• Korean Journal of Microbiology
• /
• v.38 no.3
• /
• pp.173-179
• /
• 2002

The functions of riboflavin synthesis genes ( ribI,II,III and IV) found immediately downstream of luxG in the lux operon from Photobacterium species were identified using the biochemical and genetical analysis. The ribI-III gene codes for protein corresponding to that coded by the second (riboflavin synthase), third (3,4-dihydroxy 2-butanone 4-phosphate synthase/GTP cyclohydrolase II) and fourth (lumazine synthase) gene, respectively, of Bacillus subtilis rib operon with the respective gene procuct sharing 41-50% amino acid sequence identity. Unexpectedly, the sequence of the ribIV product of Photobacterium phosphoreum does not correspond in sequence to the protein encoded by the fifth rib gene of Bacillus subtilis. Instead the gene (ribIV) codes for a polypeptide similar in sequence to GTP cyclohydrolase II of Escherichia coli and the carboxy terminal domain of the third rib gene from Bacillus subtilis. Complementation of Escherichia coli riboflavin auxotrophs showed that the function of the gene products of ribII and ribIV are DHBP synthase and GTP cyclohydrolase II, respectively. In addition the experiment, showing that increase in thermal stability of riboflavin synthase coded by ribIon coexpression with ribIII, provided indirect evidence that the latter gene codes for lumazine synthase.

• Korean Journal of Microbiology
• /
• v.53 no.4
• /
• pp.316-319
• /
• 2017

The antibiotic resistant genes (ARG) and mobile genetic elements (MGE) were investigated with the effluent of waste-water treatment plant (WWTP), and river waters of upstream and downstream in order to elucidate the effect of effluent on antibiotic resistance in a natural river. Total numbers of 134~183 of ARG and MGE were detected and the abundance of ARG and MGE was 0.063~0.422 copies per one of 16S rRNA gene in three water samples. Effluent sample contained the highest amount of the total number and abundance of ARG and MGE whereas total viable cells were observed in the lowest amount among the three samples. This indicated that the genes were originated from cells died during the wastewater treatment process. In addition, the co-relationship of abundance between ARG and MGE suggested that acquired resistance was a prevalent mechanism among the antibiotic-resistant bacteria existing in WWTP.

• BMB Reports
• /
• v.52 no.11
• /
• pp.653-658
• /
• 2019

MYB-type transcription factors (TFs) play important roles in plant growth and development, and in the rapid responses to unfavorable environmental conditions. We recently reported the isolation and characterization of a rice (Oryza sativa) MYB TF, OsMYB102, which is involved in the regulation of leaf senescence by downregulating abscisic acid (ABA) biosynthesis and the downstream signaling response. Based on the similarities of their sequences and expression patterns, OsMYB102 appears to be a homolog of the Arabidopsis thaliana AtMYB44 TF. Since AtMYB44 is a key regulator of leaf senescence and abiotic stress responses, it is important to examine whether AtMYB44 homologs in other plants also act similarly. Here, we generated transgenic Arabidopsis plants expressing OsMYB102 (OsMYB102-OX). The OsMYB102-OX plants showed a delayed senescence phenotype during dark incubation and were more susceptible to salt and drought stresses, considerably similar to Arabidopsis plants overexpressing AtMYB44. Real-time quantitative PCR (RT-qPCR) revealed that, in addition to known senescence-associated genes, genes encoding the ABA catabolic enzymes AtCYP707A3 and AtCYP707A4 were also significantly upregulated in OsMYB102-OX, leading to a significant decrease in ABA accumulation. Furthermore, protoplast transient expression and chromatin immunoprecipitation assays revealed that OsMYB102 directly activated AtCYP707A3 expression. Based on our findings, it is probable that the regulatory functions of AtMYB44 homologs in plants are highly conserved and they have vital roles in leaf senescence and the abiotic stress responses.

