• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.141-141
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• 2017

The ubiquitin-proteasome pathway is the major regulatory mechanism in a number of cellular processes for selective degradation of proteins and involves three steps: (1) ATP dependent activation of ubiquitin by E1 enzyme, (2) transfer of activated ubiquitin to E2 and (3) transfer of ubiquitin to the protein to be degraded by E3 complex. F-box proteins are subunit of SCF complex and involved in specificity for a target substrate to be degraded. F-box proteins regulate many important biological processes such as embryogenesis, floral development, plant growth and development, biotic and abiotic stress, hormonal responses and senescence. However, little is known about the F-box genes in wheat. The draft genome sequence of wheat (IWGSC Reference Sequence v1.0 assembly) used to analysis a genome-wide survey of the F-box gene family in wheat. The Hidden Markov Model (HMM) profiles of F-box (PF00646), F-box-like (PF12937), F-box-like 2 (PF13013), FBA (PF04300), FBA_1 (PF07734), FBA_2 (PF07735), FBA_3 (PF08268) and FBD (PF08387) domains were downloaded from Pfam database were searched against IWGSC Reference Sequence v1.0 assembly. RNA-seq paired-end libraries from different stages of wheat, such as stages of seedling, tillering, booting, day after flowering (DAF) 1, DAF 10, DAF 20, and DAF 30 were conducted and sequenced by Illumina HiSeq2000 for expression analysis of F-box protein genes. Basic analysis including Hisat, HTseq, DEseq, gene ontology analysis and KEGG mapping were conducted for differentially expressed gene analysis and their annotation mappings of DEGs from various stages. About 950 F-box domain proteins identified by Pfam were mapped to wheat reference genome sequence by blastX (e-value < 0.05). Among them, more than 140 putative F-box protein genes were selected by fold changes cut-offs of > 2, significance p-value < 0.01, and FDR<0.01. Expression profiling of selected F-box protein genes were shown by heatmap analysis, and average linkage and squared Euclidean distance of putative 144 F-box protein genes by expression patterns were calculated for clustering analysis. This work may provide valuable and basic information for further investigation of protein degradation mechanism by ubiquitin proteasome system using F-box proteins during wheat development stages.

• Microbiology and Biotechnology Letters
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• v.33 no.3
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• pp.169-177
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• 2005

This study focuses on investigating roles of microorganisms in decontamination of reed rhizosphere in Sunchon Bay, Korea, which is considered one of the marsh and mud environment severely affected by human activities such as agriculture and fisheries. In general, the bay is known to play the role of the buffering zone to reduce the sudden impact or change by environmental stresses. In our initial efforts to elucidate the microbial functions in decontamination process in reed rhizosphere, pure bacteria capable of degrading aromatic hydrocarbons were isolated from reed (Phragmites communis) rhizosphere of Sunchon bay by enrichment culture using either benzene, toluene, ethylbenzene, or xylene (BTEX) as a sole source of carbon and energy. Measurement of the rates of BTEX degradation and cell growth during the incubation in BTEX media under several temperature conditions demonstrated maximized degradation of BTEX at $37^{\circ}C$ in both strains. Both strains were also resistant to all the heavy metals and antibiotics tested in this study, as well as they grew well at $42^{\circ}C$. Identification of the isolates based on 16S rRNA gene sequences, and a variety of phenotypic and morphologic properties revealed that the two strains capable of BTEX catabolism were among Microbacterium sp., and Rhodococcus sp. with over $95{\%}$ confidence, designated Microbacterium sp. EMB-1 and Rhodococcus sp. EMB-2, respectively This result suggested that in the rhizosphere of reed, one of major salt marsh plants they might play an important roles in decontamination process of reed rhizosphere contaminated with petroleum such as BTEX.

• Korean Journal of Environmental Agriculture
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• v.30 no.4
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• pp.424-431
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• 2011

BACKGROUND: Tributyltin chloride is among the most toxic compounds known for aquatic ecosystems. Microorganisms are responsible for removal of TBTCl. Nevertheless, only a limited number of marine bacteria were investigated for biodegradation of TBTCl in Korea. METHODS AND RESULTS: The number of TBTCl resistant bacteria ranged from $2.5{\times}10^3$ to $3.8{\times}10^3$ cfu/mL in the seawater, and ranged from $3.2{\times}10^5$ to $9.1{\times}10^5$ cfu/g in the surface sediment, respectively. The morphological, physiological, and biochemical characteristics of TBTCl resistant bacteria were investigated by API 20NE and other tests. The most abundant species of TBTCl resistant bacteria were Vibrio spp. (19.2%), Bacillus spp. (16.2%), Aeromonas spp. (15.2%), and Pseudomonas spp. (13.1%), etc. Eleven TBTCl resistant isolates also had a resistance to heavy metals (Cd, Cu, Hg, and Zn). Among them, isolate T7 showing the strong TBTCl-resistance was selected. This isolate was identified as the genus Pantoea by 16S rRNA gene sequencing and designated as Pantoea sp. T7. In addition, this bacterium was cultivated up to the growth of 50.7% after 60 hrs at TBTCl concentration of $500{\mu}M$. TBTCl-degrading activity of Pantoea sp. T7 was measured by GC-FPD analysis. As a result of biological TBTCl-degradation at TBTCl concentration of $100{\mu}M$, TBTCl-removal efficiency of Pantoeasp. T7 was 62.7% after 40 hrs. CONCLUSION(S): These results suggest that Pantoea sp. T7 is potentially useful for the bioremediation of TBT contamination.

