• Journal of Microbiology and Biotechnology
• /
• v.18 no.6
• /
• pp.1044-1049
• /
• 2008

In order to study functional nucleotides in prototype foamy virus (PFV) DNA on specific recognition by PFV integrase (IN), we designed chimeric U5 long terminal repeat (LTR) DNA substrates by exchanging comparative sequences between human immunodeficiency virus type-1 (HIV-1) and PFV U5 LTRs, and investigated the 3'-end processing reactivity using HIV-1 and PFV INs, respectively. HIV-1 IN recognized the nucleotides present in the fifth and sixth positions at the 3'-end of the substrates more specifically than any other nucleotides in the viral DNA. However, PFV IN recognized the eighth and ninth nucleotides as distinctively as the fifth and sixth nucleotides in the reactions. In addition, none of the nucleotides present in the twelfth, sixteenth, seventeenth, eighteenth, nineteenth, and twentieth positions were not differentially recognized by HIV-1 and PFV INs, respectively. Therefore, our results suggest that the functional nucleotides that are specifically recognized by its own IN in the PFV U5 LTR are different from those in the HIV-1 U5 LTR in aspects of the positions and nucleotide sequences. Furthermore, it is proposed that the functional nucleotides related to the specific recognition by retroviral INs are present inside ten nucleotides from the 3'-end of the U5 LTR.

• Korean Journal of Agricultural Science
• /
• v.44 no.4
• /
• pp.477-486
• /
• 2017

This review provides an overview of dietary nucleotides as an alternative to in-feed antibiotics for weaning pigs. Dietary nucleotides are composed of DNA or RNA molecules and are normally contained in protein-rich feed ingredient, brewer's yeast, yeast extract, and milk. Weaning pigs are suffering from several stresses, such as environmental challenges (i.e. crowding, transportation, and feeding). Such stressors can damage the intestinal epithelium and cause an invasion by Escherichia coli, secondary inflammatory responses, and post weaning diarrhea. To overcome weaning disorder, people often use antibiotics which reduce symptoms and boost growth performance. However, since antibiotics were banned due to concerns of antibiotic resistant bacteria, researchers are studying alternative materials to antibiotics. Dietary nucleotides are one of the alternative materials for replacing antibiotics and can be used in abnormal conditions, such as weaning diarrhea, low digestibility, and disease condition. Nucleotides have substances that have important roles in cell division and cell growth, affecting growth performance, intestinal condition, and immunological effect at the weaning stage. However, nucleotides' composition is very different between sources and this aspect makes it difficult to utilize nucleotides at the weaning stage. Therefore, this review paper focuses on i) the characteristics and functions of dietary nucleotides and ii) the effect of dietary nucleotides on the growth performance and immune system of pigs.

• Journal of Microbiology and Biotechnology
• /
• v.12 no.4
• /
• pp.622-627
• /
• 2002

Diphtheria toxin repressor (DtxR) binds to approximately 30 to 35-bp regions containing an interrupted 9-bp inverted repeat within a 19-bp core sequence. The core sequence is fairly conserved and critical for DtxR binding. The flanking regions that are consisted of 5 to 8 more of nucleotides from the core are also required for DtxR binding. The nucleotides in both flanking regions are A-T rich. To examine whether the A-T nucleotides in both flanking regions from the core have significant roles for DtxR binding, a DNA fragment was constructed based on the diphtheria tox promoter/operator, and DNA fragments with substitution of A and T nucleotides In the flanking regions to G and C were also constructed. To assess the effect of these substitutions on binding of DtxR and repressibility by DtxR, $\beta$-galactosidase activity from lacZ fused to the region was assessed. Gel mobility shift of the region by purified DtxR was also examined. The DNA fragments containing the mutations in the flanking regions still exhibited repression and mobility shift with DtxR. The core segment with the mutation is still, therefore, recognized by DtxR. Nonetheless, the results from the assays indicated that the substitution significantly decreased repression of the operator by DtxR in vivo under high-iron condition and decreased binding of DtxR to the operator. These results suggest that A and T nucleotides fur both flanking regions are preferred for the binding of DtxR.

