and the other encoded a truncated protein. The S. marcescens and E. coli crp genes showed a higher degree of divergence in their nucleotide sequence with 120 changes, however, the corresponding amino acid sequences showed only two amino acid differences. Yet, an analysis of the amino acid divergence revealed that the catabolite gene activator protein, the crp gene product, was the most conserved protein observed so far. Using a crp-lac protein fusion, it was demonstrated that S. marcescens CRP could repress its own expression, probably via a mechanism similar to that previously described for the E. coli crp gene.

• Korean Journal of Breeding Science
• /
• v.42 no.5
• /
• pp.455-462
• /
• 2010

Purple acid phosphatase is important for phosphorus remobilization in plants, but its role in plant adaptation to low phosphorus availability is not known. The cDNA encoding O. sativa purple acid phosphatase (OsPAP1) has 1008 bp with an open reading frame of 335 amino acid residues. The amino acid sequence of OsPAP1 cDNA shows of 50-51% identity with other plant purple acid phosphatases. OsPAP1 was expressed in rice plants and in cell cultures in the absence of phosphate ($P_i$). The expression was organ-specific with the strongest expression in $P_i$-deprived roots. Functional expression of the OsPAP1 gene in the transgenic Arabidopsis line was confirmed by northern and western blot analysis. OsPAP1 overexpression lines had higher phosphatase activity than wild-type. Overexpression of OsPAP1 in Arabidopsis plants resulted in increased Pi accumulation under Pi sufficient condition. These results show that the OsPAP1 gene represents more efficient $P_i$ uptake and can be used to develop new transgenic dicotyledonous plants.

• Mycobiology
• /
• v.46 no.4
• /
• pp.429-439
• /
• 2018

To develop a convenient promoter analysis system for fungi, a null-pigment mutant (NPG) of Aspergillus nidulans was used with the 4'-phosphopantetheinyl transferase (PPTase) gene, npgA, which restores the normal pigmentation in A. nidulans, as a new reporter gene. The functional organization of serially deleted promoter regions of the A. nidulans trpC gene and the Cryphonectria parasitica crp gene in filamentous fungi was representatively investigated to establish a novel fungal promoter assay system that depends on color complementation of the NPG mutant with the PPTase npgA gene. Several promoter regions of the trpC and crp genes were fused to the npgA gene containing the 1,034-bp open reading frame and the 966-bp 3' downstream region from the TAA, and the constructed fusions were introduced into the NPG mutant in A. nidulans to evaluate color recovery due to the transcriptional activity of the sequence elements. Serial deletion of the trpC and crp promoter regions in this PPTase reporter assay system reaffirmed results in previous reports by using the fungal transformation step without a laborious verification process. This approach suggests a more rapid and convenient system than conventional analyses for fungal gene expression studies.

• Proceedings of the Korean Society of Plant Pathology Conference
• /
• 2003.10a
• /
• pp.147.2-148
• /
• 2003

Complete nucleotide sequence of genome RNA of a Korean isolate of Pepper mottle virus (PepMoV-Vb) from field-collected diseased paprika (Capsicum annuum var grossum) was determined in this study. Symptoms of isolates of PepMoV were divided largely into two groups, vein banding (Vb) and vein clearing (Vc) patterns. PepMoV-Vb RNA consists of 9,640 nucleotides excluding the poly(A) tail. A single open reading frame was identified beginning at nucleotide position 169 encoding a polyprotein of 3024 amino acids which is typical of the Potyvirus genus. The complete nucleotide sequence and coding regions of PepMoV-Vb were compared to that of 11 potyviruses within the genus Potyvirus. The overall nucleotide sequence identity was 94.7 and 94.1％ identical to PepMoV-C and PepMoV-FL, respectively. Full-length cDNAs of PepMoV-Vbl were synthesized from purified viral RNAs by RT-PCR and their genome structure was analysed by RFLP analysis. This is the first report on complete nucleotide sequence of PepMoV isolated from paprika in Korea.