• Journal of Physiology & Pathology in Korean Medicine
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• v.23 no.1
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• pp.127-134
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• 2009

In the present study, we investigated the anti-allergic effect of the water extract of Bopyeoyangyeong-jun(BYJ) to cytokines and transcription. To investigate the biological effect of BYJ, We examined cytotoxicity and inflammatory cytokine secretion with RBL-2H3. We examined tumor necrosis factor-alpha(TNF-$\alpha$), interleukin(IL)-4 secretion from RBL-2H3 cell after pre- treatment with Bopyeoyangyeong-jun of $1\;mg/m{\ell}$, $2\;mg/m{\ell}$. RBL-2H3 cell was stimulated with phorbol 12-myristate 13-acetate(PMA) and calcium ionophore A23187. We observed that Bopyeoyangyeong-jun reduced TNF-$\alpha$, IL-4 secretion and mRNA expression in RBL-2H3 cells. Moreover, the expression of levels of cyclooxygenase (COX)-2 mRNA, nuclear factor-kappa B (NF-${\kappa}B$) (p65) protein, ERK MAPK, and the degradation of level inhibitor kappa B-alpha ($I{\kappa}B-{\alpha}$) were down-regulated by BYJ. Taken together, these results indicate that Bopyeoyangyeong-jun hascontrols TNF-$\alpha$, IL-4 secretion on allergic reaction.

• Journal of Physiology & Pathology in Korean Medicine
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• v.31 no.2
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• pp.105-110
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• 2017

Prolonged exposure to solar ultraviolet A (UVA) radiation has been known to cause premature skin aging (photo-aging). UVA radiation generates ROS thereby induce degenerative changes of skin such as degradation of dermal collagen, elastic fibers. Matrix metalloproteinases (MMPs), the proteolytic enzymes have been implicated as a major player in the development of UVA-induced photo-aging. Many studies have been conducted to block the harmful effects of UV radiation on the skin. Recently, we are interested in the availability of fermented red ginseng (FRG) as natural matrix metalloproteinases inhibitors (MMPIs). The efficacy difference between red ginseng and FRG has been compared. Both RG and FRG have no cytotoxic effects below the concentration of $300{\mu}g/ml$. Human dermal fibroblasts (HDFs) were pretreated with FRG or RG for 24h, followed by irradiation of UVA. Then, we measured the intracellular ROS production and the expression of MMP, $IL-1{\beta}$ at the mRNA level. We also examined the intracellular localization of $NF-{\kappa}B$ and MMP-9 on the FRG or RG treated and UVA-irradiated HDFs. FRG decreased the intracellular ROS production elicited by UVA. In addition, FRG decreased the mRNA expression of MMP-3, MMP-9, and $IL-1{\beta}$ more efficiently than RG. Furthermore, FRG suppressed the nuclear localization of $NF-{\kappa}B$, and the expression of MMP-9. Taken together, our results suggest that FRG is promising agents to prevent UVA-induced photo-aging by suppressing MMP expression and inflammation.

• KSBB Journal
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• v.11 no.2
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• pp.165-172
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• 1996

To obtain a correctly folded human proinsulin, export of proinsulin using Staphylococcal protein A signal sequence-mediated secretion pathway has been attempted in E.coli. A secretion operon for proinsulin was constructed by consecutively connecting T7 promoter, SPA ribosome binding site, SPA signal sequence gene, and human proinsulin gene. Little immunoreactive proinsulin was detected in the periplasmic space and. culture medium, and not even in cytoplasmic space. The qualitative analysis of transcribed proinsulin mRNA and the in vitro transcription/translation experiment suggests that the negligible level of proinsulin export appears to be due to intracellular degradation of proinsulin, rather than due to the blockage during translocation. However, expression of proinsulin fusion protein such as MBP-proinsulin could dramatically increase export of proinsulin in E.coli.