• BMB Reports
• /
• v.52 no.2
• /
• pp.157-162
• /
• 2019

Our previous study found that two novel cancer-related genes, PRR11 and SKA2, constituted a classic gene pair that was regulated by p53 and NF-Y in lung cancer. However, their role and regulatory mechanism in breast cancer remain elusive. In this study, we found that the expression levels of PRR11 and SKA2 were upregulated and have a negative prognotic value in breast cancer. Loss-of-function experiments showed that RNAi-mediated knockdown of PRR11 and/or SKA2 inhibited proliferation, migration, and invasion of breast cancer cells. Mechanistic experiments revealed that knockdown of PRR11 and/or SKA2 caused dysregulation of several downstream genes, including CDK6, TPM3, and USP12, etc. Luciferase reporter assays demonstrated that wild type p53 significantly repressed the PRR11-SKA2 bidirectional promoter activity, but not NF-Y. Interestingly, NF-Y was only essential for and correlated with the expression of PRR11, but not SKA2. Consistently, adriamycin-induced (ADR) activation of endogenous p53 also caused significant repression of the PRR11 and SKA2 gene pair expression. Notably, breast cancer patients with lower expression levels of either PRR11 or SKA2, along with wild type p53, exhibited better disease-free survival compared to others with p53 mutations and/or higher expression levels of either PRR11 or SKA2. Collectively, our study indicates that the PRR11 and SKA2 transcription unit might be an oncogenic contributor and might serve as a novel diagnostic and therapeutic target in breast cancer.

• Animal Bioscience
• /
• v.34 no.4
• /
• pp.652-661
• /
• 2021

Objective: Wooden breast (WB) is a novel myopathy affecting modern broiler chickens, which causes substantial economic losses in the poultry industry. The objective of this study was to evaluate the effect of WB abnormality on meat quality, redox status, as well as the expression of genes of the nuclear factor-erythroid 2-related factor 2 (Nrf2) pathway. Methods: A total of 80 broilers (Ross 308, 42 days of age, about 2.6 kg body weight) raised at Jiujin farm (Suqian, Jiangsu, China) were used. Twelve unaffected (no detectable hardness of the breast area) and twelve WB-affected (diffuse remarkable hardness in the breast muscle) birds were selected from the commercial broiler farm according to the criteria proposed by previous studies. Results: The results indicated that WB showed histological lesions characterized by fiber degeneration and fibrosis, along with an increase of muscle fiber diameter (p<0.05). Moreover, higher pH value, lightness, yellowness, drip loss and cooking loss were observed in the WB group (p<0.05). Compared with the normal breast (NOR) group, the WB group showed higher formation of reactive oxygen species (p<0.05), increased level of oxidation products and antioxidant activities (p<0.05), accompanied with mitochondrial damages and lower mitochondrial membrane potential (p<0.05). Meanwhile, the relative mRNA expressions of Nrf2 and its downstream antioxidant genes including heme oxygenase-1, NAD(P)H qui none dehydrogenase 1, glutathione peroxidase, superoxide dismutase, and glutamate-cysteine ligase were higher than those of the NOR group (p<0.05). Conclusion: In conclusion, WB myopathy impairs meat quality by causing oxidative damages and mitochondrial dysfunction in broilers, even though the activated Nrf2/antioxidant response element pathway provides protection for the birds.