• Animal Bioscience
• /
• v.36 no.10
• /
• pp.1604-1611
• /
• 2023

Objective: The aim of this study was to investigate the protective effect of wheat phytase as a structural decomposer of inflammatory nucleotides, extracellular adenosine triphosphate (ATP), and uridine diphosphate (UDP) on HT-29 cells. Methods: Phosphatase activities of wheat phytase against ATP and UDP was investigated in the presence or absence of inhibitors such as L-phenylalanine and L-homoarginine using a Pi Color Lock gold phosphate detection kit. Viability of HT-29 cells exposed to intact- or dephosphorylated-nucleotides was analyzed with an EZ-CYTOX kit. Secretion levels of pro-inflammatory cytokines (IL-6 and IL-8) in HT-29 cells exposed to substrate treated with or without wheat phytase were measured with enzyme-linked immunosorbent assay kits. Activation of caspase-3 in HT-29 cells treated with intact ATP or dephosphorylated-ATP was investigated using a colorimetric assay kit. Results: Wheat phytase dephosphorylated both nucleotides, ATP and UDP, in a dose-dependent manner. Regardless of the presence or absence of enzyme inhibitors (L-phenylalanine and L-homoarginine), wheat phytase dephosphorylated UDP. Only L-phenylalanine inhibited the dephosphorylation of ATP by wheat phytase. However, the level of inhibition was less than 10%. Wheat phytase significantly enhanced the viability of HT-29 cells against ATP- and UDP-induced cytotoxicity. Interleukin (IL)-8 released from HT-29 cells with nucleotides dephosphorylated by wheat phytase was higher than that released from HT-29 cells with intact nucleotides. Moreover, the release of IL-6 was strongly induced from HT-29 cells with UDP dephosphorylated by wheat phytase. HT-29 cells with ATP degraded by wheat phytase showed significantly (13%) lower activity of caspase-3 than HT-29 cells with intact ATP. Conclusion: Wheat phytase can be a candidate for veterinary medicine to prevent cell death in animals. In this context, wheat phytase beyond its nutritional aspects might be a novel and promising tool for promoting growth and function of intestinal epithelial cells under luminal ATP and UDP surge in the gut.

• Journal of Plant Biology
• /
• v.38 no.2
• /
• pp.137-141
• /
• 1995

We isolated a cDNA clone, BLSC1, encoding 5' exon of ATP synthase CF0 subunit I from broccoli. BLSC1 is 285 nucleotides long which consists of a 5' noncoding region of 34 nucleotides, a 5' exon of 145 nucleotides and an intron of 106 nucleotides. The 5' exon codes for 48 amino acids which reveals mostly hydrophobic. The amino acid sequence deduced from BLSC1 shares 83%, 83% and 91% identities with the genes coding for atpF from wheat, rice and spinach, respectively. Genomic Southern blot analysis for BLSC1 showed a typically strong signal for a gene located in the chloroplast genome. Northern blot analysis identified three major classes of transcripts showing strong positive signals in the leaves, but only trace amounts of the transcripts were identified in the other organs like stems, flowr buds and roots.

• Journal of the Korean Society of Tobacco Science
• /
• v.18 no.2
• /
• pp.101-106
• /
• 1996

Tobacco mosaic virus (TMV) tomato strain was isolated from tomato "Seo-Kwang" in Korea. The virion was purified by density gradient centrifugation, and total viral RNA was isolated from the purified particles. Coat protein (CP) cDNA of the virus was synthesized by RT-PCR, and the purified cDNA fragment was subcloned to pBluescript II SK-. The analysis of nucleotide sequence showed that this cDNA was 693 nucleotides long from the insert of clone p1571 and p1572 which contain complete codons of the viral coat protein gene (474 nucleotides) and 3' untranslated region. The nucleotides of coat protein encoding cDNA of the strain were 6 nucleotides less than that of TMV common strain isolated from tobacco plant in Korea. The CP gene showed 70% maximum homology with that of the common strain in the nucleotide level and 86% maximum homology in amino acid level.cid level.