• Journal of Plant Biotechnology
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• v.2 no.2
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• pp.79-82
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• 2000

We have isolated a cDNA encoding a calcium-dependent protein kinase (CDPK) in Nicotiana tabacum, which was designated NtCDPK1. Accumulation of the NtCDPK1 mRNA was stimulated by various stimuli, including phytohormones, CaCl$_2$ wounding, fungal elicitors, chitin and methyl jasmonate. The NtCDPK1 gene encodes a functional Ser/Thr protein kinase of which phosphorylation activity is strongly induced by calcium. By analyzing expression of the NtCDPK1-GFP fusion protein and by immunoblotting with antibody which reacts with NtCDPK1, we found that NtCDPK1 is localized in membrane and nucleus in plant cells. Silencing expression of the NtCDPK1 transgene resulted in marked decrease of lateral root development in the transgenic tobacco plants. Yeast two hybrid screening using NtCDPK1 as a bait identified a tobacco homologue of proteasome regulatory subunit 21D7, designated Nt21D7. The 21D7 mRNA has been shown to be predominantly expressed in proliferating tissues in the cell cycledependent manner in carrot. The recombinant NtCDPK1 protein associated with Nt21D7 in vitro, and could phosphorylate the Nt21D7 protein in vitro in the presence of calcium, suggesting that Nt21D7 protein is a natural substrate of NtCDPK1 in tobacco. These results suggest that NtCDPK1 may regulate tell proliferation processes, such as lateral root formation, by regulating specificity and/or activity of proteasome-mediated protein degradation pathway.

• Microbiology and Biotechnology Letters
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• v.43 no.2
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• pp.158-163
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• 2015

In this study, we investigated the effects of 40% ethanol extract of Red Ginseng (RGE) on the productions of inflammatory proteins in Antigen I/II (Ag I/II)-N, a recombinant protein isolated from Streptococcus mutans -stimulated in RAW 264.7 cells. RGE inhibited the expression of Ag I/II-N-induced pro-inflammatory mediators, both mRNA and protein synthesis levels, without any cytotoxic effects. Moreover, RGE significantly inhibited Ag I/II-N induced NF-κB translocation into the nucleus by preventing the degradation of inhibitor κB-α. In conclusion, RGE down regulates the expression of pro-inflammatory genes involved in the synthesis of NO and iNOS in Ag I/II-N-stimulated RAW 264.7 cells by suppressing NF-κB activity.

• Journal of Microbiology and Biotechnology
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• v.16 no.11
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• pp.1728-1733
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• 2006

A Gram-negative, strictly aerobic, nonmotile, and nonspore-forming bacterial strain, designated $T5-12^T$, was isolated from compost and characterized using a polyphasic taxonomical approach. The isolate was positive for catalase and oxidase tests. It could degrade DNA, but was negative for degradation of macromolecules such as casein, collagen, starch, chitin, cellulose, and xylan. The DNA G+C content was 36.0 mol%. The predominant isoprenoid quinone was menaquinone 7 (MK-7). The major fatty acids were $iso-C_{15:0}$ (45.6%), $iso-C_{17:0}$ 3OH (17.2%), and summed feature 4 ($C_{16:0}\;{\omega}7c$ and/or $iso-C_{15:0}$ 2OH, 14.9%). Comparative 16S rRNA gene sequence analysis showed that strain $T5-12^T$ fell within the radiation of the cluster comprising members of the genus Sphingobacterium. Strain $T5-12^T$ exhibited lower than 94% of 16S rRNA gene sequence similarity with respect to the type strains of recognized Sphingobacterium species. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain $T5-12^T$ ($=KCTC\;12578^T=LMG\;23401^T=CCUG\;52467^T$) should be classified in the genus Sphingobacterium as the type strain of a novel species, for which the name Sphingobacterium composti sp. novo is proposed.

• Journal of Microbiology and Biotechnology
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• v.30 no.4
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• pp.533-539
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• 2020

A quantitative real-time polymerase chain reaction (QPCR) was applied to estimate biokinetic coefficients of Clostridium cadaveris and Clostridium sporogenes, which utilize protein as carbon source. Experimental data on changes in peptone concentration and 16S rRNA gene copy numbers of C. cadaveris and C. sporogenes were fitted to model. The fourth-order Runge-Kutta approximation with non-linear least squares analysis was employed to solve the ordinary differential equations to estimate biokinetic coefficients. The maximum specific growth rate (μ_max), half-saturation concentration (K_s), growth yield (Y), and decay coefficient (K_d) of C. cadaveris and C.sporogenes were 0.73 ± 0.05 and 1.35 ± 0.32 h^-1, 6.07 ± 1.52 and 5.67 ± 1.53 g/l, 2.25 ± 0.75 × 10¹⁰ and 7.92 ± 3.71 × 10⁹ copies/g, 0.002 ± 0.003 and 0.002 ± 0.001 h^-1, respectively. The theoretical specific growth rate of C. sporogenes always exceeded that of C. cadaveris at peptone concentration higher than 3.62 g/l. When the influent peptone concentration was 5.0 g/l, the concentration of C.cadaveris gradually decreased to the steady value of 2.9 × 10¹⁰ copies/ml at 4 h Hydraulic retention time (HRT), which indicates a 67.1% reduction of the initial population, but the wash out occurred at HRTs of 1.9 and 3.2 h. The 16S rRNA gene copy numbers of C. sporogenes gradually decreased to steady values ranging from 1.1 × 10¹⁰ to 2.9 × 10¹⁰ copies/ml. C. sporogenes species was predicted to wash out at an HRT of 1.6 h.