• Molecules and Cells
• /
• v.45 no.7
• /
• pp.454-464
• /
• 2022

DJ-1 is one of the causative genes of early-onset familial Parkinson's disease (PD). As a result, DJ-1 influences the pathogenesis of sporadic PD. DJ-1 has various physiological functions that converge to control the levels of intracellular reactive oxygen species (ROS). Based on genetic analyses that sought to investigate novel antioxidant DJ-1 downstream genes, pyruvate dehydrogenase (PDH) kinase (PDK) was demonstrated to increase survival rates and decrease dopaminergic (DA) neuron loss in DJ-1 mutant flies under oxidative stress. PDK phosphorylates and inhibits the PDH complex (PDC), subsequently downregulating glucose metabolism in the mitochondria, which is a major source of intracellular ROS. A loss-of-function mutation in PDK was not found to have a significant effect on fly development and reproduction, but severely ameliorated oxidative stress resistance. Thus, PDK plays a critical role in the protection against oxidative stress. Loss of PDH phosphatase (PDP), which dephosphorylates and activates PDH, was also shown to protect DJ-1 mutants from oxidative stress, ultimately supporting our findings. Further genetic analyses suggested that DJ-1 controls PDK expression through hypoxia-inducible factor 1 (HIF-1), a transcriptional regulator of the adaptive response to hypoxia and oxidative stress. Furthermore, CPI-613, an inhibitor of PDH, protected DJ-1 null flies from oxidative stress, suggesting that the genetic and pharmacological inhibition of PDH may be a novel treatment strategy for PD associated with DJ-1 dysfunction.

• Journal of Microbiology and Biotechnology
• /
• v.32 no.12
• /
• pp.1527-1536
• /
• 2022

Escherichia coli can use allantoin as its sole nitrogen source under anaerobic conditions. The ureidoglycolate produced by double release of ammonia from allantoin can flow into either the glyoxylate shunt or further catabolic transcarbamoylation. Although the former pathway is well studied, the genes of the latter (catabolic) pathway are not known. In the catabolic pathway, ureidoglycolate is finally converted to carbamoyl phosphate (CP) and oxamate, and then CP is dephosphorylated to carbamate by a catabolic carbamate kinase (CK), whereby ATP is formed. We identified the ybcF gene in a gene cluster containing fdrA-ylbE-ylbF-ybcF that is located downstream of the allDCE-operon. Reverse transcription PCR of total mRNA confirmed that the genes fdrA, ylbE, ylbF, and ybcF are co-transcribed. Deletion of ybcF caused only a slight increase in metabolic flow into the glyoxylate pathway, probably because CP was used to de novo synthesize pyrimidine and arginine. The activity of the catabolic CK was analyzed using purified YbcF protein. The V_max is 1.82 U/mg YbcF for CP and 1.94 U/mg YbcF for ADP, and the K_M value is 0.47 mM for CP and 0.43 mM for ADP. With these results, it was experimentally revealed that the ybcF gene of E. coli encodes catabolic CK, which completes anaerobic allantoin degradation through substrate-level phosphorylation. Therefore, we suggest renaming the ybcF gene as allK.

• Proceedings of the Plant Resources Society of Korea Conference
• /
• 2023.04a
• /
• pp.55-55
• /
• 2023

With the COVID-19 pandemic, there is increasing interest in anti-obesity strategies. According to the National Statistical Office, the obesity rate in Korea was 38.3% in 2020 and 37.1% in 2021. Obesity is a risk factor for several severe diseases, including stroke, heart disease, type 2 diabetes, and certain types of cancer. Pinus rigida × Pinus taeda is a hybrid of Pinus rigida Mill and Pinus taeda Linn, and its cones are considered a by-product. Although previous studies have investigated their pharmacological effects on antioxidant activity and protection against oxidative DNA damage, few researchers have explored their potential as functional natural materials. Therefore, we evaluated the anti-obesity effects of the cone of ethyl acetate fraction of P. rigida × P. taeda (ERT), specifically its ability to inhibit lipid accumulation. Our analysis showed that ERT contains phytochemicals (catechin and caffeic acid) which are known to improve immune function and inhibit cell damage. ERT inhibited lipid droplet accumulation at the cellular levels through Oil Red O staining. Furthermore, ERT suppressed the expression of adipogenic transcription factors (PPARγ and CEBP/α) as well as downstream lipogenic target genes (FAS and SREBP-1) thereby inhibiting adipogenesis. ERT also down-regulated key adipogenic markers, including aP2α, while inducing the phosphorylation of AMPK. It has been reported that PPARγ and CEBP/α are expressed in the early stages of adipose differentiation, while SREBP-1 is expressed in the late stage. Therefore, our findings suggest that ERT activates AMPK signaling pathways, which inhibits adipogenic transcription factors (PPARγ, C/EBPα, and SREBP1) and lipogenic genes (FAS and aP2α), thereby blocking lipid accumulation and preventing obesity and related disorders. ERT showed potential as a new resource for developing a functional material for anti-obesity agents.