• Korean Journal of Plant Resources
• /
• v.16 no.1
• /
• pp.82-88
• /
• 2003

Genomic RNA sequence of a tobamovirus infecting Eutrema wasabi plant(TMV-W) was determined. The RNA is composed 6,298 nucleotide and contains four OREs encoding the protein of 180KD(OREI), 130KD(ORE2),30KD(ORF3) and 18KD(coat protein, ORF4). ORE4, ORF 3, ORF 2 and ORF 1 are overlaped by 130, 20 and 40 nucleotides, and the overapping region can be folded into a stable hairpin styucture. This includes the 3'non-coding region of 238 nucleotides, coat protein gene(537 nucleotides,179 amino acid), 30KD movement protein gene(825 nucleotides, 275 amino acid), 13(IKD protein gene(1,896 nucleotides, 632 amino acid) and 180KD protein gene(2,958 nucleotides, 986 amino acid). The genomic RNA sequence was compared with homologous regions of eleven other tobamoviruses. TMV-WTE was similar to TMV-WSF(98.6%) in nucleotide sequence.

• The Korean Journal of Mycology
• /
• v.12 no.4
• /
• pp.141-152
• /
• 1984

Aspergillus niger van Tieghem was cultured by the method of synchronous and submerged culture. Throughout the culture, sporulation was occured. Highly phosphorylated nucleotides in sporulating mycelia were detected to assure whether the eucaryotic Aspergillus niger produce these substances or not during the differentiation. Phosphorylated nucleotides were extracted from the conidiophore, bearing mycelia and spore forming body, these nucleotides were identified by TLC with P.E.I. cellulose. Guanosine tetraphosphate was found in both phialide forming mycelia and spore forming body. The contents of free amino acids were assayed and its level was found to increase at early stage of sporulation. The effects of 8-azaguanine examined, it was found to prevent spore formation and to made abnormal structure. The effects of inosinic monophosphate and guanosine monophosphate on spore formation were examined, spore formation was enhanced by these nucleotides.

• Korean Journal of Fisheries and Aquatic Sciences
• /
• v.37 no.5
• /
• pp.366-371
• /
• 2004

Powder and liquid products of the seasoned and smoked fish were manufactured with small-sized skipjack tuna (Euthynus pelamis) captured in the East Sea, Korea. The property changes of nucleotides and their related compounds, amino acid, and sensory attribute during storage were analyzed. IMP content was the highest among the nucleotides and their related compounds followed by inosine in both powder and liquid products. Nucleotides and their related compounds of the powder product increased slightly as storage period increased, while those of liquid product were constant. Glutamic acid $(15.6{\%})$, aspartic acid $(10.7{\%})$, and lysine $(9.3{\%})$ were major amino acids of the power product, while histidine $(36.2{\%})$ and taurine $(10.6{\%})$ were high in the liquid product. Free amino acid contents of liquid product increased during storage periods. There was no significant difference In the concentration of nucleotides and their related compounds, and composition of free amino acid between the products with/without liquid smoke. Aroma and acceptance were good in both products, while bitterness and sweetness were poor.

• BMB Reports
• /
• v.45 no.4
• /
• pp.259-264
• /
• 2012

Accumulation of modified nucleotides is defective to various cellular processes, especially those involving DNA and RNA. To be viable, organisms possess a number of (deoxy)nucleotide phosphohydrolases, which hydrolyze these nucleotides removing them from the active NTP and dNTP pools. Deamination of purine bases can result in accumulation of such nucleotides as ITP, dITP, XTP and dXTP. E. coli RdgB has been characterised as a deoxyribonucleoside triphosphate pyrophosphohydrolase that can act on these nucleotides. S. cerevisiae homologue encoded by YJR069C was purified and its (d)NTPase activity was assayed using fifteen nucleotide substrates. ITP, dITP, and XTP were identified as major substrates and kinetic parameters measured. Inhibition by ATP, dATP and GTP were established. On the basis of experimental and published data, modelling and simulation of ITP, dITP, XTP and dXTP metabolism was performed. (d)ITP/(d)XTPase is a new example of enzyme with multiple substrate-specificity demonstrating that multispecificity is not a rare phenomenon