• Journal of Interdisciplinary Genomics
• /
• v.5 no.2
• /
• pp.35-41
• /
• 2023

Background: Ca²⁺ signaling plays a vital role in neuronal signaling and altered Ca²⁺ homeostasis in Parkinson's disease (PD). Overexpression of αSYN significantly promote the Ca²⁺-Calmodulin (CaM) activity and subsequent nuclear translocation of nuclear factor of activated T cells (NFAT) transcription factor in dopaminergic neurons of midbrain. However, the exact role of Ca²⁺-CaM and NFAT in PD pathology is yet to be elucidated. Methods: We designed the CaM-NFAT-oligodeoxynucleotide (ODN), a synthetic short DNA containing complementary sequence for NFAT transcription factor and CaM mRNA. Then, the effect of CaM-NFAT-ODN on 1-methyl-4-phenylpyridinium (MPP⁺)-mediated neurotoxicity was investigated in mimic PD model in vitro. Results: First, the expression of αSYN and CaM was strongly increased in substantia nigra (SN) of PD and the expression of tyrosine hydroxylase (TH) was strongly increased in control SN. Additionally, the expression of apoptosis marker proteins was strongly increased in SN of PD. Transfection of CaM-NFAT-ODN repressed CaM and pNFAT, the target genes of this ODN in rat embryo primary mesencephalic neurons. It also reduced ERK phosphorylation, a downstream target of these genes. These results demonstrated that CaM-NFAT-ODN operated successfully in rat embryo primary mesencephalic neurons. Transfection of CaM-NFAT-ODN repressed TH reduction, αSYN accumulation, and apoptosis by MPP⁺-induced neurotoxicity response through Ca²⁺ signaling and mitogen-activated protein kinases (MAPK) signaling. Conclusion: Synthetic CaM-NFAT-ODN has substantial therapeutic feasibility for the treatment of neurodegenerative diseases.

• Journal of Ginseng Research
• /
• v.48 no.1
• /
• pp.40-51
• /
• 2024

Background: Ginsenoside 20(S)-Rg3 shows promising tumor-suppressive effects in ovarian cancer via inhibiting NF-kB signaling. This study aimed to explore the downstream tumor suppressive mechanisms of ginsenoside Rg3 via this signaling pathway. Materials and methods: A systematical screening was applied to examine the expression profile of 41 kinesin family member genes in ovarian cancer. The regulatory effect of ginsenoside Rg3 on KIF20A expression was studied. In addition, we explored interacting proteins of KIF20A and their molecular regulations in ovarian cancer. RNA-seq data from The Cancer Genome Atlas (TCGA) was used for bioinformatic analysis. Epithelial ovarian cancer cell lines SKOV3 and A2780 were used as in vitro and in vivo cell models. Commercial human ovarian cancer tissue arrays were used for immunohistochemistry staining. Results: KIF20A is a biomarker of poor prognosis among the kinesin genes. It promotes ovarian cancer cell growth in vitro and in vivo. Ginsenoside Rg3 can suppress the transcription of KIF20A. GST pull-down and co-immunoprecipitation (IP) assays confirmed that KIF20A physically interacts with BTRC (β-TrCP1), a substrate recognition subunit for SCF^β-TrCP E3 ubiquitin ligase. In vitro ubiquitination and cycloheximide (CHX) chase assays showed that via interacting with BTRC, KIF20A reduces BTRC-mediated CDC25A poly-ubiquitination and enhances its stability. Ginsenoside Rg3 treatment partly abrogates KIF20A overexpression-induced CDC25A upregulation. Conclusion: This study revealed a novel anti-tumor mechanism of ginsenoside Rg3. It can inhibit KIF20A transcription and promote CDC25A proteasomal degradation in epithelial ovarian cancer.